Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China.
J Integr Plant Biol. 2022 Jun;64(6):1246-1263. doi: 10.1111/jipb.13266. Epub 2022 May 31.
Pre-harvest sprouting (PHS), which reduces grain yield and quality, is controlled by seed dormancy genes. Because few dormancy-related genes have been cloned, the genetic basis of seed dormancy in rice (Oryza sativa L.) remains unclear. Here, we performed a genome-wide association study and linkage mapping to dissect the genetic basis of seed dormancy in rice. Our findings suggest that Seed Dormancy4 (Sdr4), a central modulator of seed dormancy, integrates the abscisic acid and gibberellic acid signaling pathways at the transcriptional level. Haplotype analysis revealed that three Sdr4 alleles in rice cultivars already existed in ancestral Oryza rufipogon accessions. Furthermore, like the semi-dwarf 1 (SD1) and Rc loci, Sdr4 underwent selection during the domestication and improvement of Asian cultivated rice. The distribution frequency of the Sdr4-n allele in different locations in Asia is negatively associated with local annual temperature and precipitation. Finally, we developed functional molecular markers for Sdr4, SD1, and Rc for use in molecular breeding. Our results provide clues about the molecular basis of Sdr4-regulated seed dormancy. Moreover, these findings provide guidance for utilizing the favorable alleles of Sdr4 and Rc to synergistically boost PHS resistance, yield, and quality in modern rice varieties.
采前发芽（PHS）会降低谷物的产量和质量，其受到种子休眠基因的控制。由于休眠相关基因的克隆数量较少，因此水稻（Oryza sativa L.）种子休眠的遗传基础仍不清楚。在这里，我们进行了全基因组关联研究和连锁图谱构建，以剖析水稻种子休眠的遗传基础。我们的研究结果表明，作为种子休眠的中央调节剂，种子休眠 4 号基因（Sdr4）在转录水平上整合了脱落酸和赤霉素信号通路。单倍型分析表明，水稻品种中的三个 Sdr4 等位基因已经存在于祖先 Oryza rufipogon 中。此外，与半矮秆 1 号（SD1）和 Rc 位点一样，Sdr4 在亚洲栽培稻的驯化和改良过程中经历了选择。亚洲不同地区 Sdr4-n 等位基因的分布频率与当地的年平均温度和降水量呈负相关。最后，我们开发了用于 Sdr4、SD1 和 Rc 的功能性分子标记，可用于分子育种。我们的研究结果为 Sdr4 调控种子休眠的分子基础提供了线索。此外，这些发现为利用 Sdr4 和 Rc 的有利等位基因协同提高现代水稻品种的 PHS 抗性、产量和品质提供了指导。
