Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes
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.
Vyšlo v časopise:
Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes. PLoS Genet 7(6): e32767. doi:10.1371/journal.pgen.1002100
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1002100
Souhrn
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.
Zdroje
1. Mekel-BobrovNGilbertSLEvansPDVallenderEJAndersonJR 2005 Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens. Science 309 1720 1722
2. YuFHillRSSchaffnerSFSabetiPCWangET 2007 Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens". Science 316 370
3. PattersonNRichterDJGnerreSLanderESReichD 2006 Genetic evidence for complex speciation of humans and chimpanzees. Nature 441 1103 1108
4. TingCTTsaurSCWuCI 2000 The phylogeny of closely related species as revealed by the genealogy of a speciation gene, Odysseus. Proc Natl Acad Sci U S A 97 5313 5316
5. ZhouRZengKWuWChenXYangZ 2007 Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves. Mol Biol Evol 24 2746 2754
6. OkaH 1988 Origin of Cultivated Rice. Tokyo/Amsterdam Japan Scientific Societies Press
7. SangTGeS 2007 Genetics and phylogenetics of rice domestication. Curr Opin Genet Dev 17 533 538
8. ChengCMotohashiRTsuchimotoSFukutaYOhtsuboH 2003 Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs. Mol Biol Evol 20 67 75
9. LondoJPChiangYCHungKHChiangTYSchaalBA 2006 Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc Natl Acad Sci U S A 103 9578 9583
10. MaJBennetzenJL 2004 Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A 101 12404 12410
11. VitteCIshiiTLamyFBrarDPanaudO 2004 Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.). Mol Genet Genomics 272 504 511
12. LiCZhouASangT 2006 Rice domestication by reducing shattering. Science 311 1936 1939
13. OnishiKTakagiKKontaniMTanakaTSanoY 2007 Different patterns of genealogical relationships found in the two major QTLs causing reduction of seed shattering during rice domestication. Genome 50 757 766
14. ZhangLBZhuQWuZQRoss-IbarraJGautBS 2009 Selection on grain shattering genes and rates of rice domestication. New Phytol 184 708 720
15. DruleyTEVallaniaFLWegnerDJVarleyKEKnowlesOL 2009 Quantification of rare allelic variants from pooled genomic DNA. Nat Methods 6 263 265
16. ShendureJJiH 2008 Next-generation DNA sequencing. Nat Biotechnol 26 1135 1145
17. ZhouRLingSZhaoWOsadaNChenS 2011 Population genetics in non-model organisms: II. Natural selection in marginal habitats revealed by deep sequencing on dual platforms. Mol Biol Evol doi:10.1093/molbev/msr102
18. LynchM 2009 Estimation of allele frequencies from high-coverage genome-sequencing projects. Genetics 182 295 301
19. WattersonGA 1975 On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7 256 276
20. CaicedoALWilliamsonSHHernandezRDBoykoAFledel-AlonA 2007 Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet 3 e163 doi:10.1371/journal.pgen.0030163
21. TangTLuJHuangJHeJMcCouchSR 2006 Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication. PLoS Genet 2 e199 doi:10.1371/journal.pgen.0020199
22. GarrisAJTaiTHCoburnJKresovichSMcCouchS 2005 Genetic structure and diversity in Oryza sativa L. Genetics 169 1631 1638
23. MatherKACaicedoALPolatoNROlsenKMMcCouchS 2007 The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics 177 2223 2232
24. TanLLiXLiuFSunXLiC 2008 Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet 40 1360 1364
25. Lindblad-TohKWadeCMMikkelsenTSKarlssonEKJaffeDB 2005 Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438 803 819
26. OkaHMorishimaH 1967 Variation in the breeding systems of a wild rice, Oryza perennis. Evolution 21 249 258
27. WeirBSCockerhamCC 1984 Estimating F-Statistics for the Analysis of Population-Structure. Evolution 38 1358 1370
28. SweeneyMTThomsonMJChoYGParkYJWilliamsonSH 2007 Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genet 3 e133 doi:10.1371/journal.pgen.0030133
29. KovachMJSweeneyMTMcCouchSR 2007 New insights into the history of rice domestication. Trends Genet 23 578 587
30. ConoverWJ 1971 Practical Nonparametric Statistics. New York John Wiley & Sons
31. SweeneyMTThomsonMJPfeilBEMcCouchS 2006 Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. Plant Cell 18 283 294
32. BrennerSJohnsonMBridghamJGoldaGLloydDH 2000 Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18 630 634
33. BryanGTWuKSFarrallLJiaYHersheyHP 2000 A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta. Plant Cell 12 2033 2046
34. SiegfriedKREshedYBaumSFOtsugaDDrewsGN 1999 Members of the YABBY gene family specify abaxial cell fate in Arabidopsis. Development 126 4117 4128
35. HuangXWeiXSangTZhaoQFengQ 2010 Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42 961 967
36. YuYTangTQianQWangYYanM 2008 Independent losses of function in a polyphenol oxidase in rice: differentiation in grain discoloration between subspecies and the role of positive selection under domestication. Plant Cell 20 2946 2959
37. DoyleJDoyleJ 1987 A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19 11 15
38. LiHRuanJDurbinR 2008 Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 18 1851 1858
39. HudsonRR 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18 337 338
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2011 Číslo 6
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