Genome-wide patterns of nucleotide polymorphism in domesticated rice

PLoS Genetics

Volumn 3, Issue 9, 2007, Pages 1745-1756

  Caicedo, Ana L ^a,e   Williamson, Scott H ^b   Hernandez, Ryan D ^b   Boyko, Adam ^b   Fledel Alon, Adi ^b,f   York, Thomas L ^b   Polato, Nicholas R ^c   Olsen, Kenneth M ^a,g   Nielsen, Rasmus ^b,h   McCouch, Susan R ^c   Bustamante, Carlos D ^b   Purugganan, Michael D ^a,d  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b Plant Breeding and Genetics Section in the School of Integrative Plant Science   (United States)

^c Department of Obstetrics Gynecology   (United States)

^d NEW YORK UNIVERSITY   (United States)

^e UNIVERSITY OF MASSACHUSETTS   (United States)

^f UNIVERSITY OF CHICAGO   (United States)

^g WASHINGTON UNIVERSITY   (United States)

^h UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

PLANT DNA;

ARTICLE; DNA POLYMORPHISM; DNA SEQUENCE; DOMESTICATED PLANT; GENE FLOW; GENETIC VARIABILITY; GENOME; MOLECULAR EVOLUTION; NONHUMAN; PLANT GENETICS; RICE; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; BASE PAIRING; BASE SEQUENCE; COMPUTER SIMULATION; CROPS, AGRICULTURAL; EVOLUTION, MOLECULAR; FOUNDER EFFECT; GENE FREQUENCY; GENETICS, POPULATION; GENOME, PLANT; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC; SELECTION (GENETICS); SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

ORYZA SATIVA;

EID: 34848916049     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0030163     Document Type: Article

References (59)

1. Hancock JF (2004) Plant evolution and the origin of crop species. Cambridge (Massachusetts): CABI Publishing. 313 p.
2. Mannion AM (1999) Domestication and the origins of agriculture: an appraisal. Prog Phys Geogr 23: 37-56.
3. Darwin C (1859) On the origin of species. London: John Murray.
4. Darwin C (1868) The variation of animals and plants under domestication. London: John Murray.
5. Armelagos GJ, Harper KN (2005) Genomics at the origins of agriculture, part one. Evol Anthropol 14: 68-77.
6. Diamond J (2002) Evolution, consequences and future of plant and animal domestication. Nature 418: 700-707.
7. FAO (2005) FAOSTAT data, in last update 2003. http://faostat.fao.org/ site/346/DesktopDefault.aspx?PageID1/4346. Accessed 1 August 2007.
8. Yu J, Hu SN, Wang J, Wong GKS, Li SG, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp indica). Science 296: 79-92.
9. Goff SA, Ricke D, Lan TH, Presting G, Wang RL, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp japonica). Science 296: 92-100.
10. IRGSP (2005) The map-based sequence of the rice genome. Nature 436: 793-800.
11. Takahashi N, Hamamura K, Tsunoda S, Sakamoto S, Sato Y (1997) Differentiation of ecotypes in cultivated rice. In: Matsuo T, Futsuhara Y, Kikuchi F, Yamaguchi H, editors. Science of the rice plant. Tokyo: Food and agriculture policy research center. pp. 112-160.
12. Jackson MT (1997) Conservation of rice genetic resources: the role of the International Rice Genebank at IRRI. Plant Mol Biol 35: 61-67.
13. Oka HI (1988) Origin of cultivated rice. Tokyo: Japan Scientific Societies Press and Elsevier Science Publishers. 254 p.
14. Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169: 1631-1638.
15. Glaszmann JC (1987) Isozymes and classification of Asian rice varieties. Theor Appl Genet 74: 21-30.
16. Tenaillon MI, Sawkins MC, Anderson LK, Stack SM, Doebley J, et al. (2002) Patterns of diversity and recombination along chromosome 1 of maize (Zea mays ssp mays L.). Genetics 162: 1401-1413.
17. Schmid KJ, Ramos-Onsins S, Ringys-Beckstein H, Weisshaar B, Mitchell-Olds T (2005) A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism. Genetics 169: 1601-1615.
18. Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, et al. (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 3: 1289-1299.
19. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
20. Cheng CY, Motohashi R, Tsuchimoto S, Fukuta Y, Ohtsubo H, et al. (2003) Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs. Mol Biol Evol 20: 67-75.
21. Zhu QH, Ge S (2005) Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytol 167: 249-265.
22. Vitte C, Ishii T, Lamy F, Brar D, Panaud O (2004) Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.). Mol Genet Genomics 272: 504-511.
23. Londo JP, Chiang YC, Hung KH, Chiang TY, Schaal BA (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.
24. Second G (1982) Origin of the genic diversity of cultivated rice (Oryza-Spp) - study of the polymorphism scored at 40 isoenzyme loci. Jpn J Genet 57: 25-57.
25. Tajima F (1989) Statistical-method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
26. Fay JC, Wu CI (2000) Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
27. Wright SI (2005) The effects of artificial selection on the maize genome. Science 310: 54-54.
28. Tenaillon MI, U'Ren J, Tenaillon O, Gaut BS (2004) Selection versus demography: a multilocus investigation of the domestication process in maize. Mol Biol Evol 21: 1214-1225.
29. Eyre-Walker A, Gaut RL, Hilton H, Feldman DL, Gaut BS (1998) Investigation of the bottleneck leading to the domestication of maize. Proc Natl Acad Sci U S A 95: 4441-4446.
30. Takahata N (1991) Genealogy of neutral genes and spreading of selected mutations in a geographically structured population. Genetics 129: 585-595.
31. Tachida H, Iizuka M (1991) Fixation probability in spatially changing environments. Genet Res 58: 243-251.
32. Maruyama T (1970) On fixation probability of mutant genes in a subdivided population. Genet Res 15: 221-&.
33. Lu HY, Liu ZX, Wu NQ, Berne S, Saito Y, et al. (2002) Rice domestication and climatic change: phytolith evidence from East China. Boreas 31: 378-385.
34. Zhao ZJ (1998) The middle Yangtze region in China is one place where rice was domesticated: phytolith evidence from the Diaotonghuan cave, northern Jiangxi. Antiquity 72: 885-897.
35. Normile D (1997) Archaeology - Yangtze seen as earliest rice site. Science 275: 309-309.
36. Wakeley J, Hey J (1997) Estimating ancestral population parameters. Genetics 145: 847-855.
37. Kim Y, Stephan W (2003) Selective sweeps in the presence of interference among partially linked loci. Genetics 164: 389-398.
38. Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, et al. (2005) Genomic scans for selective sweeps using SNP data. Genome Res 15: 1566-1575.
39. Durrett R, Schweinsberg J (2004) Approximating selective sweeps. Theor Popul Biol 66: 129-138.
40. Nordborg M (2000) Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization. Genetics 154: 923-929.
41. Burnham KP, Anderson DR (1998) Model selection and inference: a practical information-theoretic approach. New York: Springer-Verlag. 353 p.
42. Vigouroux Y, Mitchell S, Matsuoka Y, Hamblin M, Kresovich S, et al. (2005) An analysis of genetic diversity across the maize genome using microsatellites. Genetics 169: 1617-1630.
43. Thuillet AC, Bataillon T, Poirier S, Santoni S, David JL (2005) Estimation of long-term effective population sizes through the history of durum wheat using microsatellite data. Genetics 169: 1589-1599.
44. Muller MH, Poncet C, Prosperi JM, Santoni S, Ronfort J (2006) Domestication history in the Medicago sativa species complex: inferences from nuclear sequence polymorphism. Mol Ecol 15: 1589-1602.
45. Li C, Zhou A, Sang T (2006) Rice domestication by reducing shattering. Science 311: 1936-1939.
46. Sweeney MT, Thomson MJ, Cho Y, Park YJ, Williamson SH (2007) Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genet 3: e133. doi:10.1371/journal.pgen.0030133
47. Maynard Smith J, Haigh J (2004) The hitch-hiking effect of a favourable gene. Genet Res 23: 23-35.
48. Kaplan NL, Hudson RR, Langley CH (1989) The hitchhiking effect revisited. Genetics 123: 887-899.
49. McCouch SR, Kochert G, Yu ZH, Wang ZY, Khush GS, et al. (1988) Molecular mapping of rice chromosomes. Theor Appl Genet 76: 815-829.
50. Wu JZ, Maehara T, Shimokawa T, Yamamoto S, Harada C, et al. (2002) A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 14: 525-535.
51. Rozen S, Skaletsky HJ (2000) In: Krawetz S, Misener S, editors. Bioinformatics methods and protocols: methods in molecular biology. Totowa (New Jersey): Humana Press. pp. 365-386.
52. Olsen KM, Caicedo AL, Polato N, McClung A, McCouch S, et al. (2006) Selection under domestication: evidence for a sweep in the rice Waxy genomic region. Genetics 173: 975-983.
53. Swofford DL (2000) PAUP* Phylogenetic analysis using parsimony (* and other methods). Sunderland, Massachusetts: Sinauer Associates.
54. Sawyer SA, Hartl DL (1992) Population-genetics of polymorphism and divergence. Genetics 132: 1161-1176.
55. Bustamante CD, Wakeley J, Sawyer S, Hartl DL (2001) Directional selection and the site-frequency spectrum. Genetics 159: 1779-1788.
56. Bustamante CD, Nielsen R, Hartl DL (2003) Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data. Theor Popul Biol 63: 91-103.
57. Williamson S, Fledel-Alon A, Bustamante CD (2004) Population genetics of polymorphism and divergence for diploid selection models with arbitrary dominance. Genetics 168: 463-475.
58. Williamson S, Perry SM, Bustamante CD, Orive ME, Stearns MN, et al. (2005) A statistical characterization of consistent patterns of human immunodeficiency virus evolution within infected patients. Mol Biol Evol 22: 456-468.
59. Hudson RR (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.