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ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Functional and Applied Plant Genomics
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1546580
This article is part of the Research TopicImproving Yield and Quality of Cereal Crops: Exploring and Utilizing Genes for Green and Efficient TraitsView all 11 articles
Identification of Key Genes Associated with Mesocotyl Length through a Genome-Wide Association Study in Rice
Provisionally accepted- 1Yangtze University, Jingzhou, Hubei Province, China
- 2Chinese Academy of Agricultural Sciences (CAAS), Beijing, Beijing Municipality, China
- 3Sichuan Agricultural University, Chengdu, China
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Mesocotyl length is a key trait affecting seedling emergence and establishment in dry direct-seeded rice, with longer mesocotyls promoting rapid and uniform emergence, thereby forming larger effective populations. Therefore, mining genes associated with mesocotyl length will facilitate the development of rice varieties suitable for dry direct seeding. In this study, four QTLs associated with mesocotyl length and two QTLs associated with seedling emergence were identified using 300 rice varieties, with phenotypic contributions ranging from 6.96-8.48%. Among them, the mesocotyl length-related QTL qML3 located at 28.03-28.43 Mb on chromosome 3 was detected at both sowing depths. Gene annotation analysis identified nine candidate 2 genes related to plant hormones and transcription factors for qML3. Further investigation revealed three genes (LOC_Os03g49250, LOC_Os03g49400, and LOC_Os03g49510) exhibiting distinct haplotypes with significant differences in mesocotyl length, suggesting they may be causal genes for qML3. This study lays the foundation for cloning and functional characterization of the qML3 gene.
Keywords: rice, Mesocotyl length, genome-wide association analysis, haplotype, candidate gene
Received: 17 Dec 2024; Accepted: 21 Apr 2025.
Copyright: © 2025 Xue, Wang, Han, Cui, Han, Deng and Ma. 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:
Longzhi Han, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, Beijing Municipality, China
Jianxin Deng, Yangtze University, Jingzhou, Hubei Province, China
Xiaoding Ma, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, Beijing Municipality, China
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