<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE article PUBLIC "-//NLM//DTD Journal Publishing DTD v2.3 20070202//EN" "journalpublishing.dtd">
<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" article-type="research-article" dtd-version="2.3" xml:lang="EN">
<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Plant Sci.</journal-id>
<journal-title>Frontiers in Plant Science</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Plant Sci.</abbrev-journal-title>
<issn pub-type="epub">1664-462X</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fpls.2024.1459505</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Plant Science</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Identification of a recessive gene <italic>RgM4G52</italic> conferring red glume, stem, and rachis in a <italic>Triticum boeoticum</italic> mutant</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Chen</surname>
<given-names>Longyu</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/data-curation/"/>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-original-draft/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Zhang</surname>
<given-names>Junqing</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-original-draft/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Ma</surname>
<given-names>Pan</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-original-draft/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Miao</surname>
<given-names>Yongping</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1527334"/>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Wu</surname>
<given-names>Lei</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Zhou</surname>
<given-names>Ke</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Yang</surname>
<given-names>Jiaru</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Zhang</surname>
<given-names>Minghu</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Liu</surname>
<given-names>Xin</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Jiang</surname>
<given-names>Bo</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
<role content-type="https://credit.niso.org/contributor-roles/supervision/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Hao</surname>
<given-names>Ming</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/850353"/>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Huang</surname>
<given-names>Lin</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/443024"/>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/supervision/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Ning</surname>
<given-names>Shunzong</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1755965"/>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/supervision/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Chen</surname>
<given-names>Xuejiao</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/data-curation/"/>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Chen</surname>
<given-names>Xue</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Liu</surname>
<given-names>Dengcai</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/537730"/>
<role content-type="https://credit.niso.org/contributor-roles/funding-acquisition/"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
<role content-type="https://credit.niso.org/contributor-roles/supervision/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Wan</surname>
<given-names>Hongshen</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/963846"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
<role content-type="https://credit.niso.org/contributor-roles/supervision/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Zhang</surname>
<given-names>Lianquan</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1384154"/>
<role content-type="https://credit.niso.org/contributor-roles/conceptualization/"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
<role content-type="https://credit.niso.org/contributor-roles/project-administration/"/>
<role content-type="https://credit.niso.org/contributor-roles/supervision/"/>
<role content-type="https://credit.niso.org/contributor-roles/validation/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
</contrib-group>
<aff id="aff1">
<sup>1</sup>
<institution>State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University</institution>, <addr-line>Chengdu</addr-line>, <country>China</country>
</aff>
<aff id="aff2">
<sup>2</sup>
<institution>Triticeae Research Institute, Sichuan Agricultural University</institution>, <addr-line>Chengdu</addr-line>, <country>China</country>
</aff>
<aff id="aff3">
<sup>3</sup>
<institution>Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs), Crop Research Institute, Sichuan Academy of Agricultural Sciences</institution>, <addr-line>Chengdu</addr-line>, <country>China</country>
</aff>
<aff id="aff4">
<sup>4</sup>
<institution>Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Crop Research Institute, Sichuan Academy of Agricultural Sciences</institution>, <addr-line>Chengdu</addr-line>, <country>China</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>Edited by: Chongmei Dong, The University of Sydney, Australia</p>
</fn>
<fn fn-type="edited-by">
<p>Reviewed by: Xingguo Ye, Chinese Academy of Agricultural Sciences, China</p>
<p>Jindong Liu, Chinese Academy of Agricultural Sciences, China</p>
<p>Peter Sharp, The University of Sydney, Australia</p>
</fn>
<fn fn-type="corresp" id="fn001">
<p>*Correspondence: Hongshen Wan, <email xlink:href="mailto:wanhongshen@126.com">wanhongshen@126.com</email>; Lianquan Zhang, <email xlink:href="mailto:zhanglianquan1977@126.com">zhanglianquan1977@126.com</email>
</p>
</fn>
<fn fn-type="other" id="fn003">
<p>&#x2020;ORCID: Hongshen Wan, <uri xlink:href="https://orcid.org/0000-0002-3212-3561">orcid.org/0000-0002-3212-3561</uri>; Lianquan Zhang, <uri xlink:href="https://orcid.org/0000-0001-9005-8705">orcid.org/0000-0001-9005-8705</uri>
</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>26</day>
<month>08</month>
<year>2024</year>
</pub-date>
<pub-date pub-type="collection">
<year>2024</year>
</pub-date>
<volume>15</volume>
<elocation-id>1459505</elocation-id>
<history>
<date date-type="received">
<day>04</day>
<month>07</month>
<year>2024</year>
</date>
<date date-type="accepted">
<day>01</day>
<month>08</month>
<year>2024</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2024 Chen, Zhang, Ma, Miao, Wu, Zhou, Yang, Zhang, Liu, Jiang, Hao, Huang, Ning, Chen, Chen, Liu, Wan and Zhang</copyright-statement>
<copyright-year>2024</copyright-year>
<copyright-holder>Chen, Zhang, Ma, Miao, Wu, Zhou, Yang, Zhang, Liu, Jiang, Hao, Huang, Ning, Chen, Chen, Liu, Wan and Zhang</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p>
</license>
</permissions>
<abstract>
<p>Anthocyanins are plant secondary metabolites belonging to the polyphenol class of natural water-soluble phytopigments. The accumulation of anthocyanins in different plant tissues can improve plant survival under adverse conditions. In addition, plants with the resulting colorful morphology can be utilized as landscape plants. <italic>Triticum boeoticum</italic> (syn. <italic>Triticum monococcum</italic> ssp. <italic>aegilopoides</italic>, 2n=2x=14, A<sup>b</sup>A<sup>b</sup>) serves as a valuable genetic resource for the improvement of its close relative common wheat in terms of enhancing resilience to various biotic and abiotic stresses. In our previous study, the EMS-mutagenized mutant Z2921 with a red glume, stem, and rachis was generated from <italic>T. boeoticum</italic> G52, which has a green glume, stem, and rachis. In this study, the F<sub>1</sub>, F<sub>2</sub>, and F<sub>2:3</sub> generations of a cross between mutant-type Z2921 and wild-type G52 were developed. A single recessive gene, tentatively designated <italic>RgM4G52</italic>, was identified in Z2921 via genetic analysis. Using bulked segregant exome capture sequencing (BSE-Seq) analysis, <italic>RgM4G52</italic> was mapped to chromosome 6AL and was flanked by the markers <italic>KASP-58</italic> and <italic>KASP-26</italic> within a 3.40-cM genetic interval corresponding to 1.71-Mb and 1.61-Mb physical regions in the Chinese Spring (IWGSC RefSeq v1.1) and <italic>Triticum boeoticum</italic> (TA299) reference genomes, respectively, in which seven and four genes related to anthocyanin synthesis development were annotated. Unlike previously reported color morphology-related genes, <italic>RgM4G52</italic> is a recessive gene that can simultaneously control the color of glumes, stems, and rachis in wild einkorn. In addition, a synthetic <italic>Triticum dicoccum</italic>&#x2013;<italic>T. boeoticum</italic> amphiploid Syn-ABA<sup>b</sup>-34, derived from the colchicine treatment of F<sub>1</sub> hybrids between tetraploid wheat PI 352367 (<italic>T. dicoccum</italic>, AABB) and Z2921, expressed the red stems of Z2921. The flanking markers of <italic>RgM4G52</italic> developed in this study could be useful for developing additional common wheat lines with red stems, laying the foundation for marker-assisted breeding and the fine mapping of <italic>RgM4G52</italic>.</p>
</abstract>
<kwd-group>
<kwd>
<italic>Triticum boeoticum</italic>
</kwd>
<kwd>synthetic amphiploid</kwd>
<kwd>red glume</kwd>
<kwd>gene mapping</kwd>
<kwd>recessive gene</kwd>
<kwd>BSE-Seq</kwd>
</kwd-group>
<counts>
<fig-count count="5"/>
<table-count count="3"/>
<equation-count count="0"/>
<ref-count count="76"/>
<page-count count="11"/>
<word-count count="4524"/>
</counts>
<custom-meta-wrap>
<custom-meta>
<meta-name>section-in-acceptance</meta-name>
<meta-value>Plant Breeding</meta-value>
</custom-meta>
</custom-meta-wrap>
</article-meta>
</front>
<body>
<sec id="s1" sec-type="intro">
<title>Introduction</title>
<p>Anthocyanins are flavonoid pigments that are important for plant adaptation to biotic and abiotic stress conditions (<xref ref-type="bibr" rid="B37">Laikova et&#xa0;al., 2005</xref>). In common bread wheat (<italic>Triticum aestivum</italic> L.), pigmentation caused by anthocyanins can occur on leaves, stems, auricles, glumes, pericarp aleurone, coleoptiles, and anthers. Pigment accumulation in crop plants can not only be used as a morphological marker to assist in breeding and research related to impurity removal, gene functions, pigment synthesis pathways, photosynthesis, and other related theories but also provide agroecological tourism value for humans (<xref ref-type="bibr" rid="B62">Song et&#xa0;al., 2020</xref>). The anthocyanin pigmentation of different parts of plants is related to their adaptation to environmental stress conditions. In wheat, purple coleoptiles, stems, and anthers are reportedly related to resistance to bunt (<xref ref-type="bibr" rid="B7">Bogdanova et&#xa0;al., 2002</xref>). It was shown that the lines with dark-purple grains and coleoptiles demonstrated a higher seedling drought tolerance than plants with uncolored pericarp and light purple coleoptiles (<xref ref-type="bibr" rid="B57">Shoeva et&#xa0;al., 2017</xref>). The relationship between accumulation of anthocyanins in wheat coleoptiles and cold treatment has been shown (<xref ref-type="bibr" rid="B19">Gordeeva et&#xa0;al., 2013</xref>). Furthermore, the purple-grained NILs had better viability after accelerated aging compared with the recurrent parent lacking anthocyanins (<xref ref-type="bibr" rid="B18">Gordeeva and Khlestkina, 2013</xref>). The knowledge about specific features of anthocyanin biosynthesis regulation in wheat can be useful for improvement of its adaptation to biotic and abiotic stress conditions. In addition, anthocyanins are important for maintaining human health and preventing cardiovascular diseases, carcinogenesis, inflammation, and many other human pathological conditions (<xref ref-type="bibr" rid="B42">Lila, 2004</xref>).</p>
<p>Anthocyanin accumulation occurs naturally in some species. However, it has also been reported that some changes in pigment accumulation occur in mutant plant populations induced by chemical mutagens. Chemical mutagens, among which ethyl methane sulfonate (EMS) is the most widely used and effective in crop mutagenesis breeding, can induce plants to produce heritable mutants (<xref ref-type="bibr" rid="B40">Li et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B21">Greene et&#xa0;al., 2003</xref>; <xref ref-type="bibr" rid="B24">Henry et&#xa0;al., 2014</xref>). There is a high frequency of EMS-induced point mutagenesis, primarily involving G&#x2013;C to A&#x2013;T conversion, with relatively few chromosomal aberrations. Most of the mutations are easy to screen (<xref ref-type="bibr" rid="B20">Greco et&#xa0;al., 2001</xref>) and can be used to induce variation in plants, construct mutant libraries, and provide rich basic genetic material for the study of plant gene function. <xref ref-type="bibr" rid="B43">Liu et&#xa0;al. (2009)</xref> obtained a rice (<italic>Oryza sativa</italic> L.) <italic>YGL4</italic> mutant with a yellow&#x2013;green leaf color through the EMS mutagenesis of Jinhui 10 cultivar. EMS-induced mutant germplasm can be effectively used to mine new genes, facilitate functional genomics research, and accelerate breeding programs (<xref ref-type="bibr" rid="B25">Hohmann et&#xa0;al., 2005</xref>). Mutagenetic breeding techniques make it possible to overcome the disadvantages of the long conventional breeding cycle, which is slow and comes with difficulties in producing mutation variation. Moreover, mutagenic breeding techniques can bring about breakthroughs in the creation of new crop cultivars, germplasms, and genetic materials and can enable some special problems in breeding work to be solved.</p>
<p>
