title: Genomewide SNP variation reveals relationships among landraces and modern varieties of rice.
abstract: Rice, the primary source of dietary calories for half of humanity, is the first crop plant for which a high-quality reference genome sequence from a single variety was produced. We used resequencing microarrays to interrogate 100 Mb of the unique fraction of the reference genome for 20 diverse varieties and landraces that capture the impressive genotypic and phenotypic diversity of domesticated rice. Here, we report the distribution of 160,000 nonredundant SNPs. Introgression patterns of shared SNPs revealed the breeding history and relationships among the 20 varieties; some introgressed regions are associated with agronomic traits that mark major milestones in rice improvement. These comprehensive SNP data provide a foundation for deep exploration of rice diversity and gene-trait relationships and their use for future rice improvement.
authors: International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, The Philippines. k.mcnally@cgiar.org
authors: Kenneth L
authors: KL
authors: McNally
authors: Kevin L
authors: KL
authors: Childs
authors: Regina
authors: R
authors: Bohnert
authors: Rebecca M
authors: RM
authors: Davidson
authors: Keyan
authors: K
authors: Zhao
authors: Victor J
authors: VJ
authors: Ulat
authors: Georg
authors: G
authors: Zeller
authors: Richard M
authors: RM
authors: Clark
authors: Douglas R
authors: DR
authors: Hoen
authors: Thomas E
authors: TE
authors: Bureau
authors: Renee
authors: R
authors: Stokowski
authors: Dennis G
authors: DG
authors: Ballinger
authors: Kelly A
authors: KA
authors: Frazer
authors: David R
authors: DR
authors: Cox
authors: Badri
authors: B
authors: Padhukasahasram
authors: Carlos D
authors: CD
authors: Bustamante
authors: Detlef
authors: D
authors: Weigel
authors: David J
authors: DJ
authors: Mackill
authors: Richard M
authors: RM
authors: Bruskiewich
authors: Gunnar
authors: G
authors: Rätsch
authors: C Robin
authors: CR
authors: Buell
authors: Hei
authors: H
authors: Leung
authors: Jan E
authors: JE
authors: Leach
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D005787:Gene Frequency; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D008969:Molecular Sequence Data; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity