Molecular Evolution Of Rice Seed Shattering Genes

Oryzasativa L.,commonly known as Asian rice,is the third most important crop in the world and provide staple food for more than half of the world’s population.O.sativa belongs to the tribe Oryzeae of family Poaceae.Since the domestication of cultivated rice,it solves the fundamental problem of food security for our society,and laid foundation for the formation and development of Asian civilization.Seed shattering is a very important agronomic trait of rice domestication.The loss of seed shattering is a critical step in the process of rice domestication,as the gain of this trait results in the retention of grain on the panicle after its maturity,which is beneficial for the farmer to collect the grains.On the contrary,seed shattering is an advantage trait that allows the wild rice disperses its seeds under natural environment.In this study,we compared genome-wide nucleotide diversity between cultivated and wild rice based on the whole genome data.Then we calculated nucleotide diversity for six rice seed shattering related genes,including sh4,q SH1,SHAT1,Os CPL1,Os Sh1 and SH5.Population genetic analyses at these genes revealed that cultivated rice(π=0.00633)showed obviously decrease in nucleotide diversity compared with its wild progenitor(π=0.00803)at the whole genome level.Among the six rice seed shattering genes,sh4 is possibly the first target gene that was selected during rice domestication.Our results also detected signals of artificial selection at the gene Os Sh1.Regarding to the q SH1,ithas undergone selection after the divergence between temperatejaponica and indica.As for SH5,it needs further investications to determine whether SH5 has undergone selection in rice domestication.However,no signals of artificial selection were detected at the remaining genes,SHAT1 and Os CPL1.In summary,our results suggested that genes involved in the regulatory network of rice seed shattering have undergone distinct selection pressures during rice domestication,with the sh4,q SH1 and Os Sh1 showing selection signal but the remaining genes evolving under neutral model.