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ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Functional and Applied Plant Genomics
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1412953
This article is part of the Research Topic Multi-Omics, Genetic Evolution and Crop Domestication View all 4 articles

TriticeaeSSRdb: A Comprehensive Database of Simple Sequence Repeats in Triticeae

Provisionally accepted
Tingting Li Tingting Li 1,2Shaoshuai Cai Shaoshuai Cai 1*Zhibo Cai Zhibo Cai 2*Yi Fu Yi Fu 1*Wenqiang Liu Wenqiang Liu 1*Xiangdong Zhu Xiangdong Zhu 1Chongde Lai Chongde Lai 1,3*Licao Cui Licao Cui 1Wenqiu Pan Wenqiu Pan 1*Yihan Li Yihan Li 1*
  • 1 College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi Province, China
  • 2 State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, China
  • 3 Nanchang Key Laboratory of Fermentation Application Technology, Jiangxi Agricultural University, Nanchang, Jiangxi Province, China

The final, formatted version of the article will be published soon.

    Microsatellites, known as simple sequence repeats (SSRs), are short tandem repeats of 1 to 6 nucleotide motifs found in all genomes, particularly eukaryotes. They are widely used as co-dominant markers in genetic analyses and molecular breeding. Triticeae, a tribe of grasses, includes major cereal crops such as bread wheat, barley, and rye, as well as abundant forage and lawn grasses, playing a crucial role in global food production and agriculture. To enhance genetic work and expedite the improvement of Triticeae crops, we have developed TriticeaeSSRdb, an integrated and user-friendly database. It contains 3,891,705 SSRs from 21 species and offers browsing options based on genomic regions, chromosomes, motif types, and repeat motif sequences. Advanced search functions allow personalized searches based on chromosome location and length of SSR. Users can also explore the genes associated with SSRs, design customized primer pairs for PCR validation, and utilize practical tools for whole-genome browsing, sequence alignment, and in silico SSR prediction from local sequences. We continually update TriticeaeSSRdb with additional species and practical utilities. We anticipate that this database will greatly facilitate trait genetic analyses and enhance molecular breeding strategies for Triticeae crops. Researchers can freely access the database at http://triticeaessrdb.com/.

    Keywords: Genome, microsatellite, SSR, database, molecular breeding

    Received: 06 Apr 2024; Accepted: 08 May 2024.

    Copyright: © 2024 Li, Cai, Cai, Fu, Liu, Zhu, Lai, Cui, Pan and Li. 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:
    Shaoshuai Cai, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
    Zhibo Cai, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, China
    Yi Fu, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
    Wenqiang Liu, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
    Chongde Lai, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
    Wenqiu Pan, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
    Yihan Li, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China

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