Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

Abstract

Rice, the primary source of dietary calories for half of humanity, is the first crop plant for which a high-quality reference genome sequence from a single variety was produced. We used resequencing microarrays to interrogate 100 Mb of the unique fraction of the reference genome for 20 diverse varieties and landraces that capture the impressive genotypic and phenotypic diversity of domesticated rice. Here, we report the distribution of 160,000 nonredundant SNPs. Introgression patterns of shared SNPs revealed the breeding history and relationships among the 20 varieties; some introgressed regions are associated with agronomic traits that mark major milestones in rice improvement. These comprehensive SNP data provide a foundation for deep exploration of rice diversity and gene-trait relationships and their use for future rice improvement.

Fig. 1.

Annotation and distribution of SNPs. (A) Nonsynonymous (12,788) and synonymous (13,698) SNPs predicted from the MBML intersect found in select Pfam domains of rice genes with 30 or more SNPs. χ² significance of the observed nonsynonymous and synonymous SNP distributions for each Pfam group is shown. *, P < 0.05; **, P < 0.001. (B) Allele frequencies at nonrepetitive MBML-intersect sites for SNPs in all annotation groups (Top), genic SNPs (Middle), and large-effect SNPs (Bottom). Only SNP sites from the MBML-intersect with complete data for >15 varieties were considered. The numbers of varieties with alleles (SNPs) different from the reference variety, Nipponbare, are indicated on the x axis.

Fig. 2.

Phylogenetic relationships, population structure, and decay of LD in the OryzaSNPset. (A) Unweighted neighbor-joining dendrogram for nonrepetitive SNPs in the MBML-intersect data (159,879 sites). Horizontal bar indicates distance by simple matching coefficient. (B) Population structure as determined by MB inference using InStruct (24). The 3 groups correspond to indica (red), aus (brown), and japonica (blue). (C) Decay of LD, expressed as r² as a function of inter-SNP distance for filtered MBML-intersect SNPs, in the indica and japonica varieties, for each chromosome (light) and overall (bold). Limited numbers of japonica SNPs bias LD estimates.

Fig. 3.

Introgressed regions detected in rice chromosomes 1, 5, and 6. The origin of an introgression is indicated by the color of the varietal group (red from indica, blue from japonica, and brown from aus). Each vertical line corresponds to a window of 100 kb. If the source of an introgression is ambiguous, each potential donor is indicated with half of the line. The maximum frequency of introgressions of the same type at the same position is plotted at the top of each chromosome. Red arrow indicates Sd1 (chromosome 1), brown bars indicate saltol (chromosome 1) and NB-ARC regions (chromosome 6), a red bar shows shared introgressions (chromosome 5), and light blue bar indicates introgressed region in Minghui 63 (chromosome 6). See Fig. S1 for introgressions in all chromosomes.

Fig. 4.

Relationships among SNP genotypes of parental varieties, Zhenshan 97B (ZSh) and Minghui 63 (M63), QTL regions, and F₁ heterotic loci on chromosome 6. (A) Molecular marker data from 5 QTL studies (–31, 38, 39) were assembled and flanking markers were physically mapped to the rice genome (green bars). Parental genotypes at 17,317 SNP sites are shown as red (A allele), blue (B allele), or gray (missing data) lines and introgressions are shown as black bars. QTL for traits including leaf area, vascular bundle number, plant height, root number, cooking quality, amylose content, gel consistency, and shoot weight colocalize with a large introgression in M63. (B) F₁ hybrid genotypes at 1,564 SNP sites in the overlapping QTL region at 0–4 Mb. Heterozygous SNP sites are black lines; small = intergenic, medium = UTR/intron/synonymous, and large = nonsynonymous. Blue bars show heterotic loci associated with high-yield performance in heterozygous vs. homozygous individuals (32).