Genome-wide analysis of polymorphisms identified domestication-associated long low diversity region carrying important rice grain size/weight QTL

Abstract

Rice grain size and weight are major determinants of grain quality and yield and so have been under rigorous selection since domestication. However, genetic basis for contrasting grain size/weight trait among Indian germplasms and their association with domestication‐driven evolution is not well understood. In this study, two long (LGG) and two short grain (SGG) genotypes were resequenced. LGG (LGR and PB 1121) differentiated from SGG (Sonasal and Bindli) by 504,439 SNPs and 78,166 InDels. The LRK gene cluster was different and a truncation mutation in the LRK8 kinase domain was associated with LGG. Phylogeny with 3000 diverse rice accessions revealed that the four sequenced genotypes belonged to japonica group and were at the edge of the clades indicating them to be the potential source of genetic diversity available in Indian rice germplasm. Six SNPs were significantly associated with grain size/weight and top four of them could be validated in mapping population, suggesting this study as a valuable resource for high‐throughput genotyping. A contiguous ~ 6 Mb long low diversity region (LDR) carrying a major grain weight QTL (harbouring OsTOR gene) was identified on chromosome 5. This LDR was identified as an evolutionary important site with significant positive selection and multiple selection sweeps, and showed association with many domestication‐related traits including grain size/weight. The aus population retained more allelic variations in the LDR than japonica and indica populations, suggesting it to be one of the divergence loci. All the data and analyses can be accessed from RiceSzWtBase database.