Global dissemination of a single mutation conferring white pericarp in rice.
Here we report that the change from the red seeds of wild rice to the white seeds of cultivated rice (Oryza sativa) resulted from the strong selective sweep of a single mutation, a frame-shift deletion within the Rc gene that is found in 97.9% of white rice varieties today. A second mutation, also within Rc, is present in less than 3% of white accessions surveyed. Haplotype analysis revealed that the predominant mutation originated in the japonica subspecies and crossed both geographic and sterility barriers to move into the indica subspecies. A little less than one Mb of japonica DNA hitchhiked with the rc allele into most indica varieties, suggesting that other linked domestication alleles may have been transferred from japonica to indica along with white pericarp color. Our finding provides evidence of active cultural exchange among ancient farmers over the course of rice domestication coupled with very strong, positive selection for a single white allele in both subspecies of O. sativa.
Sweeney
Megan T
MT
Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America.
Thomson
Michael J
MJ
Cho
Yong Gu
YG
Park
Yong Jin
YJ
Williamson
Scott H
SH
Bustamante
Carlos D
CD
McCouch
Susan R
SR
D001208:Asia; D018556:Crops, Agricultural / Q000235:genetics; D051456:Gene Flow; D005787:Gene Frequency; D017343:Genes, Plant; D014644:Genetic Variation; D006239:Haplotypes; D007564:Japan; D008969:Molecular Sequence Data; D009154:Mutation; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D010858:Pigmentation / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide
Plant J. 2007 Jan;49(1):91-102
17163879
Science. 2006 Jun 2;312(5778):1392-6
16614172
New Phytol. 2006;170(1):185-93
16539615
Mol Genet Genomics. 2004 Dec;272(5):504-11
15503144
Science. 2002 Apr 5;296(5565):92-100
11935018
Plant Cell. 2006 Feb;18(2):283-94
16399804
Theor Appl Genet. 2003 Aug;107(3):479-93
12736777
Genetics. 2004 Mar;166(3):1503-16
15082564
Science. 2002 Apr 5;296(5565):79-92
11935017
Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12404-10
15240870
Plant Cell. 2001 Sep;13(9):2099-114
11549766
Theor Appl Genet. 2005 Apr;110(6):1108-18
15782297
Science. 2006 Mar 31;311(5769):1936-9
16527928
Genetics. 2002 Jan;160(1):313-22
11805066
Genetics. 2005 Oct;171(2):695-704
15972459
Genes Dev. 1992 May;6(5):864-75
1577278
Theor Appl Genet. 1987 May;74(1):21-30
24241451
Plant Cell. 2002 Sep;14(9):2121-35
12215510
Curr Opin Plant Biol. 2003 Apr;6(2):139-46
12667870
Genetics. 2005 Mar;169(3):1631-8
15654106
Genetics. 2006 Jun;173(2):995-1005
16582442
Proc Natl Acad Sci U S A. 2006 Jun 20;103(25):9578-83
16766658
Genetics. 2002 May;161(1):289-98
12019242