Genome-wide association studies of 14 agronomic traits in rice landraces

Zong, Y. et al. Fire and flood management of coastal swamp enabled first rice paddy cultivation in east China. Nature 449, 459–462 (2007).

Zhang, D. et al. Genetic structure and differentiation of Oryza sativa L. in China revealed by microsatellites. Theor. Appl. Genet. 119, 1105–1117 (2009).

The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299–1320 (2005).

The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851–861 (2007).

The Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447, 661–678 (2007).

Altshuler, D., Daly, M.J. & Lander, E.S. Genetic mapping in human disease. Science 322, 881–888 (2008).

Nordborg, M. & Weigel, D. Next-generation genetics in plants. Nature 456, 720–723 (2008).

Atwell, S. et al. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465, 627–631 (2010).

Gore, M.A. et al. A first-generation haplotype map of maize. Science 326, 1115–1117 (2009).

International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature 436, 793–800 (2005).

Weigel, D. & Mott, R. The 1001 genomes project for Arabidopsis thaliana. Genome Biol. 10, 107 (2009).

Clark, R.M. et al. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317, 338–342 (2007).

McNally, K.L. et al. Genome-wide SNP variation reveals relationships among landraces and modern varieties of rice. Proc. Natl. Acad. Sci. USA 106, 12273–12278 (2009).

Huang, X. et al. High-throughput genotyping by whole-genome resequencing. Genome Res. 19, 1068–1076 (2009).

Caicedo, A.L. et al. Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet. 3, 1745–1756 (2007).

Zhu, Q. et al. Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol. Biol. Evol. 24, 875–888 (2007).

Price, A.L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904–909 (2006).

Mather, K.A. et al. The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics 177, 2223–2232 (2007).

Troyanskaya, O. et al. Missing value estimation methods for DNA microarrays. Bioinformatics 17, 520–525 (2001).

Roberts, A. et al. Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows. Bioinformatics 23, i401–i407 (2007).

Yu, J. et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38, 203–208 (2006).

Zhang, Z. et al. Mixed linear model approach adapted for genome-wide association studies. Nat. Genet. 42, 355–360 (2010).

Saitoh, K. et al. Allelic diversification at the C (OsC1) locus of wild and cultivated rice: nucleotide changes associated with phenotypes. Genetics 168, 997–1007 (2004).

Sweeney, M.T., Thomson, M.J., Pfeil, B.E. & McCouch, S. Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. Plant Cell 18, 283–294 (2006).

Cui, J. et al. Characterization and fine mapping of the ibf mutant in rice. J. Integr. Plant Biol. 49, 678–685 (2007).

Gao, Z. et al. Map-based cloning of the ALK gene, which controls the gelatinization temperature of rice. Sci. China C Life Sci. 46, 661–668 (2003).

Wang, Z.Y. et al. The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy gene. Plant J. 7, 613–622 (1995).

Tian, Z. et al. Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc. Natl. Acad. Sci. USA 106, 21760–21765 (2009).

Shomura, A. et al. Deletion in a gene associated with grain size increased yields during rice domestication. Nat. Genet. 40, 1023–1028 (2008).

Fan, C. et al. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor. Appl. Genet. 112, 1164–1171 (2006).

Buckler, E.S. et al. The genetic architecture of maize flowering time. Science 325, 714–718 (2009).

Kim, S.L. et al. OsMADS51 is a short-day flowering promoter that functions upstream of Ehd1, OsMADS14, and Hd3a. Plant Physiol. 145, 1484–1494 (2007).

Zhang, Q., Li, J.Y., Xue, Y.B., Han, B. & Deng, X.W. Rice 2020: a call for an international coordinated effort in rice functional genomics. Mol. Plant 1, 715–719 (2008).

Myles, S. et al. Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21, 2194–2202 (2009).

McMullen, M.D. et al. Genetic properties of the maize nested association mapping population. Science 325, 737–740 (2009).

Huang, X. et al. Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice. Plant Physiol. 148, 25–40 (2008).

Felsenstein, J. PHYLIP: phylogeny inference package (version 3.2). Cladistics 5, 164–166 (1989).

Barrett, J.C., Fry, B., Maller, J. & Daly, M.J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263–265 (2005).

Tajima, F. Evolutionary relationship of DNA sequences in finite populations. Genetics 105, 437–460 (1983).

Nordborg, M. et al. The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol. 3, e196 (2005).

Juliano, B. Rice Chemistry and Technology 443–513 (American Association of Cereal Chemists, Saint Paul, Minnesota, USA, 1985).

Little, R.R., Hilder, G.B. & Dawson, E.H. Differential effect of dilute alkali on 25 varieties of milled white rice. Cereal Chem. 35, 111–126 (1958).