title: Open access resources for genome-wide association mapping in rice.
abstract: Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement.
authors: School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, 14850 New York, USA.|Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, 14850 New York, USA.
authors: Susan R
authors: SR
authors: McCouch
authors: School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, 14850 New York, USA.
authors: Mark H
authors: MH
authors: Wright
authors: School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, 14850 New York, USA.
authors: Chih-Wei
authors: CW
authors: Tung
authors: School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, 14850 New York, USA.
authors: Lyza G
authors: LG
authors: Maron
authors: International Rice Research Institute, DAPO Box 7777, 1301 Metro Manila, Philippines.
authors: Kenneth L
authors: KL
authors: McNally
authors: International Rice Research Institute, DAPO Box 7777, 1301 Metro Manila, Philippines.|School of Food Science, University of Queensland, St Lucia, 4072 Queensland, Australia.
authors: Melissa
authors: M
authors: Fitzgerald
authors: School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, 14850 New York, USA.
authors: Namrata
authors: N
authors: Singh
authors: School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, 14850 New York, USA.
authors: Genevieve
authors: G
authors: DeClerck
authors: School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, 14850 New York, USA.|Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, 14850 New York, USA.
authors: Francisco
authors: F
authors: Agosto-Perez
authors: School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, 14850 New York, USA.|Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, 14850 New York, USA.
authors: Pavel
authors: P
authors: Korniliev
authors: School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, 14850 New York, USA.|Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, 14850 New York, USA.
authors: Anthony J
authors: AJ
authors: Greenberg
authors: International Rice Research Institute, DAPO Box 7777, 1301 Metro Manila, Philippines.
authors: Ma Elizabeth B
authors: ME
authors: Naredo
authors: International Rice Research Institute, DAPO Box 7777, 1301 Metro Manila, Philippines.
authors: Sheila Mae Q
authors: SM
authors: Mercado
authors: School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, 14850 New York, USA.
authors: Sandra E
authors: SE
authors: Harrington
authors: School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, 14850 New York, USA.
authors: Yuxin
authors: Y
authors: Shi
authors: Transnational Learning Center, Cornell University, Ithaca, 14850 New York, USA.
authors: Darcy A
authors: DA
authors: Branchini
authors: School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, 14850 New York, USA.
authors: Paula R
authors: PR
authors: Kuser-Falcão
authors: International Rice Research Institute, DAPO Box 7777, 1301 Metro Manila, Philippines.
authors: Hei
authors: H
authors: Leung
authors: National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, 305-8602 Ibaraki, Japan.
authors: Kowaru
authors: K
authors: Ebana
authors: National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, 305-8602 Ibaraki, Japan.
authors: Masahiro
authors: M
authors: Yano
authors: USDA-ARS Dale Bumpers National Rice Research Center, 2890 Hwy. 130 E., Stuttgart, Arkansas 72160, USA.
authors: Georgia
authors: G
authors: Eizenga
authors: USDA-ARS Dale Bumpers National Rice Research Center, 2890 Hwy. 130 E., Stuttgart, Arkansas 72160, USA.
authors: Anna
authors: A
authors: McClung
authors: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, 14850 New York, USA.
authors: Jason
authors: J
authors: Mezey
mesh_terms: D022126:Access to Information; D000383:Agriculture; D000483:Alleles; D002874:Chromosome Mapping; D019295:Computational Biology; D030541:Databases, Genetic; D002523:Edible Grain / Q000033:anatomy & histology / Q000235:genetics*; D004843:Epistasis, Genetic; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D055106:Genome-Wide Association Study; D005838:Genotype; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D000069600:Plant Breeding; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D040641:Quantitative Trait Loci / Q000235:genetics*