<italic>Triticum boeoticum</italic> (Syn. <italic>Triticum monococcum</italic> ssp. <italic>aegilopoides</italic>, 2n=2x=14, A<sup>b</sup>A<sup>b</sup>), the wild progenitor of <italic>Triticum monococcum</italic> ssp. <italic>monococcum</italic> (2n=2x=14, A<sup>m</sup>A<sup>m</sup>), represents a valuable genetic resource for improving the ability of its close relative common wheat in terms of coping with various biotic and abiotic stresses (<xref ref-type="bibr" rid="B9">Budak et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B1">Ahmed et&#xa0;al., 2023</xref>; <xref ref-type="bibr" rid="B67">Wang et&#xa0;al., 2023</xref>). In addition, <italic>T. boeoticum</italic> is one of the sources of the blue grain trait controlled by blue aleurone layer 2 (<italic>Ba2</italic>) (<xref ref-type="bibr" rid="B72">Zeller et&#xa0;al., 1991</xref>; <xref ref-type="bibr" rid="B71">Zeven, 1991</xref>; <xref ref-type="bibr" rid="B13">Dubcovsky et&#xa0;al., 1996</xref>; <xref ref-type="bibr" rid="B59">Singh et&#xa0;al., 2007</xref>; <xref ref-type="bibr" rid="B69">Yu et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B47">Liu et&#xa0;al., 2021</xref>). To date, the salt tolerance genes <italic>Nax2</italic> and <italic>Nax1</italic>; the powdery mildew resistance genes <italic>Pm25</italic>, <italic>PmTb7A.1</italic>, and <italic>PmTb7A.2</italic>; the leaf rust resistance gene <italic>Sr22</italic>; the stripe rust resistance locus <italic>QYrtb.pau-5A</italic>; and the stripe rust resistance gene <italic>YrZ15-1370</italic> have been successfully introduced into common wheat (<xref ref-type="bibr" rid="B54">Paull et&#xa0;al., 1994</xref>; <xref ref-type="bibr" rid="B56">Shi et&#xa0;al., 1998</xref>; <xref ref-type="bibr" rid="B11">Chhuneja et&#xa0;al., 2008</xref>; <xref ref-type="bibr" rid="B52">Munns et&#xa0;al., 2012</xref>; <xref ref-type="bibr" rid="B65">Tounsi et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B14">Elkot et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B74">Zhang et&#xa0;al., 2021</xref>).</p>
<p>Synthetic amphiploids play an important role in wheat breeding and evolutionary studies (<xref ref-type="bibr" rid="B16">Gill et&#xa0;al., 1988</xref>; <xref ref-type="bibr" rid="B51">Megyeri et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B2">Ahmed et&#xa0;al., 2014</xref>; <xref ref-type="bibr" rid="B4">Badaeva et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B39">Li et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B46">Liu et&#xa0;al., 2022</xref>, <xref ref-type="bibr" rid="B45">2023</xref>). Many studies have aimed to generate amphidiploids from hybrids of wheat with related species from the genera <italic>Aegilops</italic>, <italic>Secale</italic>, <italic>Thinopyrum</italic>, and <italic>Triticum</italic> (<xref ref-type="bibr" rid="B53">Nemeth et&#xa0;al., 2015</xref>). Recently, 18 synthetic <italic>Triticum turgidum</italic>&#x2013;<italic>Triticum boeoticum</italic> amphiploids were identified using cytological methods, and their nutritional compositions were evaluated (<xref ref-type="bibr" rid="B45">Liu et&#xa0;al., 2023</xref>). Artificial amphidiploids are regarded as a source of genetic variation for improving wheat (<xref ref-type="bibr" rid="B36">Kroupin et&#xa0;al., 2019</xref>).</p>
<p>Since the first mention of the expression of purple color traits in wheat, studies on the inheritance of these characteristics have made great progress in revealing the molecular-genetic mechanisms of anthocyanin pigment biosynthesis and its regulation in wheat (<xref ref-type="bibr" rid="B58">Shoeva and Khlestkina, 2015</xref>). In our previous study, a mutant, Z2921, with a red glume, stem, and rachis was produced from an EMS-mutagenized population of <italic>T. boeoticum</italic> G52 in M<sub>4</sub> generation. In addition, a synthetic <italic>T. dicoccum</italic>&#x2013;<italic>T. boeoticum</italic> amphiploid, Syn-ABA<sup>b</sup>-34, derived from the colchicine treatment of F<sub>1</sub> hybrids of <italic>T. dicoccum</italic> PI 352367 and Z2921, expressed the red stem from Z2921. The objectives of the present study were (1) to identify and map the genes conferring resistance to the red glume, stem, and rachis in Z2921 by using bulked segregant exome capture sequencing (BSE-Seq) analysis and (2) to characterize the new synthetic <italic>T. dicoccum</italic>&#x2013;<italic>T. boeoticum</italic> amphiploid Syn-ABA<sup>b</sup>-34 via cytological methods.</p>
</sec>
<sec id="s2" sec-type="materials|methods">
<title>Materials and methods</title>
<sec id="s2_1">
<title>Plant materials</title>
<p>
<italic>T. boeoticum</italic> G52, the Z2921 mutant, <italic>T. dicoccum</italic> PI352367, and the synthetic <italic>T. dicoccum</italic>&#x2013;<italic>T. boeoticum</italic> amphiploid Syn-ABA<sup>b</sup>-34 were used in this study. The M<sub>4</sub> generation of Z2921, which originated from the 0.4% EMS treatment of 3,000 seeds of the <italic>T. boeoticum</italic> accession G52, was used. Syn-ABA<sup>b</sup>-34 was derived from the colchicine treatment of F<sub>1</sub> hybrids from PI 352367&#xd7;Z2921. G52 was kindly provided by George Fedak at the Ottawa Research and Development Centre for Agriculture and Agri-Food (Ottawa, ON, Canada) in 2012. PI 352367 was kindly provided by the USDA-ARS germplasm bank (<ext-link ext-link-type="uri" xlink:href="http://www.ars-grin.gov">http://www.ars-grin.gov</ext-link>). All materials used in this study were kept at the Triticeae Research Institute of Sichuan Agricultural University.</p>
</sec>
<sec id="s2_2">
<title>Cytological observations</title>
<p>Sc-GISH was conducted using <italic>T. boeoticum</italic> genomic DNA as a probe according to previously published methods (<xref ref-type="bibr" rid="B66">Wang et&#xa0;al., 2019</xref>). Total genomic DNA from G52 was labeled with fluorescein-12-dUTP (Roche Diagnostics Australia, Castle Hill, NSW) using nick translation. The chromosomes were counterstained with 4&#x2032;,6-diamidino-2-phenylindole (DAPI) and pseudocolored red. Hybridization signals were visualized and captured using an Olympus BX-63 epifluorescence microscope equipped with a Photometric SenSys DP70 CCD camera (Olympus, Tokyo, Japan). The raw images were processed using Photoshop v.7.1 (Adobe Systems Inc., San Jose, CA, USA).</p>
<p>Chromosome pairing observation in pollen mother cells (PMCs) was performed as described previously (<xref ref-type="bibr" rid="B73">Zhang et&#xa0;al., 2007</xref>). For meiotic analysis, at least 50 PMCs were observed for Z5471. Ring bivalents (ring II) and rod bivalents (rod II) were counted, and their average numbers were calculated.</p>
</sec>
<sec id="s2_3">
<title>Phenotypic investigation</title>
<p>Field evaluations of glumes, stems, and rachides in G52, Z2921, PI 352367, Syn-ABA<sup>b</sup>-34, G52&#xd7;Z2921 F<sub>1</sub>, and G52&#xd7;Z2921 F<sub>2</sub> individuals as well as their corresponding F<sub>2:3</sub> families were performed at the experimental field of the Triticeae Research Institute, Sichuan Agricultural University, Wenjiang. The colors of the glumes, stems, and rachides were recorded as red or green from the jointing stage to the mature stage during the growth cycle. Each plant was 10 cm apart within rows and 30 cm apart between rows and was 1.5 m in length. The color phenotypes of all the materials in each generation were investigated.</p>
</sec>
<sec id="s2_4">
<title>Bulked segregant exome capture sequencing</title>
<p>Genomic DNA was extracted via the CTAB method (<xref ref-type="bibr" rid="B10">Chatterjee et&#xa0;al., 2002</xref>). Phenotypically contrasting F<sub>2:3</sub> families with different glume/stem/rachis colorations in the field were used to construct red and green glume/stem/rachis DNA pools for BSE-Seq. Equal amounts of DNA from 20 homozygous red-phenotype families and 20 homozygous green-phenotype families were pooled for bulked segregant exome capture sequencing (<xref ref-type="bibr" rid="B27">Ji et&#xa0;al., 2023</xref>). The DNA samples were subjected to exome capture sequencing, a technology developed by Chengdu Tcuni Technology (Chengdu, China). Sequence quality was controlled using Trimmomatic v0.36 software (<xref ref-type="bibr" rid="B8">Bolger et&#xa0;al., 2014</xref>). DNA reads of the wild-type and mutant bulks were aligned to the reference genome sequence of Chinese Spring v1.1 (<xref ref-type="bibr" rid="B26">IWGSC, 2018</xref>) using STARv2.5.1b software (<xref ref-type="bibr" rid="B12">Dobin et&#xa0;al., 2013</xref>). The unique and high-confidence alignments were applied to call SNP variants using GATK v3.6 software (<xref ref-type="bibr" rid="B50">McKenna et&#xa0;al., 2010</xref>). SNP variants with Fisher&#x2019;s exact test (FET) <italic>P</italic> values &lt;&#x2009;1e<sup>&#x2212;8</sup> and allele frequency difference (AFD) &gt;0.6 were considered associated with the red glume/stem/rachis phenotype and were then used as templates to develop SNP markers (<xref ref-type="bibr" rid="B41">Li et&#xa0;al., 2020</xref>).</p>
</sec>
<sec id="s2_5">
<title>Kompetitive allele&#x2212;specific PCR assays</title>
<p>The red-phenotype-related SNPs and the 500-bp flanking sequences were used to design the Kompetitive allele&#x2212;specific PCR (KASP) primers and test polymorphisms in the parental lines and the wild-type and mutant DNA bulks. Polymorphic markers that could be reliably scored were genotyped in the F<sub>2</sub> segregation population of G52&#xd7;Z2921. For each KASP assay, a 10-&#xb5;l reaction volume containing 5 &#xb5;l of 2 KASP master mix (Biosearch Technologies), 1.4 &#xb5;l of primer mix (a mixture of 0.168 &#xb5;M each forward A1 and A2 primer and 0.42 &#xb5;M of reverse primer), 100 ng of genomic DNA, and 2.6 &#xb5;l of ddH<sub>2</sub>O was prepared. The CFX96 Touch&#x2122; real-time PCR detection system (Bio-Rad, USA) was used for amplification under the following conditions: 15 min at 94&#xb0;C, 10 touchdown cycles of 20 s at 94&#xb0;C, 60 s at 65&#xb0;C&#x2013;57&#xb0;C (decreasing by 0.8&#xb0;C per cycle), and 32 cycles of 20 s at 94&#xb0;C, 60 s at 57&#xb0;C.</p>
</sec>
<sec id="s2_6">
<title>Data analysis</title>
<p>Chi-square (<italic>&#x3c7;<sup>2</sup>
</italic>) tests were used to determine the goodness of fit for the observed segregation and expected ratios of the F<sub>2</sub> and F<sub>2:3</sub> populations. Linkage analysis was performed using MAPMAKER/EXP v3.0b (<xref ref-type="bibr" rid="B38">Lander et&#xa0;al., 1987</xref>). The Kosambi function was used to convert recombination values to genetic distances (<xref ref-type="bibr" rid="B35">Kosambi, 1943</xref>). A logarithmic odds (LOD) ratio of 3.0 and a maximum distance of 50.0 cM were set as the thresholds for the declaration of linkage. The genetic linkage map was drawn using MapDraw v2.1 software (<xref ref-type="bibr" rid="B44">Liu and Meng, 2003</xref>).</p>
</sec>
<sec id="s2_7">
<title>Candidate gene analysis</title>
<p>The corresponding sequences of the markers <italic>KASP-58</italic> and <italic>KASP-26</italic> linked to <italic>RgM4G52</italic> were subjected to BLAST searches against the genomes of common wheat cv. Chinese Spring v1.1 (<xref ref-type="bibr" rid="B3">Appels et&#xa0;al., 2018</xref>) and the genome of <italic>Triticum boeoticum</italic> TA299 (<xref ref-type="bibr" rid="B1">Ahmed et&#xa0;al., 2023</xref>). Gene annotations between the flanking markers of the two genomes were retrieved from the databases Ensembl Plants (<ext-link ext-link-type="uri" xlink:href="http://plants.ensembl.org/index.html">http://plants.ensembl.org/index.html</ext-link>) and Swiss-Prot (<ext-link ext-link-type="uri" xlink:href="http://www.gpm-aw.com/html/swi-ss-prot.html">http://www.gpm-aw.com/html/swi-ss-prot.html</ext-link>). Collinearity analysis was performed on the DEGs related to the function of anthocyanin synthesis among the parents and mixed pools.</p>
</sec>
</sec>
<sec id="s3" sec-type="results">
<title>Results</title>
<sec id="s3_1">
<title>Genetic analysis of genes related to red glumes, stems, and rachides</title>
<p>From the jointing stage to the mature stage, the EMS mutant Z2921 exhibited red glumes, stems and rachides (<xref ref-type="fig" rid="f1">
<bold>Figures&#xa0;1A&#x2013;D</bold>
</xref>), and G52 exhibited green glumes, stems, and rachides. Z2921 was crossed with G52 to develop F<sub>1</sub>, F<sub>2</sub>, and F<sub>2:3</sub> populations for genetic analysis of the genes conferring red glumes, stems, and rachides in Z2921. The glume, stem, and rachis coloration of all the F<sub>1</sub> plants were similar to those of the parent G52 plants, with green glumes, stems, and rachides (<xref ref-type="fig" rid="f1">
<bold>Figures&#xa0;1E&#x2013;H</bold>
</xref>). The F<sub>2</sub> population segregated into 46 green-phenotype and 18 red-phenotype strains (<xref ref-type="fig" rid="f1">
<bold>Figures&#xa0;1I&#x2013;L</bold>
</xref>), fitting a 1G:3R ratio (&#x3c7;<sup>2 =</sup> 0.333, p=0.564) (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>), indicating that the red phenotype was conferred by a single recessive gene, tentatively designated <italic>RgM4G52</italic>. The segregation rate of the F<sub>2:3</sub> population composed of 64 families was 14 (homozygous green type):30 (heterozygous):17 (homozygous red type) (&#x3c7;<sub>1:2:1</sub>
<sup>2 =</sup> 0.097, <italic>p</italic> = 0.953), which is consistent with the segregation results of the F<sub>2</sub> population (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>).</p>
<fig id="f1" position="float">
<label>Figure&#xa0;1</label>
<caption>
<p>The coloration of spikes <bold>(A)</bold>, spikelets (glumes) <bold>(B)</bold>, stems <bold>(C)</bold> and rachides <bold>(D)</bold> of Z2921 and G52; The coloration of spikes <bold>(E)</bold>, spikelets (glumes) <bold>(F)</bold>, stems <bold>(G)</bold>, and rachides <bold>(H)</bold> of G52&#xd7;Z2921 F<sub>1;</sub> The coloration of spikes <bold>(I)</bold>, spikelets (glumes) <bold>(J)</bold>, stems <bold>(K)</bold>, and rachides <bold>(L)</bold> of G52&#xd7;Z2921 F<sub>2</sub> individual plants.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-15-1459505-g001.tif"/>
</fig>
<table-wrap id="T1" position="float">
<label>Table&#xa0;1</label>
<caption>
<p>Genetic analysis of red genes in F<sub>1</sub>, F<sub>2</sub>, and F<sub>2:3</sub> families of Z2921 &#xd7; G52.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" rowspan="2" align="center">Parents and cross</th>
<th valign="middle" rowspan="2" align="center">Generation<sup>a</sup>
</th>
