Abstract
The origin and domestication of rice has been a subject of considerable debate in the post-genomic era. Rice varieties have been categorized based on isozyme and DNA markers into two broad cultivar groups, Indica and Japonica. Among other well-known cultivar groups Aus varieties are closer to Indica and Aromatic varieties including Basmati are closer to Japonica, while deep-water rice varieties share kinship to both Indica and Japonica cultivar groups. Here, we analyzed haplotype networks and phylogenetic relationships in a diverse set of genotypes including Indian Oryza nivara/Oryza rufipogon wild rice accessions and representative varieties of four rice cultivar groups based on pericarp color (Rc), grain size (GS3) and eight different starch synthase genes (GBSSI, SSSI, SSIIa, SSIIb, SSIIIa, SSIIIb, SSIVa, and SSIVb). Aus cultivars appear to have the most ancient origin as they shared the maximum number of haplotypes with the wild rice populations, while Indica, Japonica and Aromatic cultivar groups showed varying phylogenetic origins of these genes. Starch synthase genes showed higher variability in cultivated rice than wild rice populations, suggesting diversified selection during and after domestication. O. nivara/O. rufipogon wild rice accessions belonging to different sub-populations shared common haplotypes for all the 10 genes analyzed. Our results support polyphyletic origin of cultivated rice with a complex pattern of migration of domestication alleles from wild to different rice cultivar groups. The findings provide novel insights into evolutionary and domestication history of rice and will help utilization of wild rice germplasm for genetic improvement of rice cultivars.
Highlights
Rice is the most important food crop of Asia, and its domestication began at least 9,000 years ago, geographical location(s) of its origin has become controversial (Zeder, 2011; Zou et al, 2015)
Two major hypotheses have been proposed on the origin and domestication of rice: (i) single origin model suggesting that Indica and Japonica cultivars were domesticated at a single location from the wild rice O. rufipogon (Molina et al, 2011; Huang et al, 2012). (ii) Independent domestication at more than one location model suggesting that the major groups of rice cultivars were domesticated separately in different parts of Asia from separate wild rice ancestors (Vitte et al, 2004; Londo et al, 2006; Civan et al, 2015; Singh et al, 2015)
Most recent study on 286 diverse O. rufipogon accessions originating from 15 countries using 113,739 nuclear single nucleotide polymorphisms (SNPs) and 25 polymorphic sites in chloroplast sequence has confirmed that three separate wild rice sub-populations were genetically and geographically closely related to Indica, Aus, and Japonica cultivar groups of O. sativa (Kim et al, 2016)
Summary
Rice is the most important food crop of Asia, and its domestication began at least 9,000 years ago, geographical location(s) of its origin has become controversial (Zeder, 2011; Zou et al, 2015). The loss of function mutation in this gene prevents development of a pigmented pericarp layer (Sweeney et al, 2006) Another crucial trait involved in rice domestication is grain size, which in addition to other minor genes is controlled by a major gene GS3 located on rice chromosome 3. In the present study we investigated the SNP haplotype variation in Rc gene for pericarp color, GS3 gene for grain size and eight different starch synthase genes in a large set of wild rice accessions together with representative varieties of major rice cultivar groups to understand the process of rice evolution and domestication by employing haplotype network and phylogenetic analysis
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