Migration, isolation and hybridization in island crop populations: The case of Madagascar rice

Molecular Ecology

Volumn 19, Issue 22, 2010, Pages 4892-4905

  Mather, Kristie A ^a   Molina, Jeanmaire ^a   Flowers, Jonathan M ^a   Rubinstein, Samara ^a   Rauh, Brad L ^b   Lawton Rauh, Amy ^b   Caicedo, Ana L ^c   McNally, Kenneth L ^d   Purugganan, Michael D ^a  

^a NEW YORK UNIVERSITY   (United States)

^b CLEMSON UNIVERSITY   (United States)

^c UNIVERSITY OF MASSACHUSETTS   (United States)

^d INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

Author keywords

domestication; hybrid; indica; isolated population; japonica; linkage disequilibrium; recombination

Indexed keywords

ARTICLE; CLASSIFICATION; CROP; GENE LINKAGE DISEQUILIBRIUM; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HUMAN; HYBRIDIZATION; MADAGASCAR; PHYLOGENY; POPULATION GENETICS; RICE; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE;

CROPS, AGRICULTURAL; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; HUMANS; HYBRIDIZATION, GENETIC; LINKAGE DISEQUILIBRIUM; MADAGASCAR; ORYZA SATIVA; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SPECIES SPECIFICITY;

JAPONICA; ORYZA SATIVA;

EID: 78449267531     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2010.04845.x     Document Type: Article

References (42)

