NS  Vol.2 No.4 , April 2010
Genetic structure associated with diversity and geographic distribution in the USDA rice world collection
Abstract: Cultivated rice (Oryza sativa L.) is structured into five genetic groups, indica, aus, tropical japonica, temperate japonica and aromatic. Genetic characterization of rice germplasm collections will enhance their utilization by the global research community for improvement of rice. The USDA world collection of rice germ-plasm that was initiated in 1904 has resulted in over 18,000 accessions from 116 countries, but their ancestry information is not available. A core subset, including 1,763 accessions repre-senting the collection, was genotyped using 72 genome-wide SSR markers, and analyzed for genetic structure, genetic relationship, global distribution and genetic diversity. Ancestry analysis proportioned this collection to 35% indica, 27% temperate japonica, 24% tropical japonica, 10% aus and 4% aromatic. Graphing model-based ancestry coefficients demon-strated that tropical japonica showed up mainly in the American continents and part of the South Pacific and Oceania, and temperate japonica in Europe and the North Pacific far from the equator, which matched the responses to tem-perature. Indica is adapted to the warm areas of Southern Asia, South China, Southeast Asia, South Pacific and Central Africa and around the equator while aus and aromatic are special types of rice that concentrates in Bangladesh and India. Indica and aus were highly diversified while temperate and tropical japonicas had low diversity, indicated by average alleles and pri-vate alleles per locus. Aromatic has the most polymorphic information content. Indica and aromatic were genetically closer to tropical ja-ponica than temperate japonica. This study of global rice has found significant population stratification generally corresponding to major geographic regions of the world.
Cite this paper: Agrama, H. , Yan, W. , Jia, M. , Fjellstrom, R. and McClung, A. (2010) Genetic structure associated with diversity and geographic distribution in the USDA rice world collection. Natural Science, 2, 247-291. doi: 10.4236/ns.2010.24036.

[1]   FAO (2005) FAOSTAT data. 346/DesktopDefault.aspx?PageID=346.

[2]   Yu, J., Hu, S.N., Wang, J., Wong, G.K., Li, S.G., et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp Indica). Science, 296(5565), 79-92.

[3]   Goff, S.A., Ricke, D., Lan, T.H., Presting, G. and Wang, R.L. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp Japonica). Science, 296(5565), 92-100.

[4]   Khush, G.S. (1997) Origin, dispersal, cultivation and variation of rice. Plant Molecular Biology, 35(1-2), 25-34.

[5]   Vaughan, D.A. (1989) The genus Oryza L: Current status of taxonomy. IRRI Research Paper Series, 138, 1-21.

[6]   Mackill, D.J. (1995) Classifying japonica rice cultivars with RAPD markers. Crop Science, 35(3), 889-894.

[7]   Zhang, Q.F., Maroof, M.A.S., Lu, T.Y. and Shen, B.Z. (1992) Genetic diversity and differentiation of Indica and Japonica rice detected by RFLP analysis. Theoretical and Applied Genetics, 83(4), 495-499.

[8]   Zhang, Q.F., Liu, K.D., Yang, G.P., Maroof, M.A.S., Xu, C.G. and Zhou, Z.Q. (1997) Molecular marker diversity and hybrid sterility in Indica-Japonica rice crosses. Theo-retical and Applied Genetics, 95(1-2), 112-118.

[9]   Williams, C.E., Yanagihara, S., McCouch, S.R., Mackill, D.J. and Ronald, P.C. (1997) Predicting success of In-dica/Japonica crosses in rice, based on a PCR marker for the S-5n allele at a hybrid-sterility locus. Crop Science, 37(6), 1910-1912.

[10]   Matsuo, T., Futsuhara, Y., Kikuchi, F. and Yamaguchi, H. (1997) Science of the rice plant. Food and Agriculture Policy Research Center, Tokyo.

[11]   Glaszmann, J.C. (1987) Isozymes and classification of Asian rice varieties. Theoretical and Applied Genetics, 74(1), 21-30.

[12]   Izawa, T. (2008) The process of rice domestication: A new model based on recent data. Rice, 1(2), 127-134.

[13]   Vaughan, D.A., Lu, B.R. and Tomooka, N. (2008) Was Asian rice (Oryza sativa) domesticated more than once? Rice, 1(1), 16-24.

[14]   Joshi, S.P., Gupta, V.S., Aaggarwal, R.K., Ranjekar, P.K. and Brar, D.S. (2000) Genetic diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theoretical and Applied Genetics, 100(8), 1311-1320.

[15]   Kovach, M.J., Sweeney, M.T. and McCouch, S.R. (2007) New insights into the history of rice domestication. Trends in Genetics, 23(11), 578-587.

[16]   Caicedo, A.L., Williamson, S.H., Hernandez, R.D. and Boyko, A. (2007) Genome-wide patterns of nucleotide polymorphism in domecticated rice. PloS Genetics, 3(9), 1745-1756.

[17]   Garris, A.J., Tai, T.H., Coburn, J., Kresovich, S. and McCouch, S. (2005) Genetic structure and diversity in Oryza sativa L. Genetics, 169(3), 1631-1638.

[18]   Li, H.B., Zhang, Q., Liu, A.M., Zou, J.S. and Chen, Z.M. (1996) A genetic analysis of low-temperature-sensitive sterility in Indica-Japonica rice hybrids. Plant Breeding, 115(5), 305-309.

[19]   Xiao, J., Li, J., Yuan, L. and McCouch, S.R. (1996) Ge-netic diversity and its relationship to hybrid performance and heterosis in rice as revealed by PCR-based markers. Theoretical and Applied Genetics, 92(6), 637-643.

[20]   Xu, Y.B. (2003) Developing marker-assisted selection strategies for breeding hybrid rice. In: Janick, J., Ed., Plant Breeding Reviews, John Wiley & Sons, Inc., Ho-boken, 23, 73-174.

[21]   FAO (Food and Agriculture Organization of the United Nations) (2004) Rice is life. International Year of Rice ’04, Rome, 22-27 November 2004.

[22]   Negrao, S., Oliveira, M.M., Jena, K.K. and Mackill, D. (2008) Integration of genomic tools to assist breeding in the japonica subspecies of rice. Molecular Breeding, 22(2), 159-168.

[23]   Agrama, H.A. and Eizenga, G.C. (2008) Molecular di-versity and genome-wide linkage disequilibrium patterns in a worldwide collection of Oryza sativa and its wild relatives. Euphytica, 160(3), 339-355.

[24]   Thomson, M.J., Septiningsin, E.M., Suwardjo, F., San-toso, T.J., Silitonga, T.S. and McCouch, S.R. (2007) Ge-netic diversity analysis of traditional and improved In-donesian rice (Oryza sativa L.) germplasm using mi-crosatellite markers. Theoretical and Applied Genetics, 114(3), 559-568.

[25]   Jayamani, P., Negrao, S., Martins, M., Macas, B. and Oliveira, M.M. (2007) Genetic relatedness of Portuguese rice accessions from diverse origins as assessed by mi-crosatellite markers. Crop Science, 47(2), 879-886.

[26]   Xu, Y.B., Beachell, H. and McCouch, S.R. (2004) A marker-based approach to broading the genetic base of rice in the USA. Crop Science, 44(6), 1947-1959.

[27]   Zhang, D., Zhang, H., Wang, M., Sun, J., Qi, Y., Wang, F., Wei, X., Han, L., Wang, X. and Li, Z. (2009) Genetic structure and differentiation of Oryza sativa L. in China revealed by microsatellites. Theoretical and Applied Ge-netics, 119(6), 1105-1117.

[28]   Pritchard, J.K., Stephens, M. and Donnelly, P. (2000) Inference of population structure using multilocus geno-type data. Genetics, 155(2), 945-959.

[29]   Falush, D., Stephens, M. and Pritchard, J.K. (2003) In-ference of population structure using multilocus geno-type data: Linked loci and correlated allele frequencies. Genetics, 164(4), 1567-1587.

[30]   Falush, D., Stephens, M. and Pritchard, J.K. (2007) In-ference of population structure using multilocus geno-type data: Dominant markers and null alleles. Molecular Ecology Notes, 7(4), 574-578.

