Association Mapping for Fruit, Plant and Leaf Morphology Traits in Eggplant
An eggplant (Solanum melongena) association panel of 191 accessions, comprising a mixture of breeding lines, old varieties and landrace selections was SNP genotyped and phenotyped for key breeding fruit and plant traits at two locations over two seasons. A genome-wide association (GWA) analysis was...
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| creator | Portis, Ezio Cericola, Fabio Barchi, Lorenzo Toppino, Laura Acciarri, Nazzareno Pulcini, Laura Sala, Tea Lanteri, Sergio Rotino, Giuseppe Leonardo |
| description | An eggplant (Solanum melongena) association panel of 191 accessions, comprising a mixture of breeding lines, old varieties and landrace selections was SNP genotyped and phenotyped for key breeding fruit and plant traits at two locations over two seasons. A genome-wide association (GWA) analysis was performed using the mixed linear model, which takes into account both a kinship matrix and the sub-population membership of the accessions. Overall, 194 phenotype/genotype associations were uncovered, relating to 30 of the 33 measured traits. These associations involved 79 SNP loci mapping to 39 distinct chromosomal regions distributed over all 12 eggplant chromosomes. A comparison of the map positions of these SNPs with those of loci derived from conventional linkage mapping showed that GWA analysis both validated many of the known controlling loci and detected a large number of new marker/trait associations. Exploiting established syntenic relationships between eggplant chromosomes and those of tomato and pepper recognized orthologous regions in ten eggplant chromosomes harbouring genes influencing breeders' traits. |
| doi_str_mv | 10.1371/journal.pone.0135200 |
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A genome-wide association (GWA) analysis was performed using the mixed linear model, which takes into account both a kinship matrix and the sub-population membership of the accessions. Overall, 194 phenotype/genotype associations were uncovered, relating to 30 of the 33 measured traits. These associations involved 79 SNP loci mapping to 39 distinct chromosomal regions distributed over all 12 eggplant chromosomes. A comparison of the map positions of these SNPs with those of loci derived from conventional linkage mapping showed that GWA analysis both validated many of the known controlling loci and detected a large number of new marker/trait associations. Exploiting established syntenic relationships between eggplant chromosomes and those of tomato and pepper recognized orthologous regions in ten eggplant chromosomes harbouring genes influencing breeders' traits.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0135200</identifier><identifier>PMID: 26284782</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Arabidopsis ; Arabidopsis thaliana ; Breeding ; Chromosome Mapping ; Chromosomes ; Comparative analysis ; Crops ; Enzymes ; Fruit - genetics ; Fruits ; Gene mapping ; Genetic engineering ; Genomes ; Genomics ; Genotypes ; Loci ; Mapping ; Mathematical analysis ; Matrix methods ; Morphology ; Phenotype ; Phenotypes ; Plant breeding ; Plant Leaves - genetics ; Polymorphism, Single Nucleotide ; Proteins ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Solanum melongena ; Solanum melongena - genetics ; Stem cells ; Synteny ; Tomatoes</subject><ispartof>PloS one, 2015-08, Vol.10 (8), p.e0135200-e0135200</ispartof><rights>COPYRIGHT 2015 Public Library of Science</rights><rights>2015 Portis 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>2015 Portis et al 2015 Portis et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c758t-657cdd7df0ec8127b4ee2ab2e9b5a02c18b6b53a80f9e3c01de3986a6d2f2153</citedby><cites>FETCH-LOGICAL-c758t-657cdd7df0ec8127b4ee2ab2e9b5a02c18b6b53a80f9e3c01de3986a6d2f2153</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4540451/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4540451/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2100,2926,23865,27923,27924,53790,53792,79371,79372</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26284782$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Ezura, Hiroshi</contributor><creatorcontrib>Portis, Ezio</creatorcontrib><creatorcontrib>Cericola, Fabio</creatorcontrib><creatorcontrib>Barchi, Lorenzo</creatorcontrib><creatorcontrib>Toppino, Laura</creatorcontrib><creatorcontrib>Acciarri, Nazzareno</creatorcontrib><creatorcontrib>Pulcini, Laura</creatorcontrib><creatorcontrib>Sala, Tea</creatorcontrib><creatorcontrib>Lanteri, Sergio</creatorcontrib><creatorcontrib>Rotino, Giuseppe Leonardo</creatorcontrib><title>Association Mapping for Fruit, Plant and Leaf Morphology Traits in Eggplant</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>An eggplant (Solanum melongena) association panel of 191 accessions, comprising a mixture of breeding lines, old varieties and landrace selections was SNP genotyped and phenotyped for key breeding fruit and plant traits at two locations over two seasons. A genome-wide association (GWA) analysis was performed using the mixed linear model, which takes into account both a kinship matrix and the sub-population membership of the accessions. Overall, 194 phenotype/genotype associations were uncovered, relating to 30 of the 33 measured traits. These associations involved 79 SNP loci mapping to 39 distinct chromosomal regions distributed over all 12 eggplant chromosomes. A comparison of the map positions of these SNPs with those of loci derived from conventional linkage mapping showed that GWA analysis both validated many of the known controlling loci and detected a large number of new marker/trait associations. Exploiting established syntenic relationships between eggplant chromosomes and those of tomato and pepper recognized orthologous regions in ten eggplant chromosomes harbouring genes influencing breeders' traits.