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Genetic Structure and Domestication History of the Grape

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Genetic Structure and Domestication History of the Grape Genetic structure and domestication history of the grape Sean Mylesa,b,c,d,1, Adam R. Boykob, Christopher L. Owense, Patrick J. Browna, Fabrizio Grassif, Mallikarjuna K. Aradhyag, Bernard Prinsg, Andy Reynoldsb, Jer-Ming Chiah, Doreen Wareh,i, Carlos D. Bustamanteb, and Edward S. Bucklera,i aInstitute for Genomic Diversity, Cornell University, Ithaca, NY 14853; bDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305; cDepartment of Biology, Acadia University, Wolfville, NS, Canada B4P 2R6; dDepartment of Plant and Animal Sciences, Nova Scotia Agricultural College, Truro, NS, Canada B2N 5E3; eGrape Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Cornell University, Geneva, NY 14456; fBotanical Garden, Department of Biology, University of Milan, 20133 Milan, Italy; gNational Clonal Germplasm Repository, United States Department of Agriculture-Agricultural Research Service, University of California, Davis, CA 95616; hCold Spring Harbor Laboratory, United States Department of Agriculture-Agricultural Research Service, Cold Spring Harbor, NY 11724; and iRobert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Cornell University, Ithaca, NY14853 Edited* by Barbara A. Schaal, Washington University, St. Louis, MO, and approved December 9, 2010 (received for review July 1, 2010) The grape is one of the earliest domesticated fruit crops and, since sociations using linkage mapping. Because of the grape’s long antiquity, it has been widely cultivated and prized for its fruit and generation time (generally 3 y), however, establishing and wine. Here, we characterize genome-wide patterns of genetic maintaining linkage-mapping populations is time-consuming and variation in over 1,000 samples of the domesticated grape, Vitis expensive. Thus, genome-wide association (GWA) (6) and ge- vinifera subsp. vinifera, and its wild relative, V. vinifera subsp. nomic selection (GS) (7) are attractive alternatives to traditional sylvestris from the US Department of Agriculture grape germ- linkage mapping in the grape and other long-lived perennial plasm collection. We find support for a Near East origin of vinifera fruit crops. and present evidence of introgression from local sylvestris as the Well-powered GWA and GS require a genome-wide assess- grape moved into Europe. High levels of genetic diversity and ment of genetic diversity, patterns of population structure, and rapid linkage disequilibrium (LD) decay have been maintained in the decay of linkage disequilibrium (LD). To this end, we re- vinifera, which is consistent with a weak domestication bottleneck cently discovered over 70,000 high-quality SNPs in the grape followed by thousands of years of widespread vegetative propa- using next-generation DNA sequencing (4). From this SNP set, gation. The considerable genetic diversity within vinifera, how- we developed and validated a 9,000-SNP genotyping array (the ever, is contained within a complex network of close pedigree Vitis9kSNP array). Here, we present an analysis of genotype data relationships that has been generated by crosses among elite cul- from 950 vinifera and 59 sylvestris accessions using the fi tivars. We show that rst-degree relationships are rare between Vitis9kSNP array as part of an effort to characterize an entire wine and table grapes and among grapes from geographically US Department of Agriculture (USDA) germplasm collection distant regions. Our results suggest that although substantial ge- on a genome-wide scale. We provide a refined model of the do- netic diversity has been maintained in the grape subsequent to mestication and breeding history of vinifera by evaluating levels of domestication, there has been a limited exploration of this diver- haplotype diversity, the decay of LD, and patterns of population sity. We propose that the adoption of vegetative propagation was vinifera sylvestris fi structure in and its progenitor, . In addition, our a double-edged sword: Although it provided a bene t by ensuring analyses reveal extensive clonal relationships among cultivars true breeding cultivars, it also discouraged the generation of and a complex pedigree structure within vinifera that are the unique cultivars through crosses. The grape currently faces severe result of widespread vegetative propagation. We suggest that the pathogen pressures, and the long-term sustainability of the grape last several thousand years of grape breeding explored only and wine industries will rely on the exploitation of the grape’s a small fraction of possible genetic combinations and that future tremendous natural genetic diversity. marker-assisted breeding efforts therefore have tremendous di- versity at their disposal to produce desirable wine and table genomics | SNP array | positive selection | genome-wide association grapes with resistance to existing and future pathogens. he grape is the most valuable horticultural crop in the world. Results ’ ∼ TThe fruit from the world s 8 million ha of vineyard is