Genome wide association study of 5 agronomic traits in olive (Olea europaea L.)
Olive ( Olea europaea L.) is one of the most economically and historically important fruit crops worldwide. Genetic progress for valuable agronomic traits has been slow in olive despite its importance and benefits. Advances in next generation sequencing technologies provide inexpensive and highly re...
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| Veröffentlicht in: | Scientific reports 2019-12, Vol.9 (1), p.18764-14, Article 18764 |
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| creator | Kaya, Hilal Betul Akdemir, Deniz Lozano, Roberto Cetin, Oznur Sozer Kaya, Hulya Sahin, Mustafa Smith, Jenny L. Tanyolac, Bahattin Jannink, Jean-Luc |
| description | Olive (
Olea europaea
L.) is one of the most economically and historically important fruit crops worldwide. Genetic progress for valuable agronomic traits has been slow in olive despite its importance and benefits. Advances in next generation sequencing technologies provide inexpensive and highly reproducible genotyping approaches such as Genotyping by Sequencing, enabling genome wide association study (GWAS). Here we present the first comprehensive GWAS study on olive using GBS. A total of 183 accessions (FULL panel) were genotyped using GBS, 94 from the Turkish Olive GenBank Resource (TOGR panel) and 89 from the USDA-ARS National Clonal Germplasm Repository (NCGR panel) in the USA. After filtering low quality and redundant markers, GWAS was conducted using 24,977 SNPs in FULL, TOGR and NCGR panels. In total, 52 significant associations were detected for leaf length, fruit weight, stone weight and fruit flesh to pit ratio using the MLM_K. Significant GWAS hits were mapped to their positions and 19 candidate genes were identified within a 10-kb distance of the most significant SNP. Our findings provide a framework for the development of markers and identification of candidate genes that could be used in olive breeding programs. |
| doi_str_mv | 10.1038/s41598-019-55338-w |
| format | Article |
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Olea europaea
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Olea europaea
L.) is one of the most economically and historically important fruit crops worldwide. Genetic progress for valuable agronomic traits has been slow in olive despite its importance and benefits. Advances in next generation sequencing technologies provide inexpensive and highly reproducible genotyping approaches such as Genotyping by Sequencing, enabling genome wide association study (GWAS). Here we present the first comprehensive GWAS study on olive using GBS. A total of 183 accessions (FULL panel) were genotyped using GBS, 94 from the Turkish Olive GenBank Resource (TOGR panel) and 89 from the USDA-ARS National Clonal Germplasm Repository (NCGR panel) in the USA. After filtering low quality and redundant markers, GWAS was conducted using 24,977 SNPs in FULL, TOGR and NCGR panels. In total, 52 significant associations were detected for leaf length, fruit weight, stone weight and fruit flesh to pit ratio using the MLM_K. Significant GWAS hits were mapped to their positions and 19 candidate genes were identified within a 10-kb distance of the most significant SNP. Our findings provide a framework for the development of markers and identification of candidate genes that could be used in olive breeding programs.</description><subject>45/23</subject><subject>45/43</subject><subject>631/449/2491</subject><subject>631/449/711</subject><subject>Chromosome Mapping</subject><subject>Crops, Agricultural - genetics</subject><subject>Fruit crops</subject><subject>Fruits</subject><subject>Genetic Markers - genetics</subject><subject>Genome, Plant</subject><subject>Genome-wide association studies</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Humanities and Social Sciences</subject><subject>Microsatellite Repeats</subject><subject>multidisciplinary</subject><subject>Olea - genetics</subject><subject>Olea europaea</subject><subject>Plant Breeding</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Quantitative Trait Loci</subject><subject>Science</subject><subject>Science (multidisciplinary)</subject><subject>Seed Bank</subject><subject>Turkey</subject><subject>United States</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kUtLAzEUhYMotlT_gAsJuNHFaJ7TZCNI8QWFbnQd0kxSU6aTmsy0-O9NrdbHwmxy4X735J4cAE4wusSIiqvEMJeiQFgWnFMqivUe6BPEeEEoIfs_6h44TmmO8uFEMiwPQY9iQciwRH0wubdNWFi49pWFOqVgvG59aGBqu-oNBgc51LMYMuQNbKP2bYK-gaH2KwvPJ7XV0HYxLHUuxpcXR-DA6TrZ4897AJ7vbp9GD8V4cv84uhkXhg1ZW8jSEOGooQJzJLnmjklKyilGhBldOSmMGLoKcWy4EwZnr6aStuKGIOGMowNwvdVddtOFrYxt8m61Wka_0PFNBe3V707jX9QsrFQpEWNcZIHzT4EYXjubWrXwydi61o0NXVL555jEZMhYRs_-oPPQxSbb21CUUcZxmSmypUwMKUXrdstgpDaRqW1kKkemPiJT6zx0-tPGbuQroAzQLZByq5nZ-P32P7LvdU-haA</recordid><startdate>20191210</startdate><enddate>20191210</enddate><creator>Kaya, Hilal Betul</creator><creator>Akdemir, Deniz</creator><creator>Lozano, Roberto</creator><creator>Cetin, Oznur</creator><creator>Sozer Kaya, Hulya</creator><creator>Sahin, Mustafa</creator><creator>Smith, Jenny L.</creator><creator>Tanyolac, Bahattin</creator><creator>Jannink, Jean-Luc</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</scope><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>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-0760-4977</orcidid></search><sort><creationdate>20191210</creationdate><title>Genome wide association study of 5 agronomic traits in olive (Olea europaea L.)</title><author>Kaya, Hilal Betul ; 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Olea europaea
L.) is one of the most economically and historically important fruit crops worldwide. Genetic progress for valuable agronomic traits has been slow in olive despite its importance and benefits. Advances in next generation sequencing technologies provide inexpensive and highly reproducible genotyping approaches such as Genotyping by Sequencing, enabling genome wide association study (GWAS). Here we present the first comprehensive GWAS study on olive using GBS. A total of 183 accessions (FULL panel) were genotyped using GBS, 94 from the Turkish Olive GenBank Resource (TOGR panel) and 89 from the USDA-ARS National Clonal Germplasm Repository (NCGR panel) in the USA. After filtering low quality and redundant markers, GWAS was conducted using 24,977 SNPs in FULL, TOGR and NCGR panels. In total, 52 significant associations were detected for leaf length, fruit weight, stone weight and fruit flesh to pit ratio using the MLM_K. Significant GWAS hits were mapped to their positions and 19 candidate genes were identified within a 10-kb distance of the most significant SNP. Our findings provide a framework for the development of markers and identification of candidate genes that could be used in olive breeding programs.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>31822760</pmid><doi>10.1038/s41598-019-55338-w</doi><tpages>14</tpages><orcidid>https://orcid.org/0000-0003-0760-4977</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | 45/23 45/43 631/449/2491 631/449/711 Chromosome Mapping Crops, Agricultural - genetics Fruit crops Fruits Genetic Markers - genetics Genome, Plant Genome-wide association studies Genome-Wide Association Study Genomes Humanities and Social Sciences Microsatellite Repeats multidisciplinary Olea - genetics Olea europaea Plant Breeding Polymorphism, Single Nucleotide Quantitative Trait Loci Science Science (multidisciplinary) Seed Bank Turkey United States |
| title | Genome wide association study of 5 agronomic traits in olive (Olea europaea L.) |
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