<th valign="middle" rowspan="2" align="center">No. of plants/families</th>
<th valign="middle" colspan="3" align="center">Observed ratio<sup>b</sup>
</th>
<th valign="middle" rowspan="2" align="center">Actual ratio</th>
<th valign="middle" rowspan="2" align="center">Expected ratio</th>
<th valign="middle" rowspan="2" align="center">&#x3c7;<sup>2</sup>
</th>
<th valign="middle" rowspan="2" align="center">
<italic>P-value</italic>
</th>
</tr>
<tr>
<th valign="middle" align="center">G</th>
<th valign="middle" align="center">Seg</th>
<th valign="middle" align="center">R</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" align="center">G52</td>
<td valign="middle" align="center">Pg</td>
<td valign="middle" align="center">10</td>
<td valign="middle" align="center">10</td>
<td valign="bottom" align="center"/>
<td valign="bottom" align="center"/>
<td valign="bottom" align="center"/>
<td valign="bottom" align="center"/>
<td valign="bottom" align="center"/>
<td valign="bottom" align="center"/>
</tr>
<tr>
<td valign="middle" align="center">Z2921</td>
<td valign="middle" align="center">P<sub>R</sub>
</td>
<td valign="middle" align="center">10</td>
<td valign="bottom" align="center"/>
<td valign="bottom" align="center"/>
<td valign="middle" align="center">10</td>
<td valign="bottom" align="center"/>
<td valign="bottom" align="center"/>
<td valign="bottom" colspan="2" align="center"/>
</tr>
<tr>
<td valign="middle" rowspan="3" align="center">Pg &#xd7; P<sub>R</sub>
</td>
<td valign="middle" align="center">F<sub>1</sub>
</td>
<td valign="middle" align="center">10</td>
<td valign="bottom" align="center">10</td>
<td valign="bottom" align="center"/>
<td valign="middle" align="center"/>
<td valign="bottom" align="center"/>
<td valign="bottom" align="center"/>
<td valign="bottom" align="center"/>
<td valign="bottom" align="center"/>
</tr>
<tr>
<td valign="middle" align="center">F<sub>2</sub>
</td>
<td valign="middle" align="center">64</td>
<td valign="middle" align="center">46</td>
<td valign="bottom" align="center"/>
<td valign="middle" align="center">18</td>
<td valign="middle" align="center">2.6:1</td>
<td valign="middle" align="center">3:1</td>
<td valign="middle" align="center">0.333</td>
<td valign="middle" align="center">0.564</td>
</tr>
<tr>
<td valign="middle" align="center">F<sub>2:3</sub>
</td>
<td valign="middle" align="center">61</td>
<td valign="middle" align="center">16</td>
<td valign="middle" align="center">28</td>
<td valign="middle" align="center">17</td>
<td valign="middle" align="center">1:1.75:1.06</td>
<td valign="middle" align="center">1:2:1</td>
<td valign="middle" align="center">0.097</td>
<td valign="middle" align="center">0.953</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>
<sup>a</sup>P<sub>S</sub>, wild-type (green color) parent G52; P<sub>Ss</sub>, mutant type (red color) parent Z2921.</p>
</fn>
<fn>
<p>
<sup>b</sup>R, homozygous red; Seg, segregating within F<sub>2:3</sub> families; G, homozygous green.</p>
</fn>
</table-wrap-foot>
</table-wrap>
</sec>
<sec id="s3_2">
<title>BSE-Seq analysis</title>
<p>The DNA samples of the red bulk and the green bulk were subjected to BSE-Seq analysis, which generated 224,290,036 and 177,194,890 raw reads, respectively. After quality control, 224,266,906 and 177,176,312 high-quality reads from the red bulk and the green bulk, respectively, were uniquely mapped to the Chinese Spring genome (IWGSC RefSeq v1.1). A total of 5651 SNPs (<italic>p</italic>&lt;&#x2009;1<sup>e-8</sup> and |AFD|&gt;0.6) were identified from these reads using GATK v4.0 software (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2B</bold>
</xref>). A total of 348 SNPs were located within a 5-Mb genomic interval (555 Mb&#x2013;560 Mb) on the long arm of chromosome 6A (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2A</bold>
</xref>) in the Chinese Spring reference genome; these SNPs were regarded as candidate SNPs linked to <italic>RgM4G52</italic>.</p>
<fig id="f2" position="float">
<label>Figure&#xa0;2</label>
<caption>
<p>Distribution of SNPs from DNA bulks. <bold>(A)</bold> Number of SNPs (|AFD| &gt; 0.6, <italic>P</italic> value &lt;1e<sup>&#x2212;8</sup>) distributed on different wheat chromosomes; <bold>(B)</bold> enrichment of SNPs within a 1-Mb window size on wheat chromosomes.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-15-1459505-g002.tif"/>
</fig>
</sec>
<sec id="s3_3">
<title>Molecular mapping of <italic>RgM4G52</italic>
</title>
<p>There were 59 of the 171 clustered SNPs on 6AL 555&#x2013;560 Mb (<italic>p&lt;1<sup>e-8</sup>
</italic> and |AFD|&gt;0.6) chosen for the development of KASP markers. Four of them were successfully converted into KASP markers (<italic>KASP-7</italic>, <italic>KASP-26</italic>, <italic>KASP-58</italic>, <italic>KASP-59</italic>) (<xref ref-type="table" rid="T2">
<bold>Table&#xa0;2</bold>
</xref>) and scored reliably on the parents as well as the red and green bulks (<xref ref-type="table" rid="T3"><bold>Table 3</bold></xref>). These KASP markers were subsequently used to genotype 64 F<sub>2</sub> plants derived from a cross between green-type G52 and red-type Z2921. Linkage analysis indicated that <italic>KASP-58</italic> was mapped 2.73 cM distal and that <italic>KASP-26</italic> was located 0.67 cM proximal to <italic>RgM4G52</italic> (<xref ref-type="fig" rid="f3">
<bold>Figures&#xa0;3A&#x2013;C</bold>
</xref>).</p>
<table-wrap id="T2" position="float">
<label>Table&#xa0;2</label>
<caption>
<p>Primer sequences of KASP markers used for genetic mapping of <italic>RgM4G52</italic>.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" align="center">Marker</th>
<th valign="middle" align="center">Physical position (bp)</th>
<th valign="middle" align="center">Allele 1 primer<sup>a</sup>
</th>
<th valign="middle" align="center">Allele 2 primer<sup>b</sup>
</th>
<th valign="middle" align="center">Common/reverse primer</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" align="center">
<italic>KASP-7</italic>
</td>
<td valign="middle" align="center">556979833</td>
<td valign="middle" align="center">GGGATTGGGGGAGCAGAGCA</td>
<td valign="middle" align="center">GGGATTGGGGGAGCAGAGCG</td>
<td valign="middle" align="center">GAGACGTCCTGTTGACTCCT</td>
</tr>
<tr>
<td valign="middle" align="center">
<italic>KASP-26</italic>
</td>
<td valign="middle" align="center">557091256</td>
<td valign="middle" align="center">ACGTTATTCATACCAGAGCGTT</td>
<td valign="middle" align="center">ACGTTATTCATACCAGAGCGTG</td>
<td valign="middle" align="center">TGGAGGGAAAGGATGACACT</td>
</tr>
<tr>
<td valign="middle" align="center">
<italic>KASP-58</italic>
</td>
<td valign="middle" align="center">558796229</td>
<td valign="middle" align="center">TGTGGACACCTTCAAGATGATC</td>
<td valign="middle" align="center">TGTGGACACCTTCAAGATGATT</td>
<td valign="middle" align="center">CTTCTTGCACTTGCCTTCCG</td>
</tr>
<tr>
<td valign="middle" align="center">
<italic>KASP-59</italic>
</td>
<td valign="middle" align="center">559401024</td>
<td valign="middle" align="center">AGATCGAGCACGCCACGA</td>
<td valign="middle" align="center">AGATCGAGCACGCCACGG</td>
<td valign="middle" align="center">TCACTCCTCTCGTCCTTCCC</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>a A1 primer labeled with FAM: GAAGGTGACCAAGTTCATGCT.</p>
</fn>
<fn>
<p>b A2 primer labeled with HEX: GAAGGTCGGAGTCAACGGATT.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<fig id="f3" position="float">
<label>Figure&#xa0;3</label>
<caption>
<p>Genetic linkage map of the <italic>RgM4G52</italic> gene on chromosome 6AL showing the physical location of <italic>RgM4G52</italic>. <bold>(A)</bold> Linkage map of <italic>RgM4G52</italic>; <bold>(B)</bold> physical interval (blue) where the four KASP markers are linked to <italic>RgM4G52</italic> anchored in Chinese Spring, with orange dots representing centromeres and dotted lines indicating the physical positions of each marker; <bold>(C)</bold> physical intervals anchored by markers linked to <italic>RgM4G52</italic> in <italic>T. boeoticum.</italic> Collinearity relationship of candidate genes in the <italic>RgM4G52</italic> gene mapping interval between <italic>T. aestivum</italic> Chinese Spring and <italic>T. boeoticum</italic> TA299. <bold>(D)</bold> Genetic linkage map of <italic>RgM4G52</italic>; <bold>(E, F)</bold> physical mapping of candidate genes in Chinese Spring and TA299.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-15-1459505-g003.tif"/>
</fig>
<table-wrap id="T3" position="float">
<label>Table&#xa0;3</label>
<caption>
<p>Genotyping of Z2921 and G52 using KASP markers linked to <italic>RgM4G52</italic>.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" rowspan="2" align="center">Parents</th>
<th valign="top" colspan="4" align="center">Marker&#xad;genotype<sup>a</sup>
</th>
</tr>
<tr>
<th valign="middle" align="center">
<italic>KASP-7</italic>
</th>
<th valign="middle" align="center">
<italic>KASP-26</italic>
</th>
<th valign="middle" align="center">
<italic>KASP-58</italic>
</th>
<th valign="middle" align="center">
<italic>KASP-59</italic>
</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" align="center">Z2921</td>
<td valign="middle" align="center">AA</td>
<td valign="middle" align="center">TT</td>
<td valign="middle" align="center">CC</td>
<td valign="middle" align="center">AA</td>
</tr>
<tr>
<td valign="middle" align="center">G52</td>
<td valign="middle" align="center">GG</td>
<td valign="middle" align="center">GG</td>
<td valign="middle" align="center">TT</td>
<td valign="middle" align="center">GG</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>
<sup>a</sup> AA, CC, GG, and TT represent the haplotype results of SNP genotyping.</p>
</fn>
</table-wrap-foot>
</table-wrap>
</sec>
<sec id="s3_4">
<title>Gene analysis of the <italic>RgM4G52</italic> genomic region</title>
<p>The sequences of the closely linked markers <italic>KASP-26</italic> and <italic>KASP-58</italic> were subjected to BLAST searches against the genome of Chinese Spring and that of <italic>T. boeoticum</italic> TA299 to determine their physical positions. <italic>RgM4G52</italic> was physically mapped to a 1.71-Mb region between the 557.09-Mb and 558.97-Mb regions of the Chinese Spring 6AL chromosome (IWGSC RefSeq v1.1) and between the 580.72-Mb and 582.33-Mb regions (1.61 Mb) of the TA299 6A<sup>b</sup>L chromosome (<italic>T. boeoticum</italic>) (<xref ref-type="fig" rid="f3"><bold>Figures 3A&#x2013;C</bold></xref>). There were 40 and 42 predicted genes in the target physical regions in Chinese Spring and <italic>T. boeoticum</italic> TA299, respectively (IWGSC RefSeq v1.1; <italic>T. boeoticum</italic> TA299, <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Tables&#xa0;S1, S2</bold>
</xref>). In the Chinese Spring genome, seven genes may be associated with the anthocyanin biosynthesis pathway, including four cytochrome P450 family protein-related genes (<xref ref-type="bibr" rid="B64">Tanaka et&#xa0;al., 2009</xref>; <xref ref-type="bibr" rid="B68">Yang et&#xa0;al., 2004</xref>) (<italic>TraesCS6A02G509500LC</italic>, <italic>TraesCS6A02G323900</italic>, <italic>TraesCS6A02G324000</italic>, <italic>TraesCS6A02G510200LC</italic>), one universal stress protein family gene (<xref ref-type="bibr" rid="B60">Song et&#xa0;al., 2023a</xref>, <xref ref-type="bibr" rid="B61">2023b</xref>; <xref ref-type="bibr" rid="B17">Gonzalez et&#xa0;al., 2008</xref>; <xref ref-type="bibr" rid="B5">Baudry et&#xa0;al., 2004</xref>; <xref ref-type="bibr" rid="B63">Stracke et&#xa0;al., 2010</xref>). (<italic>TraesCS6A02G323800</italic>), one peroxidase gene (<italic>TraesCS6A02G324200</italic>) (<xref ref-type="bibr" rid="B22">Grommeck and Markakis, 1964</xref>; <xref ref-type="bibr" rid="B70">Zapata et&#xa0;al., 1995</xref>; <xref ref-type="bibr" rid="B28">Kader et&#xa0;al., 2002</xref>; <xref ref-type="bibr" rid="B76">Zhang et&#xa0;al., 2005</xref>), and one F-box family protein-encoding gene (<xref ref-type="bibr" rid="B75">Zhang et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B15">Feder et&#xa0;al., 2015</xref>) (<italic>TraesCS6A02G324300</italic>). Four genes, namely, one cytochrome P450 protein-related gene (<italic>Tm.TA299.r1.6AG0120810</italic>), one peroxidase gene (<italic>Tm.TA299.r1.6AG0120940</italic>), a universal stress protein family gene, <italic>Tm.TA299.r1.6AG0120790</italic>, and an F-box family protein-encoding gene, <italic>Tm.TA299.r1.6AG0121100LC</italic>, were found in the <italic>T. boeoticum</italic> (TA299) genome and had a good collinear relationship with those of Chinese Spring (<xref ref-type="fig" rid="f3">
<bold>Figures&#xa0;3D&#x2013;F</bold>
</xref>).</p>
</sec>
<sec id="s3_5">
<title>Phenotypic and cytological molecular characterization of the amphiploid Syn-ABA<sup>b</sup>-34</title>
<p>An investigation of the number of chromosomes in the root tip showed that seven plants had 42 chromosomes and 2 plants had 41 chromosomes in the nine plants tested from amphiploid Syn-ABA<sup>b</sup>-34. Plants with 42 chromosomes were used for mc-GISH identification and chromosome pairing observation. Mc-GISH revealed 28 A-genome chromosomes among the amphiploid Syn-ABA<sup>b</sup>-34 chromosomes in the A-genome of Z5471 (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4A</bold>
</xref>). Chromosome pairing in PMCs (observed PMCs &gt;50) at meiotic metaphase I was 2.58 rod II+17.92 ring II+0.16 I+0.16 III+0.08 IV in these plants with 42 chromosomes (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4B</bold>
</xref>), indicating the cytological stability of amphiploid Syn-ABA<sup>b</sup>-34. The amphiploid Syn-ABA<sup>b</sup>-34 was detected using the KASP markers <italic>KASP-26</italic> and <italic>KASP-58</italic> linked to <italic>RgM4G52</italic>; the results indicated that Syn-ABAb-34 carried the gene <italic>RgM4G5</italic>2 (<xref ref-type="fig" rid="f4">
<bold>Figures&#xa0;4C, D</bold>
</xref>). Field evaluation revealed that the color of stem changes from green to purple over time and finally changes from purple to red. Syn-ABA<sup>b</sup>-34 exhibited stem pigment accumulation similar to the diploid parent Z2921, whereas no pigment accumulation was detected in the tetraploid parent PI352367 (<xref ref-type="fig" rid="f5">
