Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

ABSTRACT: Intensive rice breeding over the past 50 y has dramatically increased productivity especially in the indica subspecies, but our knowledge of the genomic changes associated with such improvement has been limited. In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions from 73 countries, including landraces and modern cultivars. We identified two major subpopulations, indica I (IndI) and indica II (IndII), in the indica subspecies, which corresponded to the two putative heterotic groups resulting from independent breeding efforts. We detected 200 regions spanning 7.8% of the rice genome that had been differentially selected between IndI and IndII, and thus referred to as breeding signatures. These regions included large numbers of known functional genes and loci asso

SUBMITTER: Xie W 

PROVIDER: S-EPMC4593105 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature