Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes

State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-Sen University, Guangzhou, China.
PLoS Genetics (Impact Factor: 8.17). 06/2011; 7(6):e1002100. DOI: 10.1371/journal.pgen.1002100
Source: PubMed

ABSTRACT Genealogical patterns in different genomic regions may be different due to the joint influence of gene flow and selection. The existence of two subspecies of cultivated rice provides a unique opportunity for analyzing these effects during domestication. We chose 66 accessions from the three rice taxa (about 22 each from Oryza sativa indica, O. sativa japonica, and O. rufipogon) for whole-genome sequencing. In the search for the signature of selection, we focus on low diversity regions (LDRs) shared by both cultivars. We found that the genealogical histories of these overlapping LDRs are distinct from the genomic background. While indica and japonica genomes generally appear to be of independent origin, many overlapping LDRs may have originated only once, as a result of selection and subsequent introgression. Interestingly, many such LDRs contain only one candidate gene of rice domestication, and several known domestication genes have indeed been "rediscovered" by this approach. In summary, we identified 13 additional candidate genes of domestication.

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Available from: Tony Greenberg, Aug 27, 2015
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    • "Xu et al. (2012) directly resequenced 50 accessions of cultivated and wild rice, and identified genome-wide variation patterns including the identification of more than 6.5 million high-quality SNPs, 808,000 InDels, 94,700 SVs (>100 bp) and 1,676 CNVs. In another study, 66 accessions from three taxa (22 each from O. sativa indica, O. sativa japonica and O. rufipogon) were chosen for whole genome sequencing (He et al. 2011). Huang et al. (2012a) also generated genome sequences from 446 geographically diverse accessions of the wild rice species O. rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties, to construct a comprehensive map of rice genome variation. "
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    • "The dense, genome-wide SNP marker coverage afforded by NGS genotyping [reviewed by Davey et al. (2011)] is now readily applied in genetic mapping of domestication-related traits, including in mapping populations derived from traditional biparental crosses (e.g., crop X wild parents ), advanced intercrossed populations derived from diverse parental lines [e.g., nested association mapping (NAM); Buckler et al., 2009; McMullen et al., 2009; Larsson et al., 2013, and genome-wide association mapping in populations of unrelated individuals (GWAS); Ramsay et al., 2011; Harper et al., 2012; Huang et al., 2012b; Riedelsheimer et al., 2012]. Genome resequencing and/or genome-wide SNP scans are also being used to identify candidate genomic regions bearing molecular signatures of selection during domestication (e.g., low nucleotide diversity, augmented linkage disequilibrium) (He et al., 2011; Harper et al., 2012; Huang et al., 2012a; Cavanagh et al., 2013; Hufford et al., 2013). Unlike methods based on trait mapping, such selection screens do not require any a priori assumptions about the traits that were subject to selection during domestication , and they can thus potentially reveal genes underlying subtle phenotypic changes such as metabolic shifts (e.g., Hufford et al., 2012). "
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    • "Because three of those were rare alleles, their exclusion made it impossible to evaluate the gene. OsRMC extreme conservation may be due its close proximity to sh4 (locus responsible for reducing grain shattering along rice domestication, located 34 020 Kb apart) (He et al., 2011). Another 18 SNPs, identified as rare in the target genes, could not be analysed in our association panel. "
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