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...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23029069/?tool=EBI |
| _version_ | 1818435277123747840 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-14T16:50:19Z |
| format | Article |
| id | doaj.art-7c6405f730a44ba7aabf7d11d0955acc |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-14T16:50:19Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
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| series | PLoS ONE |
| spelling | doaj.art-7c6405f730a44ba7aabf7d11d0955acc2022-12-21T22:54:04ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0179e4552010.1371/journal.pone.0045520High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding.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 FrancisThe 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.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23029069/?tool=EBI |
| spellingShingle | 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. PLoS ONE |
| title | 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_short | 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 |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23029069/?tool=EBI |
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