1. Ahmadi N, Becquer T, Larroque C, etal. (1988) Genetic variability of rice in Madagascar. Agronomie Tropicale, 43, 209-221.
2. Ahmadi N, Glaszmann JC, Rabary E, (1991) Traditional highland rices originating from intersubspecific recombination in Madagascar. In: Rice Genetics II: Proceedings of the Second International Rice Genetics Symposium 14-18 May 1990. pp. 67-79, IRRI Press, Manila.
3. Allibert C, (2008) Austronesian migration and the establishment of the Malagasy civilization: contrasted readings in linguistics, archaeology, genetics and cultural anthropology. Diogenes, 55, 7-15.
4. Ashikari M, Matsuoka M, (2006) Identification, isolation and pyramiding of quantitative trait loci for rice breeding. Trends Plant Science, 11, 344-350.
5. Burney DA, Burney LP, Godfrey LR, etal. (2004) A chronology for late prehistoric Madagascar. Journal of Human Evolution, 47, 25-63.
6. Caicedo AL, Williamson SH, Hernandez RD, etal. (2007) Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLOS Genetics, 3, 1745-1756.
7. Chen J, Jihua D, Yidan O, etal. (2008) A triallelic system of S5 is a major regulator of the reproductive barrier and compatibility of indica-japonica hybrids in rice. Proceedings of the National Academy of Sciences USA, 105, 11436-11441.
8. Clark RM, Tavare S, Doebley J, (2005) Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus. Molecular Biology and Evolution, 22, 2304-2312.
9. Depaulis F, Mousset S, Veuille M, (2003) Power of neutrality tests to detect bottlenecks and hitchhiking. Journal of Molecular Evolution, 57, S190-S200.
10. Dewar RE, Wright HE, (1993) The culture history of Madagascar. Journal of World Prehistory, 7, 417-466.
11. Diamond J, (2002) Evolution, consequences and future of plant and animal domestication. Nature, 418, 700-707.
12. Dlugosch KM, Parker I, (2008) Founding events in species invasions: genetic variation, adaptive evolution, and the role of multiple introductions. Molecular Ecology, 17, 431-449.
13. Evanno G, Regnaut S, Goudet J, (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14, 2611-2620.
14. Excoffier L, Laval G, Schneider S, (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47-50.
15. Falush D, Stephens M, Pritchard JK, (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164, 1567-1587.
16. Farrell BD, Sequeira AS, O'meara BC, etal. (2001) The evolution of agriculture in beetles (Curculionidae: Scolytinae and Platypodinae). Evolution, 55, 2011-2027.
17. Gao H, Williamson S, Bustamante CD, (2007) An MCMC approach for joint inference of population structure and inbreeding rates from multi-locus genotype data. Genetics (online), 176: 1635-1651.
18. Garris AJ, Tai TH, Coburn J, etal. (2005) Genetic structure and diversity in Oryza sativa L. Genetics, 169, 1631-1638.
19. Hartl DL, Clark AG, (1997) Principles of Population Genetics. 3rd edn, Sinauer Associates, Sunderland, Massachusetts.
20. Harushima Y, Nakagahra M, Yano M, etal. (2002) Diverse variation of reproductive barriers in three intraspecific rice crosses. Genetics, 160, 313-322.
21. Hey J, Nielsen R, (2007) Integration within the Felsenstein equation for improved Markov -chain Monte Carlo methods in population genetics. Proceedings of the National Academy of Sciences USA, 104, 2785-2790.
22. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature, 436, 793-800.
23. Khush GS, (1997) Origin, dispersal, cultivation and variation of rice. Plant Molecular Biology, 35, 25-34.
24. Kimura M, (1980) A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111-120.
25. Koji T, (1997) Malayan cultivated rice and its expansion. Agricultural Archaeology, 1, 73-78.
26. Li ZK, Pinson SRM, Paterson AH, etal. (1997) Genetics of hybrid sterility and hybrid breakdown in an intersubspecific rice (Oryza sativa L) population. Genetics, 145, 1139-1148.
27. Londo JP, Chiang YC, Hung KH, etal. (2006) Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proceedings of the National Academy of Sciences USA, 103, 9578-9583.
28. Mather KA, Caicedo AL, Polato NR, etal. (2007) The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics, 177, 2223-2232.
29. Oka HI, (1988) Origin of Cultivated Rice. Elsevier/JSSP, Amsterdam/Tokyo.
30. Olsen KM, Caicedo AL, Polato N, etal. (2006) Selection under domestication: evidence for a sweep in the rice Waxy genomic region. Genetics, 173, 975-983.
31. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
32. Purugganan MD, Fuller D, (2009) The nature of selection during plant domestication. Nature, 457, 843-848.
33. Rabary E, Noyer JL, Benyayer P, etal. (1989) Variabilité génétique du riz (Oryza sativa L.) à Madagascar: origine de types nouveaux. L-Agrononomie tropicale, 44, 305-312.
34. Regueiro M, Mirabal S, Lacau H, etal. (2008) Austronesian genetic signature in East African Madagascar and Polynesia. J. Hum. Genetics, 53, 106-120.
35. Rozen S, Skaletsky HJ, (2000) Primer3 on the WWW for general users and for biologist programmers. In: Bioinformatics Methods and Protocols: Methods in Molecular Biology (eds, Krawetz S, Misener S,), pp. 365-386, Humana Press, Totowa, NJ.
36. Saitou N, Nei M, (1987) The neighbor-joining method-a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406-425.
37. Schultz TR, Brady SG, (2008) Major evolutionary transitions in ant agriculture. Proceedings of the National Academy of Sciences USA, 105, 5435-5440.
38. Tamura K, Nei M, Kumar S, (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proceedings of the National Academy of Sciences USA, 101, 11030-11035.
39. Tamura K, Dudley J, Nei M, etal. (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596-1599.
40. Thornton K, (2003) Libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics, 19, 2325-2327.
41. Varilo T, Peltonen L, (2004) Founder events and mapping: isolates and their potential use in complex gene mapping efforts. Current Opinion in Genetics and Development, 14, 316-323.
42. Vaughan DA, Miyazaki S, Miyashita K, (2004) The rice genepool and human migrations. In: Biological Resources and Migration (ed., Wener D,), pp. 1-14. Springer, Berlin.