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Genetic diversity and structure of indica rice varieties from two heterotic pools of southern China and IRRI

  • Fangming Xie (a1), Longbiao Guo (a2), Guangjun Ren (a3), Peisong Hu (a2), Feng Wang (a4), Jianlong Xu (a5), Xinqi Li (a6), Fulin Qiu (a1) and Madonna Angelita dela Paz (a1)...

Investigation of genetic diversity and the relationships among varieties and breeding lines is of great importance to facilitate parental selection in the development of inbred and hybrid rice varieties and in the construction of heterotic groups. The technology of single nucleotide polymorphism (SNP) is being advanced for the assessment of population diversity and genetic structures. We characterized 215 widely cultivated indica rice varieties developed in southern China and at the International Rice Research Institute (IRRI) using IRRI-developed SNP oligonucleotide pooled assay (OPA) to provide grouping information of rice mega-varieties for further heterotic pool study. The results revealed that the Chinese varieties were more divergent than the IRRI varieties. Two major subpopulations were clustered for the varieties using a model-based grouping method. The IRRI varieties were closely grouped and separated clearly from the majority of the Chinese varieties. The Chinese varieties were subclustered into three subgroups, but there was no clear evidence to separate the Chinese varieties into subgroups geographically, indicating a great degree of genetic integration of alleles and shared ancestries among those high-yielding modern varieties.

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Boppenmaier J, Melchinger AE, Seitz G, Geiger HH and Herrmann RG (1993) Genetic diversity for RFLPs in European maize inbreds III. Performance of crosses within versus between heterotic groups for grain traits. Plant Breeding 111: 217226.
Cavalli-Sforza LL and Edwards AWF (1967) Phylogenetic analysis: models and estimation procedures. American Journal of Human Genetics 19: 233257.
Chen HD, He H, Zou YJ, Chen W, Yu RB, Liu X, Yang Y, Gao YM, Xu JL, Fan LM, Li Y, Li ZK and Deng XW (2011) Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.). Theoretical and Applied Genetics 123: 869879.
Collard BCY, Vera Cruz CM, McNally KL, Virk PS and Mackill DJ (2008) Rice molecular breeding laboratories in the genomics era: current status and future considerations. International Journal of Plant Genomics, Article ID 524847: 25.
Dudley JW, Saghai Maroof MA and Rufener GK (1991) Molecular markers and grouping of parents in maize breeding programs. Crop Science 31: 718723.
Evanno G, Regnaut S and Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 26112620.
Falush D, Stephens M and Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 15671587.
Lee M, Godshalk EB, Lamkey KR and Woodman WW (1989) Association of restriction fragment length polymorphisms among maize inbreds with agronomic performance of their crosses. Crop Science 94: 10231030.
Liu K and Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 21282129.
Lu ZM and Xu BQ (2010) On significance of heterotic group theory in hybrid rice breeding. Rice Science 17: 9498.
McCouch SR, Zhao K, Wright M, Tung CW, Ebana K, Thomson M, Reynolds A, Wang D, DeClerck G, Ali ML, McClung A, Eizenga G and Bustamante C (2010) Development of genome-wide SNP assays for rice. Breeding Science 60: 524535.
McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE, Stokowski R, Ballinger DG, Frazer KA, Cox DR, Padhukasahasram B, Bustamante CD, Weigel D, Mackill DJ, Bruskiewich RM, Ratsch G, Buell CB, Leung H and Leach JE (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proceedings of the National Academy of Sciences of the United States of America 106: 1227312278.
Moose SP and Mumm RH (2008) Molecular plant breeding as the foundation of the 21st century crop improvement. Plant Physiology 147: 969977.
Murray MG and Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research 8: 43214326.
Peakall R and Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288295.
Pritchard JK, Stephens M and Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945959.
Reif JC, Melchinger AE, Xia XC, Warburton ML, Hoisington DA, Vasal SK, Srinivasan G, Bohn M and Frisch M (2003) Genetic distance based on simple sequence repeats and heterosis in tropical maize populations. Crop Science 43: 12751282.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M and Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 27312739.
Thomson MJ, Zhao K, Wright M, McNally KL, Rey J, Tung CW, Reynolds A, Scheffler B, Eizenga G, McClung A, Kim H, Ismail AM, Ocampo M, Mojica C, Reveche MY, Dilla-Ermita CJ, Mauleon R, Leung H, Bustamante C and McCouch SR (2012) High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform. Molecular Breeding 29: 875886.
Wright MH, Tung CW, Zhao K, Reynolds A, McCouch SR and Bustamante CD (2010) ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations. Bioinformatics 26: 29522960.
Xie FM (1993) Hybrid performance and genetic diversity as revealed by RFLPs in Rice (Oryza sativa L.). PhD Thesis, Texas A&M University.
Yuan LP (1977) Practice and theory of breeding hybrid rice. Scientia Agricultura Sinica 10: 2731.
Zhang Q, Gao YJ, Yang S, Ragab R, Saghai Maroof MA and Li ZB (1994) A diallel analysis of heterosis in elite hybrid rice based on RFLPs and microsatellites. Theoretical and Applied Genetics 89: 185192.
Zhang Q, Gao YJ, Saghai Maroof MA, Yang SH and Li JX (1995) Molecular divergence and hybrid performance in rice. Molecular Breeding 1: 133142.
Zhao K, Wright MH, Kimball J, Eizenga G, McClung AM, Kovach M, Tyagi W, Ali ML, Tung CW, Reynolds A, Bustamante CD and McCouch SR (2010) Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS ONE 5: 111.
Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, Reynolds A, Mezey J, McClung AM, Bustamante CD and McCouch SR (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nature Communication 2: 467.
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Plant Genetic Resources
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