<bold>Figures&#xa0;5A&#x2013;C</bold>
</xref>). Additionally, it was observed that the average length and width of 10 grains of Syn-ABA<sup>b</sup>-34 were greater than those of the parents Z2921 and PI352367 (<xref ref-type="fig" rid="f5">
<bold>Figures&#xa0;5D, E</bold>
</xref>).</p>
<fig id="f4" position="float">
<label>Figure&#xa0;4</label>
<caption>
<p>Cytological observations of the <italic>T. dicoccum&#x2013;T. boeoticum</italic> amphiploid Syn-ABA<sup>b</sup>-34 and molecular detection using KASP markers linked to <italic>RgM4G52</italic>. <bold>(A)</bold> GISH identification of Syn-ABA<sup>b</sup>-34 using G52 genomic DNA as a probe; <bold>(B)</bold> chromosome pairing of PMCs in Syn-ABA<sup>b</sup>-34 with 21 bivalents; <bold>(C)</bold> molecular marker detection of Syn-ABA<sup>b</sup>-34 and its parents G52 and Z2921 using the KASP marker <italic>KASP-26</italic>, which is linked to <italic>RgM4G52</italic>. G52 in blue, Z2921 and Syn-ABA<sup>b</sup>-34 in yellow; <bold>(D)</bold> molecular marker detection of Syn-ABA<sup>b</sup>-34 and its parents G52 and Z2921 using the KASP marker <italic>KASP-58</italic> linked to <italic>RgM4G52</italic>. G52, blue; Z2921 and Syn-ABA<sup>b</sup>-34, yellow.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-15-1459505-g004.tif"/>
</fig>
<fig id="f5" position="float">
<label>Figure&#xa0;5</label>
<caption>
<p>Phenotype of the <italic>T. dicoccum&#x2013;T. boeoticum</italic> amphiploid Syn-ABA<sup>b</sup>-34 and its parents PI 352367 and Z2921. <bold>(A)</bold> The coloration of different stems from <italic>T. dicoccum&#x2013;T. boeoticum</italic> amphiploid Syn-ABA<sup>b</sup>-34; <bold>(B)</bold> the stem coloration of Syn-ABA<sup>b</sup>-34 and its parents Z2921 and PI352367; <bold>(C)</bold> the plants of Syn-ABA<sup>b</sup>-34 and its parents Z2921 and PI352367; <bold>(D)</bold> the seed length of Syn-ABA<sup>b</sup>-34 and its parents Z2921 and PI352367; <bold>(E)</bold> the seed width of Syn-ABA<sup>b</sup>-34 and its parents Z2921 and PI352367.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-15-1459505-g005.tif"/>
</fig>
</sec>
</sec>
<sec id="s4" sec-type="discussion">
<title>Discussion</title>
<p>Anthocyanins cause pigmentation in plant tissues and enhance plant resistance to biotic and abiotic stresses (<xref ref-type="bibr" rid="B37">Laikova et&#xa0;al., 2005</xref>). To date, there have been some reports of genes associated with pigmentation on leaves, glume shells, culms, seeds, etc., in wheat. <italic>Rg</italic> genes control glume shell color in diploid, tetraploid, and hexaploid wheat and are located on chromosomes 1A, 1B, 1D, and 2A (<xref ref-type="bibr" rid="B32">Khlestkina et&#xa0;al., 2010</xref>; <xref ref-type="bibr" rid="B49">McIntosh et&#xa0;al., 2013</xref>). Among these genes, <italic>Rg-A1b</italic> and <italic>Rg-A1c</italic> control the red and black (dark brown) glumes of diploid, tetraploid, and hexaploid wheat, respectively (<xref ref-type="bibr" rid="B6">Blanco et&#xa0;al., 1998</xref>; <xref ref-type="bibr" rid="B55">Salina et&#xa0;al., 2006</xref>) whereas <italic>Rg-D1b</italic> and <italic>Rg-D1c</italic> control the red (brown) and gray glumes, respectively, of hexaploid wheat (<xref ref-type="bibr" rid="B33">Khlestkina and Salina, 2006</xref>, <xref ref-type="bibr" rid="B34">2009b</xref>, <xref ref-type="bibr" rid="B29">2002a</xref>, <xref ref-type="bibr" rid="B30">2002b</xref>). Three homoeologous genes for purple stems (<italic>Pc-A1</italic>, <italic>Pc-B1</italic>, <italic>Pc-D1</italic>), three homoeologs for purple leaf sheaths (<italic>Pls-A1</italic>, <italic>Pls-B1</italic>, <italic>Pls-D1</italic>), and three homoeologs for purple leaf blades (<italic>Plb-A1</italic>, <italic>Plb-B1</italic>, <italic>Plb-D1</italic>) have been mapped in close linkage with the red coleoptile genes <italic>Rc-A1</italic>, <italic>Rc-B1</italic>, and <italic>Rc-D1</italic> in wheat (<xref ref-type="bibr" rid="B31">Khlestkina et&#xa0;al., 2009a</xref>, <xref ref-type="bibr" rid="B32">2010</xref>). Two genes responsible for purple anthers (<italic>Pan-A1</italic> and <italic>Pan-D1</italic>) have been mapped on chromosomes 7A (<xref ref-type="bibr" rid="B6">Blanco et&#xa0;al., 1998</xref>) and 7D (<xref ref-type="bibr" rid="B31">Khlestkina et&#xa0;al., 2009a</xref>) at short distances from <italic>Rc-A1</italic> and <italic>Rc-D1</italic>, respectively.</p>
<p>However, there have only been a few reports of pigmentation in glumes, culms, and rachides being simultaneously controlled by a single gene. In this study, a new pigmentation gene, <italic>RgM4G52</italic>, conferring red glumes, stems, and rachides, was identified in the <italic>T. boeoticum</italic> mutant Z2921 and mapped on chromosome arm 6AL flanked by the markers <italic>KASP-26</italic> and <italic>KASP-58</italic> within a 3.40-cM genetic interval corresponding to a 1.71-Mb physical region in the Chinese Spring genome (IWGSC RefSeq v1.1).</p>
<p>
<italic>RgM4G52</italic> was physically mapped to a 1.61-Mb region between 580.72 Mb and 582.33 Mb on the TA299 6A<sup>b</sup>L chromosome arm (<italic>T. boeoticum</italic> TA299) (<xref ref-type="fig" rid="f3">
<bold>Figures&#xa0;3A&#x2013;C</bold>
</xref>). Based on the gene functional annotation, there were four protein-coding genes, <italic>Tm.TA299.r1.6AG0120790</italic>, <italic>Tm.TA299.r1.6AG0120810</italic>, <italic>Tm.TA299.r1.6AG0120940</italic>, and <italic>Tm.TA299.r1.6AG0121100LC</italic>, in the target physical regions of the <italic>T. boeoticum</italic> genome (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Tables&#xa0;S1, S2</bold>
</xref>; <xref ref-type="fig" rid="f3">
<bold>Figures&#xa0;3D, E</bold>
</xref>).</p>
<p>
<italic>Tm.TA299.r1.6AG0120790</italic> was not annotated, and the homologous gene of <italic>Tm.TA299.r1.6AG0120790</italic> in Chinese Spring was <italic>TraesCS6A02G323800</italic>. Its functional annotation was that of a universal stress protein family gene. The universal stress protein family is involved in UV-B-induced flavonoid biosynthesis, and <italic>VcUSP</italic>s are coexpressed mainly with transcription factors from the MYB, AP2, zinc finger, and bHLH families (<xref ref-type="bibr" rid="B60">Song et&#xa0;al., 2023a</xref>, <xref ref-type="bibr" rid="B61">2023b</xref>; <xref ref-type="bibr" rid="B17">Gonzalez et&#xa0;al., 2008</xref>; <xref ref-type="bibr" rid="B5">Baudry et&#xa0;al., 2004</xref>; <xref ref-type="bibr" rid="B63">Stracke et&#xa0;al., 2010</xref>). <italic>Tm.TA299.r1.6AG0121100LC</italic> was not annotated, and the homologous gene of <italic>Tm.TA299.r1.6AG0121100LC</italic> in the Chinese Spring is <italic>TraesCS6A02G324300</italic>. Its functional annotation was that of an F-box family protein. Members of the F-box serve as crucial negative regulators by mediating <italic>CHS</italic> and <italic>PAL</italic> degradation, which coordinately controls flavonoid biosynthesis (<xref ref-type="bibr" rid="B75">Zhang et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B15">Feder et&#xa0;al., 2015</xref>).</p>
<p>
<italic>Tm.TA299.r1.6AG0120810</italic> was annotated as a desmethyl-deoxy-podophyllotoxin synthase, and the homologous gene of <italic>Tm.TA299.r1.6AG0120810</italic> in Chinese Spring was <italic>TraesCS6A02G323900</italic>. Its functional annotation was that of a cytochrome P450 protein-related gene. The enzymes flavonoid 3&#x2032;-hydroxylase (F3&#x2032;H) and flavonoid 3&#x2032;,5&#x2032;-hydroxylase (F3&#x2032;5&#x2032;H) play important roles in the anthocyanin biosynthesis pathway, and the genes encoding flavonoid 3&#x2032;5&#x2032;-hydroxylase (F3&#x2032;5&#x2032;h) and flavonoid 3&#x2032;-hydroxylase (F3&#x2032;h) belong to the cytochrome P450 monooxygenase gene family (<xref ref-type="bibr" rid="B64">Tanaka et&#xa0;al., 2009</xref>). There are no data on the cloning and/or mapping of these genes in wheat, except regarding one partial nucleotide sequence, F3&#x2032;5&#x2032;h (<xref ref-type="bibr" rid="B68">Yang et&#xa0;al., 2004</xref>). In the present study, <italic>Tm.TA299.r1.6AG0120940</italic> was annotated as a peroxidase gene, and the gene homologous to <italic>Tm.TA299.r1.6AG0120940</italic> in Chinese Spring was <italic>TraesCS6A02G324200</italic>. Its functional annotation was the same as that for <italic>Tm.TA299.r1.6AG0120940</italic>. All flavonoids have shown great binding affinity to peroxidase, and peroxidase can be degraded by anthocyanins as direct crop plant substrates or in the presence of H<sub>2</sub>O<sub>2</sub> with anthocyanidins as substrates to oxidize and decolorize the anthocyanidins. The activity of peroxidase is negatively correlated with that of anthocyanins (<xref ref-type="bibr" rid="B22">Grommeck and Markakis, 1964</xref>; <xref ref-type="bibr" rid="B70">Zapata et&#xa0;al., 1995</xref>; <xref ref-type="bibr" rid="B28">Kader et&#xa0;al., 2002</xref>; <xref ref-type="bibr" rid="B76">Zhang et&#xa0;al., 2005</xref>). Now, the work is ongoing to clone and sequence these four genes, namely, <italic>Tm.TA299.r1.6AG0120790</italic>, <italic>Tm.TA299.r1.6AG0120810</italic>, <italic>Tm.TA299.r1.6AG0120940</italic>, and <italic>Tm.TA299.r1.6AG0121100LC</italic>. Then, candidate genes will be screened by sequence alignment. Finally, the function of candidate genes will be verified by the transgenic technique.</p>
<p>The flanking markers <italic>KASP-26</italic> and <italic>KASP-58</italic> developed in this study could be used as molecular markers to screen recombinant heterozygous plants, construct secondary F<sub>2</sub> populations and develop markers, and further narrow the location interval to finely map and clone <italic>RgM4G52</italic>. There have been rare reports of pigmentation in glumes, culms, and rachides being simultaneously controlled by a single gene. <italic>RgM4G52</italic> may be a new recessive pigmentation gene. According to previous reports on the relationship between anthocyanin accumulation and plants, the red pigment accumulation in wheat with <italic>RgM4G52</italic> may be related to their adaptation to environmental stress conditions. It may be used as a morphological marker to assist in breeding and research related to gene functions and pigment synthesis pathways. Furthermore, it can also be used as a landscape crop for agro-ecological popular science tourism.</p>
<p>The expression of superior genes has been found to decrease or be completely inhibited when foreign genes have been transferred from a lower ploidy level (<xref ref-type="bibr" rid="B48">Ma et&#xa0;al., 1997</xref>; <xref ref-type="bibr" rid="B2">Ahmed et&#xa0;al., 2014</xref>). In this study, the amphiploid Syn-ABA<sup>b</sup>-34 had red stems at the jointing stage but had green glumes and rachides, indicating that the expression of <italic>RgM4G52</italic> was suppressed in the glumes and rachides. According to <xref ref-type="bibr" rid="B23">Hao et&#xa0;al. (2019)</xref>, the amphiploid Syn-ABA<sup>b</sup>-34 can serve as a bridge to hybridize with elite wheat varieties, transferring this trait to common wheat and providing new germplasm resources for wheat breeding. Combined with molecular marker-assisted selection, the transfer of <italic>RgM4G52</italic> from diploid wheat to common wheat cultivars are ongoing using the amphiploid Syn-ABA<sup>b</sup>-34 as a bridge. The breeding of new wheat cultivars with red glumes/stems/rachides will provide new materials for the breeding of widely adaptable wheat varieties.</p>
</sec>
</body>
<back>
<sec id="s5" sec-type="data-availability">
<title>Data availability statement</title>
<p>The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Material</bold>
</xref>.</p>
</sec>
<sec id="s6" sec-type="author-contributions">
<title>Author contributions</title>
<p>LC: Data curation, Investigation, Methodology, Software, Writing &#x2013; original draft. JZ: Investigation, Methodology, Software, Writing &#x2013; original draft. PM: Investigation, Software, Writing &#x2013; original draft. YM: Investigation, Software, Writing &#x2013; review &amp; editing. LW: Investigation, Software, Writing &#x2013; review &amp; editing. KZ: Investigation, Software, Writing &#x2013; review &amp; editing. JY: Investigation, Software, Writing &#x2013; review &amp; editing. MZ: Investigation, Software, Writing &#x2013; review &amp; editing. XL: Investigation, Software, Writing &#x2013; review &amp; editing. BJ: Software, Supervision, Writing &#x2013; review &amp; editing. MH: Investigation, Software, Writing &#x2013; review &amp; editing. LH: Investigation, Supervision, Writing &#x2013; review &amp; editing. SN: Investigation, Supervision, Writing &#x2013; review &amp; editing. XJC: Data curation, Investigation, Writing &#x2013; review &amp; editing. XC: Investigation, Software, Writing &#x2013; review &amp; editing. DL: Funding acquisition, Methodology, Supervision, Writing &#x2013; review &amp; editing. HW: Methodology, Supervision, Writing &#x2013; review &amp; editing. LZ: Conceptualization, Methodology, Project administration, Supervision, Validation, Writing &#x2013; review &amp; editing.</p>
</sec>
<sec id="s7" sec-type="funding-information">
<title>Funding</title>
<p>The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was supported by the Key Research and Development Program of Sichuan Province (2021YFYZ0002), Sichuan Science and Technology Program (2022ZDZX0016; 2023NSFSC1925), the Open Fund of the Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China (ZWS2024001), and the Sichuan Provincial Finance Department (1 + 9KJGG001; YSCX2035-001).</p>
</sec>
<sec id="s8" sec-type="COI-statement">
<title>Conflict of interest</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec id="s9" sec-type="disclaimer">
<title>Publisher&#x2019;s note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
<sec id="s10" sec-type="supplementary-material">
<title>Supplementary material</title>
<p>The Supplementary Material for this article can be found online at: <ext-link ext-link-type="uri" xlink:href="https://www.frontiersin.org/articles/10.3389/fpls.2024.1459505/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fpls.2024.1459505/full#supplementary-material</ext-link>
