Evolutionary Genomics of Structural Variation in Asian Rice (Oryza sativa) Domestication

Abstract

Structural variants (SVs) are a largely unstudied feature of plant genome evolution, despite the fact that SVs contribute substantially to phenotypes. In this study, we discovered SVs across a population sample of 347 high-coverage, resequenced genomes of Asian rice (Oryza sativa) and its wild ancestor (O. rufipogon). In addition to this short-read data set, we also inferred SVs from whole-genome assemblies and long-read data. Comparisons among data sets revealed different features of genome variability. For example, genome alignment identified a large (∼4.3 Mb) inversion in indica rice varieties relative to japonica varieties, and long-read analyses suggest that ∼9% of genes from the outgroup (O. longistaminata) are hemizygous. We focused, however, on the resequencing sample to investigate the population genomics of SVs. Clustering analyses with SVs recapitulated the rice cultivar groups that were also inferred from SNPs. However, the site-frequency spectrum of each SV type-which included inversions, duplications, deletions, translocations, and mobile element insertions-was skewed toward lower frequency variants than synonymous SNPs, suggesting that SVs may be predominantly deleterious. Among transposable elements, SINE and mariner insertions were found at especially low frequency. We also used SVs to study domestication by contrasting between rice and O. rufipogon. Cultivated genomes contained ∼25% more derived SVs and mobile element insertions than O. rufipogon, indicating that SVs contribute to the cost of domestication in rice. Peaks of SV divergence were enriched for known domestication genes, but we also detected hundreds of genes gained and lost during domestication, some of which were enriched for traits of agronomic interest.

Keywords: domestication; gene gain and loss; rice; structural variation; transposable element insertions.

Fig. 1.

Features of the data and SV data sets (A) A phylogeny based on SNPs of n = 347 accessions of Asian rice with outgroups Oryza meridionalis and O. longistaminata. (B) Population structure inference based on SNPs (top) and SVs (below) for the short-read data set of 347 individuals. The accessions are arranged in the same order for the SNP and SV plots, the x-axis labels denote the different groups, with “aro,” “rufi,” and “niv” referring to aromatic, rufipogon, and O. nivara. (C) A dotplot of chromosome 6 showing the large (∼4.3 Mb) inversion in indica accessions relative to the O. longistaminata outgroup. The inversion is not shared with the japonica accessions in our sample. (D) A Venn diagram based on the combined results from three SV types (DEL, DUP, and INV) that compares SVs among three data sets based on short reads (Illumina, n = 347), long reads (SMRT, n = 10), and genome alignments (n = 14). Results for each SV type separately are available in supplementary figure S3, Supplementary Material online.

Fig. 2.

Population information about SVs. (A) The plot graphs SNP and SV average pairwise diversity (π) for the rufipogon sample across 20-kb windows of the genome, with the line indicating the correlation, which is weakly positive but significant (Pearson r = 0.0332, P = 1.07 × 10⁻⁵). Similar graphs for the japonica and indica samples are in supplementary figure S7, Supplementary Material online. Plots (B), (C), and (D) show the unfolded SFS of different types of SVs in (B) rufipogon, (C) indica, and (D) japonica. Each SFS contains synonymous SNPs (Syn), nonsynonymous SNPs (Nsyn), and SV events that fall into the duplication (DUP), deletion (DEL) translocation (TRA), mobile element insertion (MEI), and inversion (INV) categories. (E) The decay of linkage disequilibrium (LD) of SNPs and SVs measured by r² for the three population groups based on SNPs, SVs, and SNPs+SVs.

Fig. 3.

Feature of SVs associated with domestication. (A) The genetic load of SVs for rufipogon, japonica, and indica. The selfing cultivars have a higher recessive (homozygous) load and correspondingly larger total SV burden, suggesting a cost of domestication. (B) Manhattan plots of F_ST values between rufipogon, based on SVs within 20-kb windows, with japonica on the left and indica on the right. The corresponding Manhattan plots for SNPs are provided in supplementary figure S10, Supplementary Material online. (C) Manhattan plots of CLR values for japonica (left) and indica (right), based on SVs within 20-kb windows. The corresponding Manhattan plots for SNPs are provided in supplementary figure S12, Supplementary Material online. The proportion of different types of SVs under the selective sweeps detected by F_ST (D) and SweeD (E) analyses.

Fig. 4.

Features of TE diversity in rice. Plot (A) provides the SFS for ten element types along with synonymous SNPs (Syn) and nonsynonymous SNPs (Nsyn). This plot is for rufipogon; analogous plots for japonica and indica are provided in supplementary figures S14 and S15, Supplementary Material online. (B) The inferred distribution of fitness effects (DFE) in rufipogon relative to nSNPs. The y-axis provides the proportion of TE insertions, and the x-axis reports N_es. The color scheme for TE families is the same as (A). (C) The estimated proportion of adaptive variation (α) for each TE family and each of the three taxonomic groups. (D) Distributions of inferred insertion times for TE families in the Nipponbare reference. (E) The ratio of homozygous to heterozygous MEI variants in the three taxa for each TE family, which shows that the families under strong selection have relatively fewer homozygous variants.

Fig. 5.

Two example regions of complex SVs across Oryza taxa. (A) A segmental tandem duplication of an NBS-LRR-encoding gene (LOC_Os01g05600/Os01g0149350) that was found to be gained in indica and japonica relative to rufipogon. The synteny map is shown for a region corresponding to a 35-kb region in japonica (Nipponbare). (B) Gene and TE copy number variation in a 100-kb region of chromosome 9 that includes the Sub1A gene, which confers flooding tolerance. Both an indica accession and O. longistaminata contain three copies of genes. For both (A) and (B), gene copies are tracked by dotted red lines.