Estimating the Age of Domestication Genes in Rice

During rice domestication many economically important traits, such as non-shattering and erect growth, were selected by ancient farmers. As a result, the  genes underlying these traits were artificially selected. These genes are very informative about rice domestication history, allowing us to get insight into the origin of rice domestication, the divergence of rice subgroups and gene flow among different rice subgroups. It is tempting to date the fixation time of these genes, since it would provide new insight into rice domestication history. However, for the latter, there is still few methods to estimate it. Here we present a simple method to estimate allelic fixation time by counting new mutations in the selective sweep haplotype and applying molecular clock to estimate the age of the sweep. When applied to rice Sh4 and PROG1 gene, we successfully estimate their age to be ~4000y B.P. and ~7000y B.P.