</p>
<supplementary-material xlink:href="Table1.xlsx" id="SM1" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"/>
</sec>
<ref-list>
<title>References</title>
<ref id="B1">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Ahmed</surname> <given-names>H. I.</given-names>
</name>
<name>
<surname>Heuberger</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Schoen</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Koo</surname> <given-names>D. H.</given-names>
</name>
<name>
<surname>Quiroz-Chavez</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Adhikari</surname> <given-names>L.</given-names>
</name>
<etal/>
</person-group>. (<year>2023</year>). <article-title>Einkorn genomics sheds light on history of the oldest domesticated wheat</article-title>. <source>Nature</source> <volume>620</volume>, <fpage>830</fpage>&#x2013;<lpage>838</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1038/s41586-023-06389-7</pub-id>
</citation>
</ref>
<ref id="B2">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Ahmed</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Bux</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Rasheed</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Gul Kazi</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Rauf</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Mahmood</surname> <given-names>T.</given-names>
</name>
<etal/>
</person-group>. (<year>2014</year>). <article-title>Stripe rust resistance in <italic>Triticum durum</italic>&#x2013;<italic>T. monococcum</italic> and <italic>T. durum</italic>&#x2013;<italic>T. urartu</italic> amphiploids</article-title>. <source>Australas. Plant Pathol.</source> <volume>43</volume>, <fpage>109</fpage>&#x2013;<lpage>113</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s13313-013-0237-8</pub-id>
</citation>
</ref>
<ref id="B3">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Appels</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Eversole</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Stein</surname> <given-names>N.</given-names>
</name>
<name>
<surname>Feuillet</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Keller</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Jane</surname> <given-names>R.</given-names>
</name>
<etal/>
</person-group>. (<year>2018</year>). <article-title>Shifting the limits in wheat research and breeding using a fully annotated reference genome</article-title>. <source>Science</source> <volume>361</volume>, <elocation-id>eaar7191</elocation-id>. doi:&#xa0;<pub-id pub-id-type="doi">10.1126/science.aar7191</pub-id>
</citation>
</ref>
<ref id="B4">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Badaeva</surname> <given-names>E. D.</given-names>
</name>
<name>
<surname>Ruban</surname> <given-names>A. S.</given-names>
</name>
<name>
<surname>Zoshchuk</surname> <given-names>S. A.</given-names>
</name>
<name>
<surname>Surzhikov</surname> <given-names>S. A.</given-names>
</name>
<name>
<surname>Kn&#xfc;pffer</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Kilian</surname> <given-names>B.</given-names>
</name>
</person-group> (<year>2016</year>). <article-title>Molecular cytogenetic characterization of <italic>Triticum timopheevii</italic> chromosomes provides new insight on genome evolution of <italic>T. zhukovskyi</italic>
</article-title>. <source>Plant Syst. Evol.</source> <volume>302</volume>, <fpage>943</fpage>&#x2013;<lpage>956</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s00606-016-1309-3</pub-id>
</citation>
</ref>
<ref id="B5">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Baudry</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Heim</surname> <given-names>M. A.</given-names>
</name>
<name>
<surname>Dubreucq</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Caboche</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Weisshaar</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Lepiniec</surname> <given-names>L.</given-names>
</name>
</person-group> (<year>2004</year>). <article-title>TT2, TT8, and TTG1 synergistically specify the expression of <italic>BANYULS</italic> and proanthocyanidin biosynthesis in <italic>Arabidopsis thaliana</italic>
</article-title>. <source>Plant J.</source> <volume>39</volume>, <fpage>366</fpage>&#x2013;<lpage>380</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1111/j.1365-313X.2004.02138.x</pub-id>
</citation>
</ref>
<ref id="B6">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Blanco</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Bellomo</surname> <given-names>M. P.</given-names>
</name>
<name>
<surname>Cenci</surname> <given-names>A.</given-names>
</name>
<name>
<surname>De Giovanni</surname> <given-names>C.</given-names>
</name>
<name>
<surname>D&#x2019;ovidio</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Iacono</surname> <given-names>E.</given-names>
</name>
<etal/>
</person-group>. (<year>1998</year>). <article-title>A genetic linkage map of durum wheat</article-title>. <source>Theor. Appl. Genet.</source> <volume>97</volume>, <fpage>721</fpage>&#x2013;<lpage>728</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s001220050948</pub-id>
</citation>
</ref>
<ref id="B7">
<citation citation-type="confproc">
<person-group person-group-type="author">
<name>
<surname>Bogdanova</surname> <given-names>E. D.</given-names>
</name>
<name>
<surname>Sarbaev</surname> <given-names>A. T.</given-names>
</name>
<name>
<surname>Makhmudova</surname> <given-names>K. K.</given-names>
</name>
</person-group> (<year>2002</year>). &#x201c;<article-title>Resistance of common wheat to bunt</article-title>,&#x201d; in <conf-name>Proceedings of the research conference on genetics</conf-name>, <conf-loc>Moscow, Russia</conf-loc>: <publisher-name>Research Conference on Genetics</publisher-name>. <fpage>43</fpage>&#x2013;<lpage>44</lpage>.</citation>
</ref>
<ref id="B8">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Bolger</surname> <given-names>A. M.</given-names>
</name>
<name>
<surname>Lohse</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Usadel</surname> <given-names>B.</given-names>
</name>
</person-group> (<year>2014</year>). <article-title>Trimmomatic: a flexible trimmer for Illumina sequence data</article-title>. <source>Bioinformatics</source> <volume>30</volume>, <fpage>2114</fpage>&#x2013;<lpage>2120</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/bioinformatics/btu170</pub-id>
</citation>
</ref>
<ref id="B9">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Budak</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Kantar</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Yucebilgili Kurtoglu</surname> <given-names>K.</given-names>
</name>
</person-group> (<year>2013</year>). <article-title>Drought tolerance in modern and wild wheat</article-title>. <source>Sci. World J.</source> <volume>4</volume>, <fpage>66</fpage>&#x2013;<lpage>75</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1155/2013/548246</pub-id>
</citation>
</ref>
<ref id="B10">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Chatterjee</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Moulik</surname> <given-names>S. P.</given-names>
</name>
<name>
<surname>Majhi</surname> <given-names>P. R.</given-names>
</name>
<name>
<surname>Sanyal</surname> <given-names>S. K.</given-names>
</name>
</person-group> (<year>2002</year>). <article-title>Studies on surfactant&#x2013;biopolymer interaction. I. Microcalorimetric investigation on the interaction of cetyltrimethylammonium bromide (CTAB) and sodium dodecylsulfate (SDS) with gelatin (Gn), lysozyme (Lz) and deoxyribonucleic acid (DNA)</article-title>. <source>Biophys. Chem.</source> <volume>98</volume>, <fpage>313</fpage>&#x2013;<lpage>327</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1016/S0301-4622(02)00107-2</pub-id>
</citation>
</ref>
<ref id="B11">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Chhuneja</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Kaur</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Garg</surname> <given-names>T.</given-names>
</name>
<name>
<surname>Ghai</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Kaur</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Prashar</surname> <given-names>M.</given-names>
</name>
<etal/>
</person-group>. (<year>2008</year>). <article-title>Mapping of adult plant stripe rust resistance genes in diploid A genome wheat species and their transfer to bread wheat</article-title>. <source>Theor. Appl. Genet.</source> <volume>116</volume>, <fpage>313</fpage>&#x2013;<lpage>324</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s00122-007-0668-0</pub-id>
</citation>
</ref>
<ref id="B12">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Dobin</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Davis</surname> <given-names>C. A.</given-names>
</name>
<name>
<surname>Schlesinger</surname> <given-names>F.</given-names>
</name>
<name>
<surname>Drenkow</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Zaleski</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Jha</surname> <given-names>S.</given-names>
</name>
<etal/>
</person-group>. (<year>2013</year>). <article-title>STAR: ultrafast universal RNA-seq aligner</article-title>. <source>Bioinformatics</source> <volume>29</volume>, <fpage>15</fpage>&#x2013;<lpage>21</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/bioinformatics/bts635</pub-id>
</citation>
</ref>
<ref id="B13">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Dubcovsky</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Luo</surname> <given-names>M. C.</given-names>
</name>
<name>
<surname>Zhong</surname> <given-names>G. Y.</given-names>
</name>
<name>
<surname>Bransteitter</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Desai</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Kilian</surname> <given-names>A.</given-names>
</name>
<etal/>
</person-group>. (<year>1996</year>). <article-title>Genetic map of diploid wheat, <italic>Triticum monococcum</italic> L., and its comparison with maps of <italic>Hordeum vulgare</italic> L</article-title>. <source>Genetics</source> <volume>143</volume>, <fpage>983</fpage>&#x2013;<lpage>999</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/genetics/143.2.983</pub-id>
</citation>
</ref>
<ref id="B14">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Elkot</surname> <given-names>A. F. A.</given-names>
</name>
<name>
<surname>Chhuneja</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Kaur</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Saluja</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Keller</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Singh</surname> <given-names>K.</given-names>
</name>
</person-group> (<year>2015</year>). <article-title>Marker assisted transfer of two powdery mildew resistance genes <italic>PmTb7A.1</italic> and <italic>PmTb7A.2</italic> from <italic>Triticum boeoticum</italic> (Boiss.) to <italic>Triticum aestivum</italic> (L.)</article-title>. <source>PloS One</source> <volume>10</volume>, <elocation-id>e0128297</elocation-id>. doi:&#xa0;<pub-id pub-id-type="doi">10.1371/journal.pone.0128297</pub-id>
</citation>
</ref>
<ref id="B15">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Feder</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Burger</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Gao</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Lewinsohn</surname> <given-names>E.</given-names>
</name>
<name>
<surname>Katzir</surname> <given-names>N.</given-names>
</name>
<name>
<surname>Schaffer</surname> <given-names>A. A.</given-names>
</name>
<etal/>
</person-group>. (<year>2015</year>). <article-title>A Kelch domain-containing F-Box coding gene negatively regulates flavonoid accumulation in muskmelon</article-title>. <source>Plant Physio</source> <volume>169</volume>, <fpage>1714</fpage>&#x2013;<lpage>1726</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1104/pp.15.01008</pub-id>
</citation>
</ref>
<ref id="B16">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Gill</surname> <given-names>R. S.</given-names>
</name>
<name>
<surname>Dhaliwal</surname> <given-names>H. S.</given-names>
</name>
<name>
<surname>Multani</surname> <given-names>D. S.</given-names>
</name>
</person-group> (<year>1988</year>). <article-title>Synthesis and evaluation of <italic>Triticum durum</italic>-<italic>T. monococcum</italic> amphiploids</article-title>. <source>Theor. Appl. Genet.</source> <volume>75</volume>, <fpage>912</fpage>&#x2013;<lpage>916</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/BF00258053</pub-id>
</citation>
</ref>
<ref id="B17">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Gonzalez</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Zhao</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Leavitt</surname> <given-names>J. M.</given-names>
</name>
<name>
<surname>Lloyd</surname> <given-names>A. M.</given-names>
</name>
</person-group> (<year>2008</year>). <article-title>Regulation of the anthocyanin biosynthetic pathway by the TTG1/bHLH/Myb transcriptional complex in <italic>Arabidopsis</italic> seedlings</article-title>. <source>Plant J.</source> <volume>53</volume>, <fpage>814</fpage>&#x2013;<lpage>827</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1111/j.1365-313x.2007.03373.x</pub-id>
</citation>
</ref>
<ref id="B18">
<citation citation-type="confproc">
<person-group person-group-type="author">
<name>
<surname>Gordeeva</surname> <given-names>E. I.</given-names>
</name>
<name>
<surname>Khlestkina</surname> <given-names>E. K.</given-names>
</name>
</person-group> (<year>2013</year>). &#x201c;<article-title>Relationship between accumulation of anthocyanins in wheat pericarp and response to artificial ageing of seeds</article-title>,&#x201d; in <conf-name>Abstracts of conference free radicals and antioxidants in chemistry, biology and medicine, Novosibirsk</conf-name>, <conf-loc>Russian</conf-loc>.</citation>
</ref>
<ref id="B19">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Gordeeva</surname> <given-names>E. I.</given-names>
