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, 3 (8), e133

Global Dissemination of a Single Mutation Conferring White Pericarp in Rice

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Global Dissemination of a Single Mutation Conferring White Pericarp in Rice

Megan T Sweeney et al. PLoS Genet.

Abstract

Here we report that the change from the red seeds of wild rice to the white seeds of cultivated rice (Oryza sativa) resulted from the strong selective sweep of a single mutation, a frame-shift deletion within the Rc gene that is found in 97.9% of white rice varieties today. A second mutation, also within Rc, is present in less than 3% of white accessions surveyed. Haplotype analysis revealed that the predominant mutation originated in the japonica subspecies and crossed both geographic and sterility barriers to move into the indica subspecies. A little less than one Mb of japonica DNA hitchhiked with the rc allele into most indica varieties, suggesting that other linked domestication alleles may have been transferred from japonica to indica along with white pericarp color. Our finding provides evidence of active cultural exchange among ancient farmers over the course of rice domestication coupled with very strong, positive selection for a single white allele in both subspecies of O. sativa.

Conflict of interest statement

Competing interests. The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Current Distribution of the Five Major Subpopulations of Rice in Asia
For details about the geographical distribution of accessions used in this study, see Table S1.
Figure 2
Figure 2. Haplotype Data across the Rc Gene
The gene model for Rc, containing seven exons and comprising a region of approximately 8 kb, is shown horizontally along the top; arrows on the gene model and promoter region of Rc indicate positions of markers: RID-number markers amplify rice insertion/deletion polymorhisms, RM-number markers amplify rice microsatellite polymorphisms, and the RS-number marker detects a rice SNP. Physical positions along the rice Chromosome 7 pseudomolecule are indicated by the ruler below the gene model. In the tables below, allele sizes for RID marker loci are given in bp and allele sizes for RM markers show the number of repeats at each microsatellite locus. The number of varieties in each subpopulation that carry each haplotype is provided in boxed squares in the table to the right. Haplotypes found in varieties with red pericarp are shaded red.
Figure 3
Figure 3. Comparison of Rc Gene and Rice Genome-Wide Phylogenetic Trees
Sequence alignment adjusted manually in MacClade 4.05. A heuristic parsimony search was conducted on the data matrix, excluding gapped characters, with TBR branch swapping. This identified a single tree at 53 steps, with a consistency index of 0.98 (0.97 without autapomorphies) and a retention index of 0.99. Bootstrap support was estimated using 100 replications of the same search strategy. Pericarp color and subpopulation of each variety sequenced is labeled.
Figure 4
Figure 4. Japonica Introgressions in White Indica
Arrows indicate the location of markers on the physical map of Chromosome 7, numbers are in Mb. F ST values for red indica versus japonica are plotted across the chromosome using diamonds, white indica versus japonica are plotted using squares. The expanded region shows a detailed view of the 1-Mb window around the Rc gene. All varieties genotyped are white indicas containing the 14-bp deletion. DNA segments containing alleles of japonica ancestry (in the indica background) are shown in white, segments containing alleles of indica ancestry are shown in black, and segments containing a breakpoint between alleles of japonica and indica ancestry are shown in grey. Locations of the Rc and Hsh genes indicated by brackets.

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