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

Abstract Preharvest sprouting (PHS), a deleterious phenotype that occurs frequently in rice growing regions with high temperature and precipitation, negatively affects yield, quality, and processing. Seed dormancy can prevent PHS. We report discovery of qSDR3.1, a new quantitative trait locus (QTL) for seed dormancy in rice. knockout lines of qSDR3.1 exhibited significant reduction in PHS. The qSDR3.1 locus negatively regulated seed dormancy by directly inhibiting the transcriptional activity of ABSCISIC ACID INSENSITIVE5 (ABI5). Haplotype analysis showed that qSDR3.1 was divided into five haplotypes and three amino acid (aa) types. The 102nd (aa102) and 105th (aa105) amino acids of qSDR3.1 were the key amino acids responsible for the differences in dormancy between Xian and Geng. Genetic diversity analysis revealed that qSDR3.1 was artificially selected during domestication. We proposed a two-line model for the process of rice dormancy domestication from wild rice to Xian and Geng, and we provide new candidate genes and germplasm for genetic improvement of rice seed dormancy.