High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding.

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...

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Autores principales: Sung-Chur Sim, Allen Van Deynze, Kevin Stoffel, David S Douches, Daniel Zarka, Martin W Ganal, Roger T Chetelat, Samuel F Hutton, John W Scott, Randolph G Gardner, Dilip R Panthee, Martha Mutschler, James R Myers, David M Francis
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Publicado: Public Library of Science (PLoS) 2012
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Acceso en línea:https://doaj.org/article/7c6405f730a44ba7aabf7d11d0955acc
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spelling oai:doaj.org-article:7c6405f730a44ba7aabf7d11d0955acc2021-11-18T07:04:44ZHigh-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding.1932-620310.1371/journal.pone.0045520https://doaj.org/article/7c6405f730a44ba7aabf7d11d0955acc2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23029069/?tool=EBIhttps://doaj.org/toc/1932-6203The 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.Sung-Chur SimAllen Van DeynzeKevin StoffelDavid S DouchesDaniel ZarkaMartin W GanalRoger T ChetelatSamuel F HuttonJohn W ScottRandolph G GardnerDilip R PantheeMartha MutschlerJames R MyersDavid M FrancisPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 9, p e45520 (2012)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Sung-Chur Sim
Allen Van Deynze
Kevin Stoffel
David S Douches
Daniel Zarka
Martin W Ganal
Roger T Chetelat
Samuel F Hutton
John W Scott
Randolph G Gardner
Dilip R Panthee
Martha Mutschler
James R Myers
David M Francis
High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding.
description 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.
format article
author Sung-Chur Sim
Allen Van Deynze
Kevin Stoffel
David S Douches
Daniel Zarka
Martin W Ganal
Roger T Chetelat
Samuel F Hutton
John W Scott
Randolph G Gardner
Dilip R Panthee
Martha Mutschler
James R Myers
David M Francis
author_facet Sung-Chur Sim
Allen Van Deynze
Kevin Stoffel
David S Douches
Daniel Zarka
Martin W Ganal
Roger T Chetelat
Samuel F Hutton
John W Scott
Randolph G Gardner
Dilip R Panthee
Martha Mutschler
James R Myers
David M Francis
author_sort Sung-Chur Sim
title High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding.
title_short High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding.
title_full High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding.
title_fullStr High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding.
title_full_unstemmed High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding.
title_sort high-density snp genotyping of tomato (solanum lycopersicum l.) reveals patterns of genetic variation due to breeding.
publisher Public Library of Science (PLoS)
publishDate 2012
url https://doaj.org/article/7c6405f730a44ba7aabf7d11d0955acc
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