Evolutionary Insights Based on Haplotype and Phylogenetic Analysis of Red Pericarp, Grain Size and Starch Synthase Genes in Wild and Cultivated Rice

The origin and domestication of rice has been a subject of considerable debate. Rice cultivars have been categorized based on isozyme and DNA markers into two broad groups, ‘Indica’ and ‘Japonica’. Among other well-known groups of cultivated rice varieties, ‘Aus’ is closer to Indica and ‘Aromatic’ including Basmati is closer to Japonica, while deep-water rice varieties belong to both Indica and Japonica cultivar groups. Here, we analyzed haplotype network and phylogenetic relationship in a diverse rice germplasm including a large set of Indian O. nivara / O. rufipogon wild rice accessions and representative varieties of different rice cultivar groups, based on red pericarp (Rc), grain size (GS3) and eight different starch synthase genes (GBSSI, SSSI, SSIIa, SSIIb, SSIIIa, SSIIIb ,SSIVa and SSIVb). Our results show a polyphyletic origin of the cultivated rice. It further indicated that O. nivara / O.rufipogon accessions from wide geographical regions of India have the ancestral haplotypes of all the ten genes analyzed and in some cases the cultivated rice alleles were shared by wild rice populations which could be their probable progenitors. There is a complex pattern of migration of domestication alleles from wild rice to different rice cultivar groups. These findings will be useful in understanding the domestication history of rice and utilization of wild rice germplasm in genetic improvement of rice cultivars.