</description><subject>Arabidopsis</subject><subject>Arabidopsis thaliana</subject><subject>Breeding</subject><subject>Chromosome Mapping</subject><subject>Chromosomes</subject><subject>Comparative analysis</subject><subject>Crops</subject><subject>Enzymes</subject><subject>Fruit - genetics</subject><subject>Fruits</subject><subject>Gene mapping</subject><subject>Genetic engineering</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotypes</subject><subject>Loci</subject><subject>Mapping</subject><subject>Mathematical analysis</subject><subject>Matrix methods</subject><subject>Morphology</subject><subject>Phenotype</subject><subject>Phenotypes</subject><subject>Plant breeding</subject><subject>Plant Leaves - genetics</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Proteins</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><subject>Solanum melongena</subject><subject>Solanum melongena - genetics</subject><subject>Stem cells</subject><subject>Synteny</subject><subject>Tomatoes</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNkl1v0zAUhiMEYmPwDxBEQkIgrcXfTm-QqmljFZ2GoOLWchw7dZXGwXYQ-_e4bTY1aBfIF7aOn_Oe4-M3y15DMIWYw08b1_tWNtPOtXoKIKYIgCfZKZxhNGEI4KdH55PsRQgbACguGHuenSCGCsILdJp9nYfglJXRuja_kV1n2zo3zudXvrfxPP_WyDbmsq3ypZYmv3G-W7vG1Xf5yksbQ27b_LKuux32MntmZBP0q2E_y1ZXl6uL68ny9sviYr6cKE6LOGGUq6rilQFaFRDxkmiNZIn0rKQSIAWLkpUUywKYmcYKwErjWcEkq5BBkOKz7O1BtmtcEMMYgoAcFJRxRmEiFgeicnIjOm-30t8JJ63YB5yvhfTRqkaLEmINJQYGlZQUnJS8AggQAw3ADEqVtD4P1fpyqyul2-hlMxId37R2LWr3WxBKANk382EQ8O5Xr0MUWxuUbtLEtOv3fVOOCQEgoe_-QR9_3UDVMj3AtsalumonKuYE0YIjiEmipo9QaVV6a1XyjLEpPkr4OEpITNR_Yi37EMTix_f_Z29_jtn3R-xayyaug2v6nePCGCQHUHkXgtfmYcgQiJ3l76chdpYXg-VT2pvjD3pIuvc4_gtcAvom</recordid><startdate>20150818</startdate><enddate>20150818</enddate><creator>Portis, Ezio</creator><creator>Cericola, Fabio</creator><creator>Barchi, Lorenzo</creator><creator>Toppino, Laura</creator><creator>Acciarri, Nazzareno</creator><creator>Pulcini, Laura</creator><creator>Sala, Tea</creator><creator>Lanteri, Sergio</creator><creator>Rotino, Giuseppe Leonardo</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20150818</creationdate><title>Association Mapping for Fruit, Plant and Leaf Morphology Traits in Eggplant</title><author>Portis, Ezio ; Cericola, Fabio ; Barchi, Lorenzo ; Toppino, Laura ; Acciarri, Nazzareno ; Pulcini, Laura ; Sala, Tea ; Lanteri, Sergio ; Rotino, Giuseppe Leonardo</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c758t-657cdd7df0ec8127b4ee2ab2e9b5a02c18b6b53a80f9e3c01de3986a6d2f2153</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Arabidopsis</topic><topic>Arabidopsis thaliana</topic><topic>Breeding</topic><topic>Chromosome Mapping</topic><topic>Chromosomes</topic><topic>Comparative analysis</topic><topic>Crops</topic><topic>Enzymes</topic><topic>Fruit - 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A genome-wide association (GWA) analysis was performed using the mixed linear model, which takes into account both a kinship matrix and the sub-population membership of the accessions. Overall, 194 phenotype/genotype associations were uncovered, relating to 30 of the 33 measured traits. These associations involved 79 SNP loci mapping to 39 distinct chromosomal regions distributed over all 12 eggplant chromosomes. A comparison of the map positions of these SNPs with those of loci derived from conventional linkage mapping showed that GWA analysis both validated many of the known controlling loci and detected a large number of new marker/trait associations. Exploiting established syntenic relationships between eggplant chromosomes and those of tomato and pepper recognized orthologous regions in ten eggplant chromosomes harbouring genes influencing breeders' traits.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26284782</pmid><doi>10.1371/journal.pone.0135200</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Arabidopsis Arabidopsis thaliana Breeding Chromosome Mapping Chromosomes Comparative analysis Crops Enzymes Fruit - genetics Fruits Gene mapping Genetic engineering Genomes Genomics Genotypes Loci Mapping Mathematical analysis Matrix methods Morphology Phenotype Phenotypes Plant breeding Plant Leaves - genetics Polymorphism, Single Nucleotide Proteins Single nucleotide polymorphisms Single-nucleotide polymorphism Solanum melongena Solanum melongena - genetics Stem cells Synteny Tomatoes |
| title | Association Mapping for Fruit, Plant and Leaf Morphology Traits in Eggplant |
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