Genetic structure and domestication history of the grape.
The grape is one of the earliest domesticated fruit crops and, since antiquity, it has been widely cultivated and prized for its fruit and wine. Here, we characterize genome-wide patterns of genetic variation in over 1,000 samples of the domesticated grape, Vitis vinifera subsp. vinifera, and its wild relative, V. vinifera subsp. sylvestris from the US Department of Agriculture grape germplasm collection. We find support for a Near East origin of vinifera and present evidence of introgression from local sylvestris as the grape moved into Europe. High levels of genetic diversity and rapid linkage disequilibrium (LD) decay have been maintained in vinifera, which is consistent with a weak domestication bottleneck followed by thousands of years of widespread vegetative propagation. The considerable genetic diversity within vinifera, however, is contained within a complex network of close pedigree relationships that has been generated by crosses among elite cultivars. We show that first-degree relationships are rare between wine and table grapes and among grapes from geographically distant regions. Our results suggest that although substantial genetic diversity has been maintained in the grape subsequent to domestication, there has been a limited exploration of this diversity. We propose that the adoption of vegetative propagation was a double-edged sword: Although it provided a benefit by ensuring true breeding cultivars, it also discouraged the generation of unique cultivars through crosses. The grape currently faces severe pathogen pressures, and the long-term sustainability of the grape and wine industries will rely on the exploitation of the grape's tremendous natural genetic diversity.
Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA.
Sean
S
Myles
Adam R
AR
Boyko
Christopher L
CL
Owens
Patrick J
PJ
Brown
Fabrizio
F
Grassi
Mallikarjuna K
MK
Aradhya
Bernard
B
Prins
Andy
A
Reynolds
Jer-Ming
JM
Chia
Doreen
D
Ware
Carlos D
CD
Bustamante
Edward S
ES
Buckler
D002999:Clone Cells; D018556:Crops, Agricultural / Q000235:genetics* / Q000266:history*; D006239:Haplotypes / Q000235:genetics; D049690:History, Ancient; D015810:Linkage Disequilibrium / Q000235:genetics; D010375:Pedigree; D010802:Phylogeny; D011157:Population Dynamics; D025341:Principal Component Analysis; D012639:Seeds / Q000235:genetics; D014481:United States; D016885:United States Department of Agriculture; D027843:Vitis / Q000235:genetics*
BMC Genomics. 2007 Nov 19;8:424
18021442
PLoS One. 2010 Jan 13;5(1):e8219
20084295
Theor Appl Genet. 2003 Nov;107(7):1315-20
13679993
Genetics. 2007 Dec;177(4):2223-32
17947413
Am J Hum Genet. 2001 Jul;69(1):1-14
11410837
Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11479-84
11562485
Heredity (Edinb). 2010 May;104(5):431-7
19844269
PLoS Genet. 2006 Dec;2(12):e190
17194218
Genetics. 2008 Mar;178(3):1709-23
18385116
Proc Natl Acad Sci U S A. 2001 Jul 31;98(16):9161-6
11470895
J Hered. 2009 Jan-Feb;100(1):66-75
18927474
Mol Ecol. 2006 Oct;15(12):3707-14
17032268
Science. 2004 May 14;304(5673):982
15143274
Nature. 2008 Dec 11;456(7223):720-3
19079047
Nature. 2009 Sep 24;461(7263):489-94
19779445
Heredity (Edinb). 2010 Apr;104(4):351-62
19920856
Science. 1999 Sep 3;285(5433):1562-1565
10477519
Theor Appl Genet. 2006 Feb;112(4):708-16
16402190
Am J Hum Genet. 2006 Apr;78(4):629-44
16532393
Genet Res. 2003 Jun;81(3):179-92
12929909
Theor Appl Genet. 2007 Feb;114(4):723-30
17221259
Theor Appl Genet. 1990 Oct;80(4):437-48
24221000
Heredity (Edinb). 2010 Apr;104(4):331-40
19935824
Am J Hum Genet. 2007 Sep;81(3):559-75
17701901
Genetics. 2009 Nov;183(3):1127-39
19720862
Nat Rev Genet. 2008 May;9(5):356-69
18398418
Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4441-6
9539756
Evolution. 1984 Nov;38(6):1358-1370
28563791
Nat Genet. 2007 Sep;39(9):1151-5
17676040
Plant Cell. 2009 Aug;21(8):2194-202
19654263
Trends Genet. 2006 Sep;22(9):511-9
16872714
Curr Opin Plant Biol. 2006 Apr;9(2):172-6
16459128
BMC Genet. 2009 Dec 30;10:89
20042081
Nat Genet. 2006 Feb;38(2):203-8
16380716