Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm
Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collecti...
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| Veröffentlicht in: | PloS one 2015-09, Vol.10 (9), p.e0136803-e0136803 |
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| creator | Micheletti, Diego Dettori, Maria Teresa Micali, Sabrina Aramini, Valeria Pacheco, Igor Da Silva Linge, Cassia Foschi, Stefano Banchi, Elisa Barreneche, Teresa Quilot-Turion, Bénédicte Lambert, Patrick Pascal, Thierry Iglesias, Ignasi Carbó, Joaquim Wang, Li-Rong Ma, Rui-Juan Li, Xiong-Wei Gao, Zhong-Shan Nazzicari, Nelson Troggio, Michela Bassi, Daniele Rossini, Laura Verde, Ignazio Laurens, François Arús, Pere Aranzana, Maria José |
| description | Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding programs. |
| doi_str_mv | 10.1371/journal.pone.0136803 |
| format | Article |
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Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding programs.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0136803</identifier><identifier>PMID: 26352671</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Agricultural sciences ; Biodiversity ; Bioinformatics ; Breeding ; Chromosome Mapping ; Chromosomes, Plant ; Consortia ; Data collection ; Diagnostic systems ; Domestication ; Fruits ; Gene pool ; Genetic aspects ; Genetic diversity ; Genetic variability ; Genetic Variation ; Genome, Plant ; Genome-wide association studies ; Genome-Wide Association Study ; Genomes ; Genomics ; Genotype ; Genotype & phenotype ; Germplasm ; Haplotypes ; Horticulture ; Life Sciences ; Linkage analysis ; Linkage disequilibrium ; Marker-assisted selection ; Morphology ; Myzus persicae ; Parents ; Peaches ; Phenotype ; Phylogeny ; Physiological aspects ; Polymorphism, Single Nucleotide ; Population structure ; Population studies ; Populations ; Prunus ; Prunus persica ; Prunus persica - genetics ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Studies ; Variability ; Vegetal Biology</subject><ispartof>PloS one, 2015-09, Vol.10 (9), p.e0136803-e0136803</ispartof><rights>COPYRIGHT 2015 Public Library of Science</rights><rights>2015 Micheletti et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Attribution</rights><rights>2015 Micheletti et al 2015 Micheletti et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c792t-17a061ac34cd89e10667c39b74b6ed973e481b64006a0ec61bb13330641916203</citedby><cites>FETCH-LOGICAL-c792t-17a061ac34cd89e10667c39b74b6ed973e481b64006a0ec61bb13330641916203</cites><orcidid>0000-0002-7852-1418 ; 0000-0003-4095-1399</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4564248/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4564248/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,861,882,2096,2915,23847,27905,27906,53772,53774,79349,79350</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26352671$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-01210020$$DView record in HAL$$Hfree_for_read</backlink></links><search><contributor>Han, Yuepeng</contributor><creatorcontrib>Micheletti, Diego</creatorcontrib><creatorcontrib>Dettori, Maria Teresa</creatorcontrib><creatorcontrib>Micali, Sabrina</creatorcontrib><creatorcontrib>Aramini, Valeria</creatorcontrib><creatorcontrib>Pacheco, Igor</creatorcontrib><creatorcontrib>Da Silva Linge, Cassia</creatorcontrib><creatorcontrib>Foschi, Stefano</creatorcontrib><creatorcontrib>Banchi, Elisa</creatorcontrib><creatorcontrib>Barreneche, Teresa</creatorcontrib><creatorcontrib>Quilot-Turion, Bénédicte</creatorcontrib><creatorcontrib>Lambert, Patrick</creatorcontrib><creatorcontrib>Pascal, Thierry</creatorcontrib><creatorcontrib>Iglesias, Ignasi</creatorcontrib><creatorcontrib>Carbó, Joaquim</creatorcontrib><creatorcontrib>Wang, Li-Rong</creatorcontrib><creatorcontrib>Ma, Rui-Juan</creatorcontrib><creatorcontrib>Li, Xiong-Wei</creatorcontrib><creatorcontrib>Gao, Zhong-Shan</creatorcontrib><creatorcontrib>Nazzicari, Nelson</creatorcontrib><creatorcontrib>Troggio, Michela</creatorcontrib><creatorcontrib>Bassi, Daniele</creatorcontrib><creatorcontrib>Rossini, Laura</creatorcontrib><creatorcontrib>Verde, Ignazio</creatorcontrib><creatorcontrib>Laurens, François</creatorcontrib><creatorcontrib>Arús, Pere</creatorcontrib><creatorcontrib>Aranzana, Maria José</creatorcontrib><title>Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding programs.