mostly Pedigree Analysis Within vinifera. We used the Vitis9KSNP array processed into wine, but some is destined for fresh consumption (4) to generate 5,387 SNP genotypes from 950 vinifera accessions as table grapes, dried into raisins, processed into nonalcoholic (451 table grape accessions, 469 wine grape accessions, and 30 juice, and distilled into spirits (http://faostat.fao.org/). The ar- accessions of unknown type) from the grape germplasm collec- chaeological record suggests that cultivation of the domesticated tion of the USDA, one of the most comprehensive repositories Vitis vinifera vinifera – grape, subsp. , began 6,000 8,000 y ago in the of grape diversity in the world. Currently, there are over 10,000 Vitis vinifera sylvestris Near East from its wild progenitor, subsp. grape cultivar names in use worldwide (8), and their classifica- (1). The thousands of grape cultivars in use today have been tion is often confusing because of homonyms, synonyms, scarce generated since then by vegetative propagation and by crosses. Wine and table grapes currently receive intense chemical applications to combat severe pathogen pressures. This suscep- Author contributions: S.M., D.W., C.D.B., and E.S.B. designed research; S.M. and J.-M.C. tibility to disease, however, is not attributable to a lack of genetic performed research; F.G., M.K.A., and B.P. contributed new reagents/analytic tools; S.M., diversity. Vinifera harbors levels of genetic variation an order of A.R.B., C.L.O., P.J.B., and A.R. analyzed data; and S.M., C.D.B., and E.S.B. wrote the paper. magnitude greater than humans and is comparable in diversity to The authors declare no conflict of interest. maize (2, 3), with polymorphism that dates back tens of millions *This Direct Submission article had a prearranged editor. of years (4). Thus, an environmentally sustainable grape-growing Freely available online through the PNAS open access option. industry will rely on accessing and using the grape’s tremendous See Commentary on page 3457. genetic diversity to develop improved disease-resistant grape 1To whom correspondence should be addressed. E-mail: [email protected]. cultivars through marker-assisted breeding (5). Traditionally, This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. grape breeding programs have sought genotype-phenotype as- 1073/pnas.1009363108/-/DCSupplemental. 3530–3535 | PNAS | March 1, 2011 | vol. 108 | no. 9 www.pnas.org/cgi/doi/10.1073/pnas.1009363108 Downloaded by guest on September 28, 2021 B A A B SEE COMMENTARY Cultivar without (399) Unknown (19) clonal variation Table (262) 400 Pinot (17) Wine (302) Sultanina (14) Chasselas (13) Afus Ali (9) Khusaine Belyi (8) Chardonnay (7) Tebrizi (7) Number of cultivars Number of accessions Trousseau Noir (7) Ahmeur Bou Ahmeur (7) 0 100 200 300 0123456≥ 7 Muscat of Alexandria (7) 0 20 40 60 80 100 120 140 0 1 2 3 4 5 6 7 8 9 10≥ 11 Number of clones Muscat à petits grains blancs (7) Number of first degree relatives Fig. 1. Clonal relationships within the USDA grape germplasm collection. Fig. 2. First-degree relationships within the USDA grape germplasm col- (A) Number of clonal relationships was evaluated for each of the 950 vinifera lection. (A) Number of first-degree relationships was evaluated for each of accessions. Most of the accessions [551 (58%) of 950 accessions] have a clonal the 583 unique vinifera cultivars. A total of 74.8% of the unique cultivars are relationship with at least 1 other accession. (B) Degree of clonal relatedness related to at least 1 other cultivar by a first-degree relationship, and some among all 950 vinifera accessions is represented as a set of clusters. The 399 cultivars have many first-degree relationships (i.e., >10; SI Appendix, Table accessions that do not have a clonal relationship with another accession are S4). (B) Pedigree structure of vinifera is represented as a set of networks. shown as lone black dots. Accessions with six or fewer clonal relationships Edges in the network represent inferred first-degree relationships. The are grouped together with their clones and shown in gray. Clusters of clones vertices, or dots, represent grape cultivars and are colored by grape type with ≥7 accessions are colored, and their names are indicated in the legend. (legend). The sample size of each grape type is shown in parentheses. Lone Names listed in the legend are the prime names from the Vitis International dots represent cultivars with no first-degree relatives in the dataset. Note Variety Catalogue (http://www.vivc.de/). that one single interconnected network is clearly visible and includes 384 (58.3%) of the 583 unique cultivars that are interconnected by a series of first-degree relationships. or incorrect historical information, and curation error. Some cultivars have been differentiated into several through the veg- etative propagation of somatic mutants (9), and we expect clones relationships for each cultivar. The assignment of clonal and fi derived from the same cultivar to be genetically identical at the pedigree relationships from the present study will be veri ed in SCIENCES tested marker loci.
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