Genomewide SNP variation reveals relationships among landraces and modern varieties of rice.
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.
McNally
Kenneth L
KL
International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, The Philippines. k.mcnally@cgiar.org
Childs
Kevin L
KL
Bohnert
Regina
R
Davidson
Rebecca M
RM
Zhao
Keyan
K
Ulat
Victor J
VJ
Zeller
Georg
G
Clark
Richard M
RM
Hoen
Douglas R
DR
Bureau
Thomas E
TE
Stokowski
Renee
R
Ballinger
Dennis G
DG
Frazer
Kelly A
KA
Cox
David R
DR
Padhukasahasram
Badri
B
Bustamante
Carlos D
CD
Weigel
Detlef
D
Mackill
David J
DJ
Bruskiewich
Richard M
RM
Rätsch
Gunnar
G
Buell
C Robin
CR
Leung
Hei
H
Leach
Jan E
JE
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