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: 217–226.
Cavalli-Sforza, LL and Edwards, AWF (1967) Phylogenetic analysis: models and estimation procedures. American Journal of Human Genetics 19: 233–257.
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: 869–879.
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: 718–723.
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: 2611–2620.
Falush, D, Stephens, M and Pritchard, JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567–1587.
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: 1023–1030.
Liu, K and Muse, SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128–2129.
Lu, ZM and Xu, BQ (2010) On significance of heterotic group theory in hybrid rice breeding. Rice Science 17: 94–98.
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: 524–535.
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: 12273–12278.
Moose, SP and Mumm, RH (2008) Molecular plant breeding as the foundation of the 21st century crop improvement. Plant Physiology 147: 969–977.
Murray, MG and Thompson, WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research 8: 4321–4326.
Peakall, R and Smouse, PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288–295.
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.
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: 1275–1282.
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: 2731–2739.
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: 875–886.
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: 2952–2960.
Xie, FM (1993) .
Yuan, LP (1977) Practice and theory of breeding hybrid rice. Scientia Agricultura Sinica 10: 27–31.
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: 185–192.
Zhang, Q, Gao, YJ, Saghai Maroof, MA, Yang, SH and Li, JX (1995) Molecular divergence and hybrid performance in rice. Molecular Breeding 1: 133–142.
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: 1–11.
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.
