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High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding

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dc.creator Sim, Sung-Chur
dc.creator Van Deynze, Allen
dc.creator Stoffel, Kevin
dc.creator Douches, David S.
dc.creator Zarka, Daniel
dc.creator Ganal, Martin W.
dc.creator Chetelat, Roger T.
dc.creator Hutton, Samuel F.
dc.creator Scott, John W.
dc.creator Gardner, Randolph G.
dc.creator Panthee, Dilip R.
dc.creator Mutschler, Martha
dc.creator Myers, James R.
dc.creator Francis, David M.
dc.date.accessioned 2012-11-12T16:40:33Z
dc.date.available 2012-11-12T16:40:33Z
dc.date.issued 2012-09-20
dc.identifier.citation Sim S-C, Van Deynze A, Stoffel K, Douches DS, Zarka D, et al. (2012) High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding. PLoS ONE 7(9): e45520. doi:10.1371/journal.pone.0045520 en_US
dc.identifier.uri http://hdl.handle.net/1957/35037
dc.description This is the publisher’s final pdf. The published article is copyrighted by PLoS ONE and can be found at: www.plosone.org. en_US
dc.description.abstract The effects of selection on genome variation were investigated and visualized in tomato using a high-density single nucleotide polymorphism (SNP) array. 7,720 SNPs were genotyped on a collection of 426 tomato accessions (410 inbreds and 16 hybrids) and over 97% of the markers were polymorphic in the entire collection. Principal component analysis (PCA) and pairwise estimates of F-st supported that the inbred accessions represented seven sub-populations including processing, large-fruited fresh market, large-fruited vintage, cultivated cherry, landrace, wild cherry, and S. pimpinellifolium. Further divisions were found within both the contemporary processing and fresh market sub-populations. These sub-populations showed higher levels of genetic diversity relative to the vintage sub-population. The array provided a large number of polymorphic SNP markers across each sub-population, ranging from 3,159 in the vintage accessions to 6,234 in the cultivated cherry accessions. Visualization of minor allele frequency revealed regions of the genome that distinguished three representative sub-populations of cultivated tomato (processing, fresh market, and vintage), particularly on chromosomes 2, 4, 5, 6, and 11. The PCA loadings and F-st outlier analysis between these three sub-populations identified a large number of candidate loci under positive selection on chromosomes 4, 5, and 11. The extent of linkage disequilibrium (LD) was examined within each chromosome for these sub-populations. LD decay varied between chromosomes and sub-populations, with large differences reflective of breeding history. For example, on chromosome 11, decay occurred over 0.8 cM for processing accessions and over 19.7 cM for fresh market accessions. The observed SNP variation and LD decay suggest that different patterns of genetic variation in cultivated tomato are due to introgression from wild species and selection for market specialization. en_US
dc.description.sponsorship This work was supported by a grant from the United States Department of Agriculture/National Institute of Food and Agriculture (2008-55300-04757 and 2009-85606-05673). Work at TraitGenetics was supported by the German Federal Ministry of Education and Research (BMBF) through grant number 0315639A. en_US
dc.language.iso en_US en_US
dc.publisher Plos One en_US
dc.relation.ispartofseries PLoS ONE en_US
dc.relation.ispartofseries Vol. 7 no. 9 en_US
dc.subject Single nucleotide polymorphisms en_US
dc.subject Linkage disequilibrium analysis en_US
dc.subject Late blight resistance en_US
dc.subject Self pruning gene en_US
dc.subject Map based cloning en_US
dc.subject Population structure en_US
dc.subject Disease resistance en_US
dc.subject Cultivated tomato en_US
dc.subject Phytophthora infestans en_US
dc.subject Processing tomato en_US
dc.title High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding en_US
dc.type Article en_US
dc.description.peerreview yes en_US
dc.identifier.doi 10.1371/journal.pone.0045520


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