[31]   Chen, C., Durand, E., Forbes, F. and François, O. (2007) Bayesian clustering algorithms ascertaining spatial population structure: A new computer program and a comparison study. Molecular Ecology Notes, 7(5), 747-756.

[32]   François, O., Blum, M.G.B., Jakobsson, M. and Rosenberg, N.A. (2008) Demographic history of European popula-tions of Arabidopsis thaliana. PLoS Genetics, 4(5), 75.

[33]   Bockelman, H.E., Dilday, R.H., Yan, W.G. and Wesen-berg, D.M. (2003) Germplasm collection, preservation and utilization. In: Smith, C.W. and Dilday, R.H., Ed., Rice Origin, History, Technology and Production, John Wiley & Sons, Inc., Hoboken, 597-625.

[34]   NPGS (2009) Summary statistics of holdings for Oryza.

[35]   Yan, W.G., Rutger, J.N., Bryant, R.J., Bockelman, H.E., Fjellstrom, R.G., Chen, M.H., Tai, T.H. and McClung, A.M. (2007) Development and evaluation of a core sub-set of the USDA rice (Oryza sativa L.) germplasm col-lection. Crop Science, 47(2), 869-878.

[36]   Grenier, C., Hamon, P. and Bramel-Cox, P.J. (2001) Core collection of sorghum: II. Comparison of three random sampling strategies. Crop Science, 41(1), 241-246.

[37]   Yan, W.G., Rutger, J.N., Bockelman, H.E. and Tai, T.H. (2004a) Development of a core collection from the USDA rice germplasm collection. In: Norman, R.J., Meullenet, J.F. and Moldenhauer, K.A.K., Ed., Rice Re-search Studies 2003, University Arkansas, Agricultural Experiment Station, Research Series, 517, 88-96.

[38]   Yan, W.G., Rutger, J.N., Bockelman, H.E. and Tai, T.H. (2004b) Germplasm accessions resistant to straighthead in the USDA rice core collection. In Norman, R.J., Meullenet, J.F. and Moldenhauer, K.A.K. (eds.) Rice Re-search Studies 2003, University Arkansas, Agricultural Experiment Station Research Series, 517, 97-102.

[39]   Agrama, H.A., Yan, W.G., Lee, F.N., Fjellstrom, R., Chen, M., Jia, M. and McClung, A. (2009) Genetic assessment of a mini-core developed from the USDA rice genebank. Crop Science, 49, 1336-1346.

[40]   Xin, Z., Velten, J.P., Oliver, M.J. and Burke, J.J. (2003) High-throughput DNA extraction method suitable for PCR. BioTechniques, 34(4), 820-826.

[41]   Agrama, H.A. and Yan, W.G. (2009) Genetic diversity and relatedness of rice cultivars resistant to straighthead disorder. Plant Breeding, 128(4).

[42]   McNally, K.L., Bruskiewich, R., Mackill, D., Buell, C.R., Leach, J.E. and Leung, H. (2006) Sequencing multiple and diverse rice varieties: Connecting whole-genome variation with phenotypes. Plant Physiology, 141(1), 26-31.

[43]   Spiegelhalter, D.J., Best, N.G., Carlin, B.P. and van Der, L.A. (2002) Bayesian measures of model complexity and fit (with discussion). Journal of the Royal Statistical So-ciety B, 64, 583-639.

[44]   Evanno, G., Regnaut, S. and Goudet, J. (2005) Detecting the number of clusters of individuals using the software structure: a simulation. Molecular Ecology, 14(8), 2611- 2620.

[45]   Jakobsson, M. and Rosenberg, N.A. (2007) CLUMPP: A cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics, 23(14), 1801-1806.

[46]   Excoffier, L., Smouse, P.E. and Quattro, J.M. (1992) Analysis of molecular variance inferred from metric dis-tances among DNA haplotypes: Application to human mitochondrial DNA restriction sites. Genetics, 131(2), 479-491.

[47]   Schneider, S., Roessli, D. and Excoffier, L. (2000) Arle-quin: A software for population genetic data. Genetics and Biometry Laboratory, University of Geneva, Swit-zerland.