</name>
<name>
<surname>Shoeva</surname> <given-names>O. Y.</given-names>
</name>
<name>
<surname>Khlestkina</surname> <given-names>E. K.</given-names>
</name>
</person-group> (<year>2013</year>). <article-title>Cold stress response of wheat genotypes having different <italic>Rc</italic> alleles</article-title>. <source>Cereal Res. Commun.</source> <volume>41</volume>, <fpage>519</fpage>&#x2013;<lpage>526</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1556/CRC.2013.0029</pub-id>
</citation>
</ref>
<ref id="B20">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Greco</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Ouwerkerk</surname> <given-names>P. B.</given-names>
</name>
<name>
<surname>Taal</surname> <given-names>A. J.</given-names>
</name>
<name>
<surname>Favalli</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Beguiristain</surname> <given-names>T.</given-names>
</name>
<name>
<surname>Puigdomenech</surname> <given-names>P.</given-names>
</name>
<etal/>
</person-group>. (<year>2001</year>). <article-title>Early and multiple Ac transpositions in rice suitable for efficient insertional mutagenesis</article-title>. <source>Plant Mol. Biol.</source> <volume>46</volume>, <fpage>215</fpage>&#x2013;<lpage>227</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1023/A:1010607318694</pub-id>
</citation>
</ref>
<ref id="B21">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Greene</surname> <given-names>E. A.</given-names>
</name>
<name>
<surname>Codomo</surname> <given-names>C. A.</given-names>
</name>
<name>
<surname>Taylor</surname> <given-names>N. E.</given-names>
</name>
<name>
<surname>Henikoff</surname> <given-names>J. G.</given-names>
</name>
<name>
<surname>Till</surname> <given-names>B. J.</given-names>
</name>
<name>
<surname>Reynolds</surname> <given-names>S. H.</given-names>
</name>
<etal/>
</person-group>. (<year>2003</year>). <article-title>Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in <italic>Arabidopsis</italic>
</article-title>. <source>Genetics</source> <volume>164</volume>, <fpage>731</fpage>&#x2013;<lpage>740</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/genetics/164.2.731</pub-id>
</citation>
</ref>
<ref id="B22">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Grommeck</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Markakis</surname> <given-names>P.</given-names>
</name>
</person-group> (<year>1964</year>). <article-title>The effect of peroxidase on anthocyanin pigments a</article-title>. <source>J. Food Sci.</source> <volume>29</volume>, <fpage>53</fpage>&#x2013;<lpage>57</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1111/j.1365-2621.1964.tb01693.x</pub-id>
</citation>
</ref>
<ref id="B23">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Hao</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Zhao</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Dai</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Li</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Yang</surname> <given-names>W.</given-names>
</name>
<etal/>
</person-group>. (<year>2019</year>). <article-title>A breeding strategy targeting the secondary gene pool of bread wheat: introgression from a synthetic hexaploid wheat</article-title>. <source>Theor. Appl. Genet.</source> <volume>132</volume>, <fpage>2285</fpage>&#x2013;<lpage>2294</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s00122-019-03354-9</pub-id>
</citation>
</ref>
<ref id="B24">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Henry</surname> <given-names>I. M.</given-names>
</name>
<name>
<surname>Nagalakshmi</surname> <given-names>U.</given-names>
</name>
<name>
<surname>Lieberman</surname> <given-names>M. C.</given-names>
</name>
<name>
<surname>Ngo</surname> <given-names>K. J.</given-names>
</name>
<name>
<surname>Krasileva</surname> <given-names>K. V.</given-names>
</name>
<name>
<surname>Vasquez-Gross</surname> <given-names>H.</given-names>
</name>
<etal/>
</person-group>. (<year>2014</year>). <article-title>Efficient genome-wide detection and cataloging of EMS-induced mutations using exome capture and next-generation sequencing</article-title>. <source>Plant Cell</source> <volume>26</volume>, <fpage>1382</fpage>&#x2013;<lpage>1397</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1105/TPC.113.121590</pub-id>
</citation>
</ref>
<ref id="B25">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Hohmann</surname> <given-names>U.</given-names>
</name>
<name>
<surname>Jacobs</surname> <given-names>G.</given-names>
</name>
<name>
<surname>Jung</surname> <given-names>C.</given-names>
</name>
</person-group> (<year>2005</year>). <article-title>An EMS mutagenesis protocol for sugar beet and isolation of non-bolting mutants</article-title>. <source>Plant Breed</source> <volume>124</volume>, <fpage>317</fpage>&#x2013;<lpage>321</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1111/j.1439-0523.2005.01126.x</pub-id>
</citation>
</ref>
<ref id="B26">
<citation citation-type="journal">
<person-group person-group-type="author">
<collab>IWGSC</collab>
<name>
<surname>Bellec</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Berges</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Appels</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Eversole</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Stein</surname> <given-names>N.</given-names>
</name>
<etal/>
</person-group>. <article-title>Shifting the limits in wheat research and breeding using a fully annotated reference genome</article-title>. <source>Science</source>, <year>2018</year>, <volume>361</volume>:<elocation-id>6403</elocation-id>. doi:&#xa0;<pub-id pub-id-type="doi">10.1126/science.aar7191</pub-id>
</citation>
</ref>
<ref id="B27">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Ji</surname> <given-names>G.</given-names>
</name>
<name>
<surname>Xu</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Fan</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Zhou</surname> <given-names>Q.</given-names>
</name>
<name>
<surname>Chen</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Yu</surname> <given-names>Q.</given-names>
</name>
<etal/>
</person-group>. (<year>2023</year>). <article-title>Identification and validation of major QTL for grain size and weight in bread wheat (<italic>Triticum aestivum</italic> L.)</article-title>. <source>Crop J.</source> <volume>11</volume>, <fpage>564</fpage>&#x2013;<lpage>572</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1016/j.cj.2022.06.014</pub-id>
</citation>
</ref>
<ref id="B28">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Kader</surname> <given-names>F.</given-names>
</name>
<name>
<surname>Irmouli</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Nicolas</surname> <given-names>J. P.</given-names>
</name>
<name>
<surname>Metche</surname> <given-names>M.</given-names>
</name>
</person-group> (<year>2002</year>). <article-title>Involvement of blueberry peroxidase in the mechanisms of anthocyanin degradation in blueberry juice</article-title>. <source>J. Food Sci.</source> <volume>67</volume>, <fpage>910</fpage>&#x2013;<lpage>915</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1111/j.1365-2621.2002.tb09427.x</pub-id>
</citation>
</ref>
<ref id="B29">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Khlestkina</surname> <given-names>E. K.</given-names>
</name>
<name>
<surname>Pestsova</surname> <given-names>E. G.</given-names>
</name>
<name>
<surname>R&#xf6;der</surname> <given-names>M. S.</given-names>
</name>
<name>
<surname>B&#xf6;rner</surname> <given-names>A.</given-names>
</name>
</person-group> (<year>2002</year>a). <article-title>Molecular mapping, phenotypic expression and geographical distribution of genes determining anthocyanin pigmentation of coleoptiles in wheat (<italic>Triticum aestivum</italic> L.)</article-title>. <source>Theor. Appl. Genet.</source> <volume>104</volume>, <fpage>632</fpage>&#x2013;<lpage>637</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s00122-001-0788-x</pub-id>
</citation>
</ref>
<ref id="B30">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Khlestkina</surname> <given-names>E. K.</given-names>
</name>
<name>
<surname>Pestsova</surname> <given-names>E. G.</given-names>
</name>
<name>
<surname>Salina</surname> <given-names>E.</given-names>
</name>
<name>
<surname>Roder</surname> <given-names>M. S.</given-names>
</name>
<name>
<surname>Arbuzova</surname> <given-names>V. S.</given-names>
</name>
<name>
<surname>Koval</surname> <given-names>S. F.</given-names>
</name>
<etal/>
</person-group>. (<year>2002</year>b). <article-title>Genetic mapping and tagging of wheat genes using RAPD, STS and SSR markers</article-title>. <source>Cell. Mol. Biol. Let</source> <volume>7</volume>, <fpage>795</fpage>&#x2013;<lpage>802</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s00018-002-8414-x</pub-id>
</citation>
</ref>
<ref id="B31">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Khlestkina</surname> <given-names>E. K.</given-names>
</name>
<name>
<surname>Pshenichnikova</surname> <given-names>T. A.</given-names>
</name>
<name>
<surname>R&#xf6;der</surname> <given-names>M. S.</given-names>
</name>
<name>
<surname>B&#xf6;rner</surname> <given-names>A.</given-names>
</name>
</person-group> (<year>2009</year>a). <article-title>Clustering anthocyanin pigmentation genes in wheat group 7 chromosomes</article-title>. <source>Cereal. Res. Commun.</source> <volume>37</volume>, <fpage>391</fpage>&#x2013;<lpage>398</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1556/crc.37.2009.3.8</pub-id>
</citation>
</ref>
<ref id="B32">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Khlestkina</surname> <given-names>E. K.</given-names>
</name>
<name>
<surname>R&#xf6;der</surname> <given-names>M. S.</given-names>
</name>
<name>
<surname>B&#xf6;rner</surname> <given-names>A.</given-names>
</name>
</person-group> (<year>2010</year>). <article-title>Mapping genes controlling anthocyanin pigmentation on the glume and pericarp in tetraploid wheat (<italic>Triticum durum</italic> L.)</article-title>. <source>Euphytica</source> <volume>171</volume>, <fpage>65</fpage>&#x2013;<lpage>69</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s10681-009-9994-4</pub-id>
</citation>
</ref>
<ref id="B33">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Khlestkina</surname> <given-names>E. K.</given-names>
</name>
<name>
<surname>Salina</surname> <given-names>E. A.</given-names>
</name>
</person-group> (<year>2006</year>). <article-title>SNP markers: methods of analysis, ways of development, and comparison on an example of common wheat. Russian</article-title>. <source>J. Genet.</source> <volume>42</volume>, <fpage>585</fpage>&#x2013;<lpage>594</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1134/s1022795406060019</pub-id>
</citation>
</ref>
<ref id="B34">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Khlestkina</surname> <given-names>E. J.</given-names>
</name>
<name>
<surname>Salina</surname> <given-names>E. A.</given-names>
</name>
<name>
<surname>Pshenichnikova</surname> <given-names>T. A.</given-names>
</name>
<name>
<surname>R&#xf6;der</surname> <given-names>M. S.</given-names>
</name>
<name>
<surname>B&#xf6;rner</surname> <given-names>A.</given-names>
</name>
</person-group> (<year>2009</year>b). <article-title>Glume coloration in wheat: allelism test, consensus mapping and its association with specific microsatellite allele</article-title>. <source>Cereal Res. Commun.</source> <volume>37</volume>, <fpage>37</fpage>&#x2013;<lpage>43</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1556/CRC.37.2009.1.5</pub-id>
</citation>
</ref>
<ref id="B35">
<citation citation-type="book">
<person-group person-group-type="author">
<name>
<surname>Kosambi</surname> <given-names>D. D.</given-names>
</name>
</person-group> (<year>1943</year>). <article-title>The estimation of map distances from recombination values</article-title>. <source>Ann. Eugen</source>. <volume>12</volume>, <page-range>172&#x2013;175</page-range>. doi:&#xa0;<pub-id pub-id-type="doi">10.1111/j.1469-1809.1943.tb02321.x</pub-id>
</citation>
</ref>
<ref id="B36">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Kroupin</surname> <given-names>P. Y.</given-names>
</name>
<name>
<surname>Divashuk</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Karlov</surname> <given-names>G.</given-names>
</name>
</person-group> (<year>2019</year>). <article-title>Gene resources of perennial wild cereals involved in breeding to improve wheat crop</article-title>. <source>Selskokhoziaistvennaia Biol.</source> <volume>54</volume>, <fpage>409</fpage>&#x2013;<lpage>425</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.15389/agrobiology.2019.3.409eng</pub-id>
</citation>
</ref>
<ref id="B37">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Laikova</surname> <given-names>L. I.</given-names>
</name>
<name>
<surname>Arbuzova</surname> <given-names>V. S.</given-names>
</name>
<name>
<surname>Efremova</surname> <given-names>T. T.</given-names>
</name>
<name>
<surname>Popova</surname> <given-names>O. M.</given-names>
</name>
</person-group> (<year>2005</year>). <article-title>Genetic analysis of anthocyanin of the anthers and culm pigmentation in common wheat</article-title>. <source>Genetika</source> <volume>41</volume>, <fpage>1428</fpage>&#x2013;<lpage>1433</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s11177-005-0216-4</pub-id>
</citation>
</ref>
<ref id="B38">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Lander</surname> <given-names>E. S.</given-names>
</name>
<name>
<surname>Green</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Abrahamson</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Barlow</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Daly</surname> <given-names>M. J.</given-names>
</name>
<name>
<surname>Lincoln</surname> <given-names>S. E.</given-names>
</name>
<etal/>
</person-group>. (<year>1987</year>). <article-title>MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations</article-title>. <source>Genomics</source> <volume>1</volume>, <fpage>174</fpage>&#x2013;<lpage>181</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1016/j.ygeno.2008.12.003</pub-id>