</description><subject>Agricultural sciences</subject><subject>Biodiversity</subject><subject>Bioinformatics</subject><subject>Breeding</subject><subject>Chromosome Mapping</subject><subject>Chromosomes, Plant</subject><subject>Consortia</subject><subject>Data collection</subject><subject>Diagnostic systems</subject><subject>Domestication</subject><subject>Fruits</subject><subject>Gene pool</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genetic variability</subject><subject>Genetic Variation</subject><subject>Genome, Plant</subject><subject>Genome-wide association studies</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotype</subject><subject>Genotype & phenotype</subject><subject>Germplasm</subject><subject>Haplotypes</subject><subject>Horticulture</subject><subject>Life Sciences</subject><subject>Linkage analysis</subject><subject>Linkage disequilibrium</subject><subject>Marker-assisted selection</subject><subject>Morphology</subject><subject>Myzus persicae</subject><subject>Parents</subject><subject>Peaches</subject><subject>Phenotype</subject><subject>Phylogeny</subject><subject>Physiological aspects</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Population structure</subject><subject>Population studies</subject><subject>Populations</subject><subject>Prunus</subject><subject>Prunus persica</subject><subject>Prunus persica - genetics</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><subject>Studies</subject><subject>Variability</subject><subject>Vegetal 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Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm</title><author>Micheletti, Diego ; Dettori, Maria Teresa ; Micali, Sabrina ; Aramini, Valeria ; Pacheco, Igor ; Da Silva Linge, Cassia ; Foschi, Stefano ; Banchi, Elisa ; Barreneche, Teresa ; Quilot-Turion, Bénédicte ; Lambert, Patrick ; Pascal, Thierry ; Iglesias, Ignasi ; Carbó, Joaquim ; Wang, Li-Rong ; Ma, Rui-Juan ; Li, Xiong-Wei ; Gao, Zhong-Shan ; Nazzicari, Nelson ; Troggio, Michela ; Bassi, Daniele ; Rossini, Laura ; Verde, Ignazio ; Laurens, François ; Arús, Pere ; Aranzana, Maria José</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c792t-17a061ac34cd89e10667c39b74b6ed973e481b64006a0ec61bb13330641916203</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Agricultural sciences</topic><topic>Biodiversity</topic><topic>Bioinformatics</topic><topic>Breeding</topic><topic>Chromosome 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Edition</collection><collection>ProQuest Central China</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Micheletti, Diego</au><au>Dettori, Maria Teresa</au><au>Micali, Sabrina</au><au>Aramini, Valeria</au><au>Pacheco, Igor</au><au>Da Silva Linge, Cassia</au><au>Foschi, Stefano</au><au>Banchi, Elisa</au><au>Barreneche, Teresa</au><au>Quilot-Turion, Bénédicte</au><au>Lambert, Patrick</au><au>Pascal, Thierry</au><au>Iglesias, Ignasi</au><au>Carbó, Joaquim</au><au>Wang, Li-Rong</au><au>Ma, Rui-Juan</au><au>Li, Xiong-Wei</au><au>Gao, Zhong-Shan</au><au>Nazzicari, Nelson</au><au>Troggio, Michela</au><au>Bassi, Daniele</au><au>Rossini, Laura</au><au>Verde, Ignazio</au><au>Laurens, François</au><au>Arús, Pere</au><au>Aranzana, Maria José</au><au>Han, Yuepeng</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2015-09-09</date><risdate>2015</risdate><volume>10</volume><issue>9</issue><spage>e0136803</spage><epage>e0136803</epage><pages>e0136803-e0136803</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding programs.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26352671</pmid><doi>10.1371/journal.pone.0136803</doi><orcidid>https://orcid.org/0000-0002-7852-1418</orcidid><orcidid>https://orcid.org/0000-0003-4095-1399</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2015-09, Vol.10 (9), p.e0136803-e0136803 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1715677899 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS); EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Agricultural sciences Biodiversity Bioinformatics Breeding Chromosome Mapping Chromosomes, Plant Consortia Data collection Diagnostic systems Domestication Fruits Gene pool Genetic aspects Genetic diversity Genetic variability Genetic Variation Genome, Plant Genome-wide association studies Genome-Wide Association Study Genomes Genomics Genotype Genotype & phenotype Germplasm Haplotypes Horticulture Life Sciences Linkage analysis Linkage disequilibrium Marker-assisted selection Morphology Myzus persicae Parents Peaches Phenotype Phylogeny Physiological aspects Polymorphism, Single Nucleotide Population structure Population studies Populations Prunus Prunus persica Prunus persica - genetics Single nucleotide polymorphisms Single-nucleotide polymorphism Studies Variability Vegetal Biology |
| title | Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm |
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