[48]   Weir, B. and Cockerham, C.C. (1984) Estimating F sta-tistics for the analysis of population structure. Evolution, 38(6), 1358-1370.

[49]   Paun, O., Greilhuber, J., Temsch, E.M. and Hörandl, E. (2006) Patterns, sources and ecological implications of clonal diversity in apomictic Ranunculus carpaticola (Ranunculus auricomus complex, Ranunculaceae). Mo-lecular Ecology, 15(4), 897-910.

[50]   Goudet, J. (1995) FSTAT (version 1.2): A computer pro-gram to calculate F statistics. Journal of Heredity, 86(6), 485-486.

[51]   Goovaerts, P. (1992) Factorial kriging analysis: A useful tool for exploring the structure of multivariate spatial soil information. Journal of Soil Science, 43, 597-619.

[52]   Wackernagel, H. (1994) Cokriging versus kriging in re-gionalized multivariate data analysis. Geoderma, 62(1), 83-92.

[53]   Venables, W.N. and Ripley, B.D. (1998) Modern applied statistics with S+. 2nd Edition, Springer, New York.

[54]   Venables, W.N., Smith, D.M. and R Development Core Team (2008) Notes on R: A programming environment for data analysis and graphics version 2.8.1. R Founda-tion for Statistical Computing, Vienna.

[55]   Peakall, R. and Smouse, P.E. (2006) GenAlEx 6: Genetic analysis in Excel. Population genetic software for teach-ing and research. Molecular Ecology Notes, 6(1), 288-295.

[56]   Liu, K. and Muse, S. (2005) PowerMarker: An integrated analysis environment for genetic marker analysis. Bioin-formatics, 21(9), 2128-2129.

[57]   Szpiech, Z.A., Jacksson, M. and Rosenbreg, N.A. (2008) ADZE: A rarefaction approach for counting alleles pri-vate to combinations of populations. Bioinformatics, 24(21), 2498-2504.

[58]   Nei, M. (1973) The theory and estimation of genetic distance. In: Morton, N.E., Ed., Genetic Structure of Populations. University Press of Hawaii, Honolulu, 45- 54.

[59]   Nei, M. (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89(3), 583-590.

[60]   Vigouroux, Y., Glaubitz, J.C., Matsuoka, Y., Goodman, M.M., Sanchez, J. and Doebley, J. (2008) Population structure and genetic diversity of new world maize races assessed by DNA microsatellites. American Journal of Botany, 95, 1240-1253.

[61]   Morishima, H. (1989) Intra-population genetic diversity in landrace of rice. Proceedings of the 6th International Congress of SABRAO, Tsukuba, 25 August 1989.

[62]   Vaughan, D.A., Miyazaki, S. and Miyashita, K. (2004) The rice genepool and human migrations. In: Werner, D., Ed., Biological Resources and Migration, Springer, Berlin, 1-11.

[63]   Sneller, C.H., Mather, D.E. and Crepieux, S. (2009) Analytical approaches and population types for finding and utilizing QTL in complex plant populations. Crop Science, 49(5), 363-390.

[64]   Patterson, N., Price, A.L. and Reich, D. (2006) Popula-tion structure and eigenanalysis. PLoS Genetics, 2(12).

[65]   Melchinger, A.E., Utz, H.F., Piepho, H.P., Zeng, Z.B. and Schon, C.C. (2007) The role of epistasis in the manifes-tation of heterosis: A systems-oriented approach. Genet-ics, 177, 1815-1825.

[66]   Luo, L., Yin, C., Mei, H. and Wu, Y. (1996) Wide com-patibility and agronomic performance of southern US rice cultivars in China. Proceedings of 26th Rice Techni-cal Working Group, San Antonio, 25-28 February 1996, 80-81.

[67]   Sun, S.X., Gao, F.Y., Lu, X.J., Wu, X.J., Wang, X.D., Ren, G.J. and Luo, H. (2008) Genetic analysis and gene fine mapping of aroma in rice (Oryza sative L. Cyperales, Poaceae). Genetics and Molecular Biology, 31(2), 532-538.