ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Physiology
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1691426
This article is part of the Research TopicMolecular Basis of Seed Germination and Dormancy, Volume IIView all 3 articles
Mapping of Quantitative Trait Loci for Early Seed Germination Speed Using Whole-Genome Re-sequenced Chromosome Segment Substitution Lines of aus Kasalath in the Background of japonica Nipponbare
Provisionally accepted
- 1Huazhong Agricultural University College of Plant Science and Technology, Wuhan, China
- 2Chinese Academy of Agricultural Sciences Agricultural Genomics Institute at Shenzhen, Shenzhen, China
- 3Foshan University, Foshan, China
- 4China Jiliang University, Hangzhou, China
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Direct-seeding systems in rice require cultivars with enhanced seed vigor to ensure rapid and uniform germination. In this study, we analyzed a population of 42 chromosome segment substitution lines (CSSLs) derived from aus Kasalath in the japonica Nipponbare background, coupled with whole-genome resequencing data, to identify quantitative trait loci (QTLs) associated with early seed germination speed. Phenotypic traits, including germination percentage (GP), germination rate (GR), and germination index (GI), were measured over two consecutive years to ensure robustness. Six stable QTLs were identified, with qSV-1 on chromosome 1 (30.10–30.94 Mb) emerging as the most consistent across evaluations for GP and GI. Functional annotation and gene expression analysis within the 840-kb qSV-1 interval pinpointed C3H10 and OsOFP3 as the primary candidate genes for further investigation. This study underscores the effectiveness of whole-genome resequencing paired with the CSSL platform for precise QTL identification, thereby providing critical genetic resources for improving seed vigor through marker-assisted breeding and functional genomics.
Keywords: rice, seed germination, Seed vigor, Chromosome segment substitution lines (CSSL), whole-genomeresequencing
Received: 23 Aug 2025; Accepted: 06 Oct 2025.
Copyright: © 2025 Shan, Ye, Ruan, Teng and Yu. 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:
Sheng Teng, steng@cjlu.edu.cn
Min Yu, yumin@fosu.edu.cn
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