Genome-Wide Association Study for Seed Dormancy Using Re-Sequenced Germplasm under Multiple Conditions in Rice

文献类型： 外文期刊

第一作者： Chen, Dandan

作者： Chen, Dandan;Peng, Ting;Chen, Dandan;Zou, Wenli;Zhang, Mingpei;Liu, Jindong;Chen, Liang;Ye, Guoyou;Zhang, Mingpei;Zhang, Mingpei;Ye, Guoyou

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关键词： seed dormancy and germination; QTLs; candidate gene; expression level; hormone

期刊名称：INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES （ 影响因子：5.6； 五年影响因子：6.2 ）

ISSN：

年卷期： 2023 年 24 卷 7 期

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收录情况： SCI

摘要： Seed dormancy is a key factor used to determine seed germination in rice production. So far, only a few genes controlling seed dormancy have been reported, and the genetic mechanism of rice seed dormancy is still elusive. In this study, a population of 195 diverse re-sequenced accessions from 40 countries was evaluated for the seed germination rate (GR) without dormancy breaking (WDB) as a control and under dry heating (DH) and gibberellic acid (GA) treatments, as dormancy breaking agents to identify QTLs for seed dormancy. Phenotypic assessment revealed that these accessions had abundant variations in seed dormancy. GWAS using 1,120,223 high-quality single nucleotide polymorphisms (SNPs) and a mixed linear model (MLM) incorporating both principal components (PCs) and kinship (K) identified 30 QTLs on 10 chromosomes, accounting for 7.3-20.4% of the phenotypic variance in GR. Ten of the QTLs were located in the regions of previously reported QTLs, while the rest were novel ones. Thirteen high-confidence candidate genes were predicted for the four QTLs detected in two or three conditions (qGR4-4, qGR4-5, qGR8 and qGR11-4) and one QTL with a large effect (qGR3). These genes were highly expressed during seed development and were significantly regulated by various hormone treatments. This study provides new insights into the genetic and molecular basis of rice seed dormancy/germination. The accessions with moderate and strong dormancy and markers for the QTLs and candidate genes are useful for attaining a proper level of seed dormancy.

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