</citation>
</ref>
<ref id="B39">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Li</surname> <given-names>H. Y.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>X. J.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>M. H.</given-names>
</name>
<name>
<surname>Feng</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>D. C.</given-names>
</name>
<name>
<surname>Ayliffe</surname> <given-names>M.</given-names>
</name>
<etal/>
</person-group>. (<year>2018</year>). <article-title>Development and identification of new synthetic <italic>T. turgidum</italic>&#x2013;<italic>T. monococcum</italic> amphiploids</article-title>. <source>Plant Genet. Resour</source> <volume>16</volume>, <fpage>555</fpage>&#x2013;<lpage>563</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1017/S1479262118000175</pub-id>
</citation>
</ref>
<ref id="B40">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Li</surname> <given-names>W.</given-names>
</name>
<name>
<surname>Guo</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Xie</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Zhao</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Gu</surname> <given-names>J.</given-names>
</name>
<etal/>
</person-group>. (<year>2017</year>). <article-title>Identification of novel alleles induced by EMS-mutagenesis in key genes of kernel hardness and starch biosynthesis in wheat by TILLING</article-title>. <source>Genes Genom</source> <volume>39</volume>, <fpage>387</fpage>&#x2013;<lpage>395</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s13258-016-0504-5</pub-id>
</citation>
</ref>
<ref id="B41">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Li</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Shi</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Hu</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Wu</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Qiu</surname> <given-names>D.</given-names>
</name>
<name>
<surname>Qu</surname> <given-names>Y.</given-names>
</name>
<etal/>
</person-group>. (<year>2020</year>). <article-title>Identification of a recessive gene <italic>PmQ</italic> conferring resistance to powdery mildew in wheat landrace Qingxinmai using BSR-Seq analysis</article-title>. <source>Plant Dis.</source> <volume>104</volume>, <fpage>743</fpage>&#x2013;<lpage>751</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1094/PDIS-08-19-1745-RE</pub-id>
</citation>
</ref>
<ref id="B42">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Lila</surname> <given-names>M. A.</given-names>
</name>
</person-group> (<year>2004</year>). <article-title>Anthocyanins and human health: an in <italic>vitro</italic> investigative approach</article-title>. <source>J. BioMed. Biotechnol.</source> <volume>2004</volume>, <fpage>306</fpage>&#x2013;<lpage>313</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1155/S111072430440401X</pub-id>
</citation>
</ref>
<ref id="B43">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Liu</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Sang</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Ling</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Zhao</surname> <given-names>F.</given-names>
</name>
<name>
<surname>Yang</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>He</surname> <given-names>G.</given-names>
</name>
</person-group> (<year>2009</year>). <article-title>Genetic analysis and molecular mapping of a yellow green leaf gene (<italic>YGL4</italic>) in rice (<italic>Oryza sativa</italic> L.)</article-title>. <source>Acta Agro. Sin.</source> <volume>35</volume>, <fpage>1405</fpage>&#x2013;<lpage>1409</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.3724/SP.J.1006.2009.01405</pub-id>
</citation>
</ref>
<ref id="B44">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Liu</surname> <given-names>R. H.</given-names>
</name>
<name>
<surname>Meng</surname> <given-names>J.</given-names>
</name>
</person-group> (<year>2003</year>). <article-title>MapDraw: a microsoft excel macro for drawing genetic linkage maps based on given genetic linkage data</article-title>. <source>Hereditas</source> <volume>25</volume>, <fpage>317</fpage>&#x2013;<lpage>321</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.3321/j.issn:0253-9772.2003.03.019</pub-id>
</citation>
</ref>
<ref id="B45">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Liu</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Jiang</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Ye</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Shen</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Wu</surname> <given-names>L.</given-names>
</name>
<etal/>
</person-group>. (<year>2023</year>). <article-title>Molecular cytogenetic identification and nutritional composition evaluation of newly synthesized <italic>Triticum turgidum</italic>-<italic>Triticum boeoticum</italic> amphiploids (AABBA<sup>b</sup>A<sup>b</sup>)</article-title>. <source>Front. Plant Sci.</source> <volume>14</volume>. doi:&#xa0;<pub-id pub-id-type="doi">10.3389/fpls.2023.1285847</pub-id>
</citation>
</ref>
<ref id="B46">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Liu</surname> <given-names>X. J.</given-names>
</name>
<name>
<surname>Yang</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>M. H.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Peng</surname> <given-names>T.</given-names>
</name>
<name>
<surname>Hao</surname> <given-names>M.</given-names>
</name>
<etal/>
</person-group>. (<year>2022</year>). <article-title>Molecular cytogenetic identification of a new synthetic amphiploid (<italic>Triticum timococcum</italic>, A<sup>t</sup>A<sup>t</sup>GGA<sup>m</sup>A<sup>m</sup>) with a seed setting rate comparable with that of natural <italic>Triticum zhukovskyi</italic>
</article-title>. <source>Plant Breed</source> <volume>141</volume>, <fpage>558</fpage>&#x2013;<lpage>565</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1111/pbr.13030</pub-id>
</citation>
</ref>
<ref id="B47">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Liu</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Jiang</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Li</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Jia</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Hao</surname> <given-names>M.</given-names>
</name>
<etal/>
</person-group>. (<year>2021</year>). <article-title>
<italic>TbMYC4A</italic> is a candidate gene controlling the blue aleurone trait in a wheat-<italic>Triticum boeoticum</italic> substitution line</article-title>. <source>Front. Plant Sci.</source> <volume>12</volume>. doi:&#xa0;<pub-id pub-id-type="doi">10.3389/fpls.2021.762265</pub-id>
</citation>
</ref>
<ref id="B48">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Ma</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Singh</surname> <given-names>R. P.</given-names>
</name>
<name>
<surname>Mujeeb-Kazi</surname> <given-names>A.</given-names>
</name>
</person-group> (<year>1997</year>). <article-title>Resistance to stripe rust in durum wheats, A-genome diploids, and their amphiploids</article-title>. <source>Euphytica</source> <volume>94</volume>, <fpage>279</fpage>&#x2013;<lpage>286</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1023/A:1002979706378</pub-id>
</citation>
</ref>
<ref id="B49">
<citation citation-type="confproc">
<person-group person-group-type="author">
<name>
<surname>McIntosh</surname> <given-names>R. A.</given-names>
</name>
<name>
<surname>Yamazaki</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Dubcovsky</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Rogers</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Morris</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Appels</surname> <given-names>R.</given-names>
</name>
<etal/>
</person-group>. (<year>2013</year>). &#x201c;<article-title>Catalogue of gene symbols for wheat</article-title>,&#x201d; in <conf-name>Proceedings of the 12th international wheat genetics symposium</conf-name>, <conf-loc>Yokohama Japan</conf-loc>. <fpage>8</fpage>&#x2013;<lpage>13</lpage>.</citation>
</ref>
<ref id="B50">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>McKenna</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Hanna</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Banks</surname> <given-names>E.</given-names>
</name>
<name>
<surname>Sivachenko</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Cibulskis</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Kernytsky</surname> <given-names>A.</given-names>
</name>
<etal/>
</person-group>. (<year>2010</year>). <article-title>The genome analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data</article-title>. <source>Genome. Res.</source> <volume>20</volume>, <fpage>1297</fpage>&#x2013;<lpage>1303</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1101/gr.107524.110</pub-id>
</citation>
</ref>
<ref id="B51">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Megyeri</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Miko&#x2032;</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Molna&#x2032;r</surname> <given-names>I.</given-names>
</name>
<name>
<surname>Kova&#x2032;cs</surname> <given-names>G.</given-names>
</name>
</person-group> (<year>2011</year>). <article-title>Development of synthetic amphiploids based of <italic>Triticum turgidum</italic> &#xd7; T. monococcum crosses to improve the adaptability of cereals</article-title>. <source>Acta Agron. Hung</source> <volume>59</volume>, <fpage>267</fpage>&#x2013;<lpage>274</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1556/AAgr.59.2011.3.11</pub-id>
</citation>
</ref>
<ref id="B52">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Munns</surname> <given-names>R.</given-names>
</name>
<name>
<surname>James</surname> <given-names>R. A.</given-names>
</name>
<name>
<surname>Xu</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Athman</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Conn</surname> <given-names>S. J.</given-names>
</name>
<name>
<surname>Jordans</surname> <given-names>C.</given-names>
</name>
<etal/>
</person-group>. (<year>2012</year>). <article-title>Wheat grain yield on saline soils is improved by an ancestral Na<sup>+</sup> transporter gene</article-title>. <source>Nat. Biotechnol.</source> <volume>30</volume>, <fpage>360</fpage>&#x2013;<lpage>364</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1038/nbt.2120</pub-id>
</citation>
</ref>
<ref id="B53">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Nemeth</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Yang</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Kasprzak</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Hubbart</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Scholefield</surname> <given-names>D.</given-names>
</name>
<name>
<surname>Mehra</surname> <given-names>S.</given-names>
</name>
<etal/>
</person-group>. (<year>2015</year>). <article-title>Generation of amphidiploids from hybrids of wheat and related species from the genera <italic>Aegilops</italic>, <italic>Secale</italic>, <italic>Thinopyrum</italic>, and <italic>Triticum</italic> as a source of genetic variation for wheat improvement</article-title>. <source>Genome</source> <volume>58</volume>, <fpage>71</fpage>&#x2013;<lpage>79</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1139/gen-2015-0002</pub-id>
</citation>
</ref>
<ref id="B54">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Paull</surname> <given-names>J. G.</given-names>
</name>
<name>
<surname>Pallotta</surname> <given-names>M. A.</given-names>
</name>
<name>
<surname>Langridge</surname> <given-names>P.</given-names>
</name>
<name>
<surname>The</surname> <given-names>T. T.</given-names>
</name>
</person-group> (<year>1994</year>). <article-title>RFLP markers associated with <italic>Sr22</italic> and recombination between chromosome 7A of bread wheat and the diploid species <italic>Triticum boeoticum</italic>
</article-title>. <source>Theor. Appl. Genet.</source> <volume>89</volume>, <fpage>1039</fpage>&#x2013;<lpage>1045</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/BF00224536</pub-id>
</citation>
</ref>
<ref id="B55">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Salina</surname> <given-names>E. A.</given-names>
</name>
<name>
<surname>Leonova</surname> <given-names>I. N.</given-names>
</name>
<name>
<surname>Efremova</surname> <given-names>T. T.</given-names>
</name>
<name>
<surname>R&#xf6;der</surname> <given-names>M. S.</given-names>
</name>
</person-group> (<year>2006</year>). <article-title>Wheat genome structure: translocations during the course of polyploidization</article-title>. <source>Funct. Integr. Genomic</source> <volume>6</volume>, <fpage>71</fpage>&#x2013;<lpage>80</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s10142-005-0001-4</pub-id>
</citation>
</ref>
<ref id="B56">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Shi</surname> <given-names>A. N.</given-names>
</name>
<name>
<surname>Leath</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Murphy</surname> <given-names>J. P.</given-names>
</name>
</person-group> (<year>1998</year>). <article-title>A major gene for powdery mildew resistance transferred to common wheat from wild einkorn wheat</article-title>. <source>Phytopathology</source> <volume>88</volume>, <fpage>144</fpage>&#x2013;<lpage>147</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1094/PHYTO.1998.88.2.144</pub-id>
</citation>
</ref>
<ref id="B57">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Shoeva</surname> <given-names>O. Y.</given-names>
</name>
<name>
<surname>Gordeeva</surname> <given-names>E. I.</given-names>
</name>
<name>
<surname>Arbuzova</surname> <given-names>V. S.</given-names>
</name>
<name>
<surname>Khlestkina</surname> <given-names>E. K.</given-names>
</name>
</person-group> (<year>2017</year>). <article-title>Anthocyanins participate in protection of wheat seedlings from osmotic stress</article-title>. <source>Cereal Res. Commun.</source> <volume>45</volume>, <fpage>47</fpage>&#x2013;<lpage>56</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1556/0806.44.2016.044</pub-id>
