Sdr4 dominates pre‐harvest sprouting and facilitates adaptation to local climatic condition in Asian cultivated rice

Abstract

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.

ABA biosynthesis gene OsNCED3 contributes to preharvest sprouting resistance and grain development in rice

“…Domestication and improvement are usually characterized by reduced nucleotide diversity (Zhao et al, 2022). To explore this association for OsNCED3 , we compared the nucleotide diversity (π) across their genome regions using 4701 rice germplasm accessions and 451 WILD accessions.…”

“…Previous studies showed that freshly harvested seeds in different rice subpopulations exhibit distinct variations in seed dormancy (Zhao et al, 2022). Japonica subgroups had a higher mean germination rate than the IND subgroup, and AUS had the lowest mean germination rate (Zhao et al, 2022). Natural variation analysis showed that japonica rice varieties (TEJ and TRJ) mainly carried the Taken together, in this study, we made the observation that overexpressing OsNCED3 markedly enhanced PHS resistance, grain size and weight, and suggest that OsNCED3 is a valuable genetic resource for PHS resistance and grain development improvement.…”

“…Preharvest sprouting (PHS) in rice ( Oryza sativa L.), induced by long rainy and high‐temperature weather during the harvest season, often occurs in rice‐growing regions of the world, especially in southeastern Asian countries (Du et al, 2018; Lee et al, 2021; Xu et al, 2019). PHS is an undesirable trait in agricultural production owing to its impact on seed viability, grain quality and yield, resulting in significant economic losses worldwide (Chen et al, 2021; Sohn et al, 2021; Zhao et al, 2022). Seed dormancy, an indicator of PHS resistance, is an adaptive trait that allows the seeds of many plant species to remain quiescent until conditions become favorable for germination (Chen et al, 2021; Gubler et al, 2005; Shu et al, 2016; Yang et al, 2020).…”

“…A clear understanding of molecular basis for seed dormancy and germination in rice, a cereal model, would support breeding associated traits. Although much has been done in Arabidopsis with respect to genes involved in the regulation of seed dormancy, much less is known in cereals including rice (Miao et al, 2019; Sohn et al, 2021; Zhao et al, 2022). Seed dormancy is established during seed maturation and its maintenance in the mature seed is precisely regulated by environmental factors and levels of endogenous phytohormones (Chen et al, 2021; Gubler et al, 2005; Karssen et al, 1983; Shu et al, 2016).…”

Novel quantitative trait locus qSDR3.1 represses Oryza sativa. L seed dormancy

“…The proper dormancy of seeds can solve the problem of preharvest sprouting, thereby reducing losses and increasing yield. Unfortunately, during domestication, rice seed dormancy was largely lost 23 . Therefore, it is necessary to identify rice varieties that have strong dormancy and clone dormancy genes to improve rice yield.…”