Identification of Selection Signatures in Commercial Asian Rice Subspecies Deciphered Selection Footprints for Four Overrepresented Biological Processes

Abstract

BackgroundSelective breeding pressures have led to gradual genomic changes in Asian commercial rice, which have shaped selection footprints on its genome level. Tracing genomic selection footprints might be illuminative for better understanding of recent selection breeding objectives, and how breeding strategies have formed the Asian commercial rice genome. ResultsIn this study, the genotypic information (HDRA 700K) of four Asian commercial rice subspecies including Indica (n=498), Aus (n=187), Temperate japonica (n=241), and Tropical japonica (n=361) were downloaded from Rice Diversity Project database (http://www.ricediversity.org) to detect selection signatures by employing the Z-transformed of fixation index and Tajima’s D test, based on a sliding window approach. Although we could not identify overrepresented genomic regions underlying selection pressure among all aforementioned Asian commercial rice subspecies, interestingly, our findings revealed four overrepresented biological processes underlying selection pressure including proteolysis (GO:0006508), phosphorylation (GO:0016310), protein catabolic process (GO:0030163), and transmembrane transport (GO:0055085) that might be associated with immunity, senescing leaves, transporting, and absorption of ions. ConclusionsThese results can provide knowledge on how breeding efforts shaped the Asian commercial rice subspecies genome, and which genomic regions of these subspecies have been targeted in recent decades.