Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

Abstract

Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors (Oryza rufipogon and Oryza nivara) to >15 × raw data coverage. We investigated genome-wide variation patterns in rice and obtained 6.5 million high-quality single nucleotide polymorphisms (SNPs) after excluding sites with missing data in any accession. Using these population SNP data, we identified thousands of genes with significantly lower diversity in cultivated but not wild rice, which represent candidate regions selected during domestication. Some of these variants are associated with important biological features, whereas others have yet to be functionally characterized. The molecular markers we have identified should be valuable for breeding and for identifying agronomically important genes in rice.

Rapid diversification of five Oryza AA genomes associated with rice adaptation

“…We measured potential gene extinction events by estimating the number of gene families that were entirely lost in SAT while being retained in other species, and found that ∼547 genes (488 families × 1.12 genes per family) were lost in SAT after the divergence from a common ancestor with NIV. To identify gene loss events and/or novel gene creations in SAT, we performed de novo assemblies of unmapped reads from the other five AA-genome species using a previously reported methodology, with some modifications (41). We found 490 genes that were lost in the SAT genome, in agreement with the estimated number based on the loss of gene families across the AA-genome Oryza species (SI Appendix, Dataset S10a).…”

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

“…Sequence diversity analysis, including PCA, dendrogram, and diversity parameters θπ and θw, were measured as described 54 . F ST values for 31 elite cultivars and 25 landraces were calculated by using population branch statistics 55 and these values were compared using FDIST 28 .…”

A map of rice genome variation reveals the origin of cultivated rice

“…Despite the fact that rice is a major cereal and a model system for plant biology, the evolutionary origins and domestication processes of cultivated rice have long been debated. The puzzles about rice domestication include: (1) where the geographic origin of cultivated rice was, (2) which types of O. rufipogon served as its direct wild progenitor, and (3) whether the two subspecies of cultivated rice, indica and japonica, are derived from a single or multiple domestications.A wide range of genetic and archaeological studies have been carried out to examine the phylogenetic relationships of rice, and investigate the demographic history of rice domestication [10][11][12][13][14][15][16][17][18][19] . Molecular phylogenetic analyses indicated that indica and japonica originated independently 3,10,20 .…”

“…A wide range of genetic and archaeological studies have been carried out to examine the phylogenetic relationships of rice, and investigate the demographic history of rice domestication [10][11][12][13][14][15][16][17][18][19] . Molecular phylogenetic analyses indicated that indica and japonica originated independently 3,10,20 .…”

“…Recently, a demographic analysis of single-nucleotide polymorphisms (SNPs) detected from 630 gene fragments suggested a single domestication origin of rice 17 . Meanwhile, population genetics analyses of genome-wide data of cultivated and wild rice have tended to suggest that indica and japonica genomes generally appear to be of independent origin 18,19 , but many genomic segments bearing domestication alleles may have originated only once 18 . Despite these advances, wider sampling with population-scale whole-genome sequencing is needed to shed greater light on the evolutionary history of rice domestication.…”