ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Breeding
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1644153
Integrating QTL mapping, BSA-Seq and RNA-Seq to identify candidate genes regulating seed storability from Dongxiang wild rice
Provisionally accepted
- 1Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
- 2College of Agronomy, Hunan Agricultural University, Changsha, China
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Rice seed storability (SS) is crucial for germplasm preservation, agricultural production, grain storage and food security. Dongxiang wild rice (Oryza rufipogon Griff. hereafter DXWR) belongs to the common wild rice adapted in the northern most area and possesses strong SS. Xieqingzao B (XB) is a maintainer widely used in hybrid rice. DXWR and XB was crossed and then backcrossed with XB for four times to develop the strong SS line 19H19 in the BC4F2. 19H19, XB and their 120 BC5F2 lines were employed to study SS with artificially aging. A genetic map identified four quantitative trait locus (QTLs), BSA-seq identified four QTLs, and qSS6.1 was co-identified by both ways. By combining QTL mapping, BSA-seq and RNA-seq, 31 candidate genes were identified in total for SS. Among these candidate genes, the gene Os06g0287500 in qSS6.1 interval was related to 'defense response', where it was down-regulated in 19H19, but up-regulated in XB after aging because there were some non-synonymous mutations and deletions in its exon of parental XB. Genetic effects on SS of the candidate gene showed that gene Os06g0287500 was significantly associated with SS in rice. Haplotype analysis on Os06g0287500 among 141 core germplasm accessions revealed that the SS of Hap1/DXWR(19H19) type accessions was significantly stronger than that of Hap2/XB type and Hap3 under artificially aging conditions. And the Hap1/DXWR (19H19) accessions had the strongest SS among three haplotypes, no matter whether under artificially or naturally aging conditions. One gene interaction network regulating SS in rice was revealed based on STRING database assay, wherein the differentially expressed genes (DEGs) related to 'kinase activity' interacted with Os06g0287500. Therefore, Os06g0287500 was the promising candidate gene involved in SS in rice. These findings not only provide important information for understanding the genetic mechanisms on SS in rice, but also exploit new foreign genes for SS to broaden gene pool of cultivated rice and develop new rice varieties with high SS by QTL pyramiding.
Keywords: Dongxiang wild rice, Seed storability, RNA-Seq, BSA-seq, haplotype
Received: 10 Jun 2025; Accepted: 01 Jul 2025.
Copyright: © 2025 Zhou, Wu, Wang, He and Hu. 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) or licensor 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.
* Correspondence: Biaolin Hu, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
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