</citation>
</ref>
<ref id="B58">
<citation citation-type="book">
<person-group person-group-type="author">
<name>
<surname>Shoeva</surname> <given-names>O. Y.</given-names>
</name>
<name>
<surname>Khlestkina</surname> <given-names>E. K.</given-names>
</name>
</person-group> (<year>2015</year>). &#x201c;<article-title>The specific features of anthocyanin biosynthesis regulation in wheat</article-title>,&#x201d; in <source>Advances in wheat genetics: from genome to field: Proceedings of the 12th International wheat genetics symposium</source> (<publisher-name>Springer</publisher-name>, <publisher-loc>Japan</publisher-loc>), <fpage>147</fpage>&#x2013;<lpage>157</lpage>.</citation>
</ref>
<ref id="B59">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Singh</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Ghai</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Garg</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Chhuneja</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Kaur</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Schnurbusch</surname> <given-names>T.</given-names>
</name>
<etal/>
</person-group>. (<year>2007</year>). <article-title>An integrated molecular linkage map of diploid wheat based on a <italic>Triticum boeoticum</italic> &#xd7; <italic>T. monococcum</italic> RIL population</article-title>. <source>Theor. Appl. Genet.</source> <volume>115</volume>, <fpage>301</fpage>&#x2013;<lpage>312</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s00122-007-0543-z</pub-id>
</citation>
</ref>
<ref id="B60">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Song</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Ma</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Feng</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Guo</surname> <given-names>Q.</given-names>
</name>
<name>
<surname>Zhou</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>X.</given-names>
</name>
<etal/>
</person-group>. (<year>2023</year>a). <article-title>Genome-wide analysis of the universal stress protein gene family in Blueberry and their transcriptional responses to UV-B irradiation and abscisic acid</article-title>. <source>Int. J. Mol. Sci.</source> <volume>24</volume>, <elocation-id>16819</elocation-id>. doi:&#xa0;<pub-id pub-id-type="doi">10.3390/ijms242316819</pub-id>
</citation>
</ref>
<ref id="B61">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Song</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Ma</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Guo</surname> <given-names>Q.</given-names>
</name>
<name>
<surname>Zhou</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Zhou</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Ming</surname> <given-names>Z.</given-names>
</name>
<etal/>
</person-group>. (<year>2023</year>b). <article-title>MYB pathways that regulate UV-B-induced anthocyanin biosynthesis in blueberry (<italic>Vaccinium corymbosum</italic>)</article-title>. <source>Front. Plant Sci.</source> <volume>14</volume>. doi:&#xa0;<pub-id pub-id-type="doi">10.3389/fpls.2023.1125382</pub-id>
</citation>
</ref>
<ref id="B62">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Song</surname> <given-names>W. J.</given-names>
</name>
<name>
<surname>Zhong</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Yu</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Xia</surname> <given-names>W. H.</given-names>
</name>
<name>
<surname>Shu</surname> <given-names>X. L.</given-names>
</name>
<name>
<surname>Wu</surname> <given-names>D. X.</given-names>
</name>
<etal/>
</person-group>. (<year>2020</year>). <article-title>Current status on research and utilization of colored rice</article-title>. <source>Chin. J. @ Rice Sci.</source> <volume>34</volume>, <fpage>191</fpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.16819/j.1001-7216.2020.9137</pub-id>
</citation>
</ref>
<ref id="B63">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Stracke</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Jahns</surname> <given-names>O.</given-names>
</name>
<name>
<surname>Keck</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Tohge</surname> <given-names>T.</given-names>
</name>
<name>
<surname>Niehaus</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Fernie</surname> <given-names>A. R.</given-names>
</name>
<etal/>
</person-group>. (<year>2010</year>). <article-title>Analysis of PRODUCTION OF FLAVONOL GLYCOSIDES-dependent flavonol glycoside accumulation in <italic>Arabidopsis thaliana</italic> plants reveals MYB11-, MYB12-and MYB111-independent flavonol glycoside accumulation</article-title>. <source>New Phytol.</source> <volume>188</volume>, <fpage>985</fpage>&#x2013;<lpage>1000</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1111/j.1469-8137.2010.03421.x</pub-id>
</citation>
</ref>
<ref id="B64">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Tanaka</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Brugliera</surname> <given-names>F.</given-names>
</name>
<name>
<surname>Chandler</surname> <given-names>S.</given-names>
</name>
</person-group> (<year>2009</year>). <article-title>Recent progress of flower colour modification by biotechnology</article-title>. <source>Int. J. Mol. Sci.</source> <volume>10</volume>, <fpage>5350</fpage>&#x2013;<lpage>5369</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.3390/ijms10125350</pub-id>
</citation>
</ref>
<ref id="B65">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Tounsi</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Amar</surname> <given-names>S. B.</given-names>
</name>
<name>
<surname>Masmoudi</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Sentenac</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Brini</surname> <given-names>F.</given-names>
</name>
<name>
<surname>Very</surname> <given-names>A.-A.</given-names>
</name>
</person-group> (<year>2016</year>). <article-title>Characterization of two HKT1;4 transporters from <italic>Triticum monococcum</italic> to elucidate the determinants of the wheat salt tolerance Nax1 QTL</article-title>. <source>Plant Cell Physiol.</source> <volume>57</volume>, <fpage>2047</fpage>&#x2013;<lpage>2057</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/pcp/pcw123</pub-id>
</citation>
</ref>
<ref id="B66">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Wang</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Guo</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Du</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Lin</surname> <given-names>Z.</given-names>
</name>
<etal/>
</person-group>. (<year>2019</year>). <article-title>Development and genetic analysis of wheat double substitution lines carrying <italic>Hordeum vulgare</italic> 2H and <italic>Thinopyrum intermedium</italic> 2Ai# 2 chromosomes</article-title>. <source>Crop J.</source> <volume>7</volume>, <fpage>163</fpage>&#x2013;<lpage>175</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1016/j.cj.2018.11.003</pub-id>
</citation>
</ref>
<ref id="B67">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Wang</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Li</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Shen</surname> <given-names>T.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Yi</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Meng</surname> <given-names>T.</given-names>
</name>
<etal/>
</person-group>. (<year>2023</year>). <article-title>A near-complete genome sequence of einkorn wheat provides insight into the evolution of wheat A subgenomes</article-title>. <source>Plant Commun</source>. <volume>5</volume> (<issue>5</issue>), <page-range>100768</page-range>. doi:&#xa0;<pub-id pub-id-type="doi">10.1016/j.xplc.2023.100768</pub-id>
</citation>
</ref>
<ref id="B68">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Yang</surname> <given-names>G. H.</given-names>
</name>
<name>
<surname>Li</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Gao</surname> <given-names>J. W.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>J. Z.</given-names>
</name>
<name>
<surname>Zhao</surname> <given-names>X. Q.</given-names>
</name>
<name>
<surname>Zheng</surname> <given-names>Q.</given-names>
</name>
<etal/>
</person-group>. (<year>2004</year>). <article-title>Cloning and expression of two chalcone synthase and a flavonoid 3&#x2019;5&#x2019;-hydroxylase 3&#x2019;-end cDNAs from developing seeds of blue-grained wheat involved in anthocyanin biosynthetic pathway</article-title>. <source>Acta Bot. Sin.</source> <volume>46</volume>, <fpage>588</fpage>&#x2013;<lpage>594</lpage>. doi:&#xa0;1672-6650(2004)46:5&gt;588:CAEOTC&gt;2.0.TX;2-1
</citation>
</ref>
<ref id="B69">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Yu</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>D.</given-names>
</name>
<name>
<surname>Wu</surname> <given-names>W.</given-names>
</name>
<name>
<surname>Yang</surname> <given-names>W.</given-names>
</name>
<name>
<surname>Sun</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Li</surname> <given-names>X.</given-names>
</name>
<etal/>
</person-group>. (<year>2017</year>). <article-title>Development of an integrated linkage map of einkorn wheat and its application for QTL mapping and genome sequence anchoring</article-title>. <source>Theor. Appl. Genet.</source> <volume>130</volume>, <fpage>53</fpage>&#x2013;<lpage>70</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s00122-016-2791-2</pub-id>
</citation>
</ref>
<ref id="B70">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zapata</surname> <given-names>J. M.</given-names>
</name>
<name>
<surname>Calderon</surname> <given-names>A. A.</given-names>
</name>
<name>
<surname>Ros Barcelo</surname> <given-names>A.</given-names>
</name>
</person-group> (<year>1995</year>). <article-title>Actual browning and peroxidase level are not correlated in red and white berries from grapevine (<italic>Vitis vinifera</italic>) cultivars</article-title>. <source>Fruit Variet J.</source> <volume>49</volume>, <fpage>82</fpage>&#x2013;<lpage>84</lpage>.</citation>
</ref>
<ref id="B71">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zeven</surname> <given-names>A.</given-names>
</name>
</person-group> (<year>1991</year>). <article-title>Wheats with purple and blue grains: a review</article-title>. <source>Euphytica</source> <volume>56</volume>, <fpage>243</fpage>&#x2013;<lpage>258</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/BF00042371</pub-id>
</citation>
</ref>
<ref id="B72">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zeller</surname> <given-names>F. J.</given-names>
</name>
<name>
<surname>Cerme&#xf1;o</surname> <given-names>M. C.</given-names>
</name>
<name>
<surname>Miller</surname> <given-names>T. E</given-names>
</name>
</person-group> (<year>1991</year>). <article-title>Cytological analysis on the distribution and origin of the alien chromosome pair conferring blue aleurone color in several European common wheat (Triticum aestivum L.) strains</article-title>. <source>Theor Appl Genet</source>, <volume>81</volume>(<issue>4</issue>): <fpage>551</fpage>&#x2013;<lpage>558</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/BF00219448</pub-id>
</citation>
</ref>
<ref id="B73">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zhang</surname> <given-names>L. Q.</given-names>
</name>
<name>
<surname>Yen</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Zheng</surname> <given-names>Y. L.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>D. C.</given-names>
</name>
</person-group> (<year>2007</year>). <article-title>Meiotic restriction in emmer wheat is controlled by one or more nuclear genes that continue to function in derived lines</article-title>. <source>Sex Plant Reprod.</source> <volume>20</volume>, <fpage>159</fpage>&#x2013;<lpage>166</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s00497-007-0052-x</pub-id>
</citation>
</ref>
<ref id="B74">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zhang</surname> <given-names>M. H.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Peng</surname> <given-names>T.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>D. H.</given-names>
</name>
<name>
<surname>Liang</surname> <given-names>D. Y.</given-names>
</name>
<name>
<surname>Li</surname> <given-names>H. Y.</given-names>
</name>
<etal/>
</person-group>. (<year>2021</year>). <article-title>Identification of a recessive gene <italic>YrZ15-1370</italic> conferring adult plant resistance to stripe rust in wheat-<italic>Triticum boeoticum</italic> introgression line</article-title>. <source>Theor. Appl. Genet.</source> <volume>134</volume>, <fpage>2891</fpage>&#x2013;<lpage>2900</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s00122-021-03866-3</pub-id>
</citation>
</ref>
<ref id="B75">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zhang</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Lin</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Lin</surname> <given-names>W.</given-names>
</name>
<etal/>
</person-group>. (<year>2017</year>). <article-title>GA-DELLA pathway is involved in regulation of nitrogen deficiency-induced anthocyanin accumulation</article-title>. <source>Plant Cell Rep.</source> <volume>36</volume>, <fpage>557</fpage>&#x2013;<lpage>569</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s00299-017-2102-7</pub-id>
</citation>
</ref>
<ref id="B76">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zhang</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Pang</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Duan</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Ji</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Jiang</surname> <given-names>Y.</given-names>
</name>
</person-group> (<year>2005</year>). <article-title>Role of peroxidase in anthocyanin degradation in litchi fruit pericarp</article-title>. <source>Food Chem.</source> <volume>90</volume>, <fpage>47</fpage>&#x2013;<lpage>52</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1016/j.foodchem.2004.03.023</pub-id>
</citation>
</ref>
</ref-list>
</back>
</article>