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Two evolutionary histories in the genome of rice: the roles of domestication genes.

He Z, Zhai W, Wen H, Tang T, Wang Y, Lu X, Greenberg AJ, Hudson RR, Wu CI, Shi S - PLoS Genet. (2011)

Bottom Line: The existence of two subspecies of cultivated rice provides a unique opportunity for analyzing these effects during domestication.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.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-Sen University, Guangzhou, China.

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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Cumulative plots for Fst distributions in observed data and two example simulations.A) Observed cumulative plot for Fst between I and J; Fst distribution for overlapping LDRs are plotted in dashed lines. Solid lines are used for genome background. B) Observed cumulative plot for Fst between R and J. C) Simulated cumulative plot for Fst between I and J under an independent domestication history. D) Simulated cumulative plot for Fst between R and J under an independent domestication history. E) Simulated cumulative plot for Fst between I and J under a sequential domestication history. F) Simulated cumulative plot for Fst between R and J under a sequential domestication history. D measures the maximal distances between the two plotted cumulative distributions in each panel (see main text). Both observed D value in real data and maximal value across simulated replicates are shown in left upper corner of each panel.
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pgen-1002100-g004: Cumulative plots for Fst distributions in observed data and two example simulations.A) Observed cumulative plot for Fst between I and J; Fst distribution for overlapping LDRs are plotted in dashed lines. Solid lines are used for genome background. B) Observed cumulative plot for Fst between R and J. C) Simulated cumulative plot for Fst between I and J under an independent domestication history. D) Simulated cumulative plot for Fst between R and J under an independent domestication history. E) Simulated cumulative plot for Fst between I and J under a sequential domestication history. F) Simulated cumulative plot for Fst between R and J under a sequential domestication history. D measures the maximal distances between the two plotted cumulative distributions in each panel (see main text). Both observed D value in real data and maximal value across simulated replicates are shown in left upper corner of each panel.

Mentions: The observed cumulative distributions of Fst are shown in Figure 4A (for I vs. J) and Figure 4B (for R vs. J). In each panel, the distributions of the whole genome and overlapping LDRs are represented by the solid and dotted line, respectively. Similar to what we observe in Figure 2, overlapping LDRs show a pattern of population differentiation distinct from that of the genome background. We measured the largest distance between the dotted curve (for overlapping LDRs) and the solid curve (genomic background), marked D in Figure 4A and 4B. The observed D value is given in the upper left corner of each panel.


Two evolutionary histories in the genome of rice: the roles of domestication genes.

He Z, Zhai W, Wen H, Tang T, Wang Y, Lu X, Greenberg AJ, Hudson RR, Wu CI, Shi S - PLoS Genet. (2011)

Cumulative plots for Fst distributions in observed data and two example simulations.A) Observed cumulative plot for Fst between I and J; Fst distribution for overlapping LDRs are plotted in dashed lines. Solid lines are used for genome background. B) Observed cumulative plot for Fst between R and J. C) Simulated cumulative plot for Fst between I and J under an independent domestication history. D) Simulated cumulative plot for Fst between R and J under an independent domestication history. E) Simulated cumulative plot for Fst between I and J under a sequential domestication history. F) Simulated cumulative plot for Fst between R and J under a sequential domestication history. D measures the maximal distances between the two plotted cumulative distributions in each panel (see main text). Both observed D value in real data and maximal value across simulated replicates are shown in left upper corner of each panel.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3111475&req=5

pgen-1002100-g004: Cumulative plots for Fst distributions in observed data and two example simulations.A) Observed cumulative plot for Fst between I and J; Fst distribution for overlapping LDRs are plotted in dashed lines. Solid lines are used for genome background. B) Observed cumulative plot for Fst between R and J. C) Simulated cumulative plot for Fst between I and J under an independent domestication history. D) Simulated cumulative plot for Fst between R and J under an independent domestication history. E) Simulated cumulative plot for Fst between I and J under a sequential domestication history. F) Simulated cumulative plot for Fst between R and J under a sequential domestication history. D measures the maximal distances between the two plotted cumulative distributions in each panel (see main text). Both observed D value in real data and maximal value across simulated replicates are shown in left upper corner of each panel.
Mentions: The observed cumulative distributions of Fst are shown in Figure 4A (for I vs. J) and Figure 4B (for R vs. J). In each panel, the distributions of the whole genome and overlapping LDRs are represented by the solid and dotted line, respectively. Similar to what we observe in Figure 2, overlapping LDRs show a pattern of population differentiation distinct from that of the genome background. We measured the largest distance between the dotted curve (for overlapping LDRs) and the solid curve (genomic background), marked D in Figure 4A and 4B. The observed D value is given in the upper left corner of each panel.

Bottom Line: The existence of two subspecies of cultivated rice provides a unique opportunity for analyzing these effects during domestication.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.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-Sen University, Guangzhou, China.

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.

Show MeSH