Nucleotide diversity of 11S seed storage protein gene and its implications for ecological adaptation of Oryza nivara

The mechanism by which a new species arises and adapts to its environment is a fundamental question in evolutionary biology. Seed characteristics such as seed size and nutrient composition are important fitness‐related traits and have been shown to vary greatly among populations and species. However, the significance of variation in seed traits in plant adaptation and speciation remains unclear. We carried out a population genetic study on nucleotide variation of one 11S seed storage protein gene (Pss) of Oryza rufipogon Griff. and O. nivara Sharma & Shastry, two closely related wild rice species. By comparatively examining the genetic variation pattern of the regulatory and coding regions of Pss and fragments of six reference loci across different chromosomes, we found significantly lower polymorphisms at coding regions of the gene (PssI) in O. nivara relative to O. rufipogon. Neutrality tests indicated that the reduction of polymorphisms at PssI in O. nivara was caused by positive selection rather than population demography, implying a role of selection on the 11S seed protein gene. Further phylogenetic and principal component analyses also support the hypotheses that the origin of O. nivara was associated with the adaptive divergence on the coding region of Pss. It is most likely that higher reproductive effort would be favored when O. nivara arose from O. rufipogon populations and adapted to the environment change.