The ties of brotherhood between japonica and indica rice for regional adaptation

Selection of beneficial genomic variants was crucial for regional adaptation of crops during domestication, but the underlying genomic basis remains largely unexplored. Here we report a genome-wide selective-sweep analysis of 655 japonica and 1,205 indica accessions selected from 2,673 landraces through principal component analysis to identify 5,636 non-synonymous single nucleotide polymorphisms (SNPs) fixed in at least one subspecies. We classified these SNPs into three groups, jiS (japonica- and indica-selected), jS (japonica-selected only), and iS (indica-selected only), and documented evidence for selection acting on these groups, their relation to yield-related traits, such as heading date, and their practical value in cropping area prediction. We also demonstrated the role of a jiS-SNP-containing gene in temperature adaptability. Our study informs genes underpinning adaptation that may shape Green Super Rice and proposes a time-saving, cost-reducing selection strategy of genomic breeding, sweep-SNP-guided selection, for developing regionally-adapted heterosis.