A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda

A consensus genetic map for Pinus taeda (loblolly pine) and Pinus elliottii (slash pine) was constructed by merging three previously published P. taeda maps with a map from a pseudo-backcross between P. elliottii and P. taeda. The consensus map positioned 3856 markers via genotyping of 1251 individu...

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Authors: Westbrook, Jared W., Chhatre, Vikram E., Wu, Le-Shin, Chamala, Srikar, Neves, Leandro Gomide, Muñoz, Patricio, Martínez-García, Pedro J., Neale, David B., Kirst, Matias, Mockaitis, Keithanne, Nelson, C. Dana, Peter, Gary F., Davis, John M., Echt, Craig S.
Format: article
Status:Published version
Publication Date:2015
Country:España
Institution:Consejo Superior de Investigaciones Científicas (CSIC)
Repository:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/338870
Online Access:http://hdl.handle.net/10261/338870
Access Level:Open access
Keyword:Pine
Linkage mapping
Linkage disequilibrium
Population structure
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spelling A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taedaWestbrook, Jared W.Chhatre, Vikram E.Wu, Le-ShinChamala, SrikarNeves, Leandro GomideMuñoz, PatricioMartínez-García, Pedro J.Neale, David B.Kirst, MatiasMockaitis, KeithanneNelson, C. DanaPeter, Gary F.Davis, John M.Echt, Craig S.PineLinkage mappingLinkage disequilibriumPopulation structureA consensus genetic map for Pinus taeda (loblolly pine) and Pinus elliottii (slash pine) was constructed by merging three previously published P. taeda maps with a map from a pseudo-backcross between P. elliottii and P. taeda. The consensus map positioned 3856 markers via genotyping of 1251 individuals from four pedigrees. It is the densest linkage map for a conifer to date. Average marker spacing was 0.6 cM and total map length was 2305 cM. Functional predictions of mapped genes were improved by aligning expressed sequence tags used for marker discovery to full-length P. taeda transcripts. Alignments to the P. taeda genome mapped 3305 scaffold sequences onto 12 linkage groups. The consensus genetic map was used to compare the genome-wide linkage disequilibrium in a population of distantly related P. taeda individuals (ADEPT2) used for association genetic studies and a multiple-family pedigree used for genomic selection (CCLONES). The prevalence and extent of LD was greater in CCLONES as compared to ADEPT2; however, extended LD with LGs or between LGs was rare in both populations. The average squared correlations, r2, between SNP alleles less than 1 cM apart were less than 0.05 in both populations and r2 did not decay substantially with genetic distance. The consensus map and analysis of linkage disequilibrium establish a foundation for comparative association mapping and genomic selection in P. taeda and P. elliottii.J.W.W. was supported by a USDA CSREES Food and Agricultural Sciences National Needs Graduate Fellowship. V.E.C. was supported by USDA NIFA Award #2011-68002-30185 (PINEMAP) and the USDA Forest Service. L.S.W. was supported by the National Science Foundation under grant no. ABI-1062432 to Indiana University. P.M.G., D.N., and K.M. were supported in part by USDA NIFA Award #2011-67009-30030 (PineRefSeq) to University of California, Davis.Peer reviewedOxford University PressGenetics Society of AmericaNational Institute of Food and Agriculture (US)Department of Agriculture (US)US Forest ServiceNational Science Foundation (US)Indiana University - Purdue University Fort WayneUniversity of California, DavisMartínez-García, Pedro J. [0000-0002-7647-5235]202320232015info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/338870reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)InglésThe underlying dataset has been published as a supplementary material of the article in the publisher platfrorm at doi:10.1534/g3.115.019588/-/DC1https://doi.org/10.1534/g3.115.019588Noinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3388702026-05-22T06:33:51Z
dc.title.none.fl_str_mv A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda
title A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda
spellingShingle A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda
Westbrook, Jared W.
Pine
Linkage mapping
Linkage disequilibrium
Population structure
title_short A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda
title_full A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda
title_fullStr A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda
title_full_unstemmed A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda
title_sort A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda
dc.creator.none.fl_str_mv Westbrook, Jared W.
Chhatre, Vikram E.
Wu, Le-Shin
Chamala, Srikar
Neves, Leandro Gomide
Muñoz, Patricio
Martínez-García, Pedro J.
Neale, David B.
Kirst, Matias
Mockaitis, Keithanne
Nelson, C. Dana
Peter, Gary F.
Davis, John M.
Echt, Craig S.
author Westbrook, Jared W.
author_facet Westbrook, Jared W.
Chhatre, Vikram E.
Wu, Le-Shin
Chamala, Srikar
Neves, Leandro Gomide
Muñoz, Patricio
Martínez-García, Pedro J.
Neale, David B.
Kirst, Matias
Mockaitis, Keithanne
Nelson, C. Dana
Peter, Gary F.
Davis, John M.
Echt, Craig S.
author_role author
author2 Chhatre, Vikram E.
Wu, Le-Shin
Chamala, Srikar
Neves, Leandro Gomide
Muñoz, Patricio
Martínez-García, Pedro J.
Neale, David B.
Kirst, Matias
Mockaitis, Keithanne
Nelson, C. Dana
Peter, Gary F.
Davis, John M.
Echt, Craig S.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv National Institute of Food and Agriculture (US)
Department of Agriculture (US)
US Forest Service
National Science Foundation (US)
Indiana University - Purdue University Fort Wayne
University of California, Davis
Martínez-García, Pedro J. [0000-0002-7647-5235]
dc.subject.none.fl_str_mv Pine
Linkage mapping
Linkage disequilibrium
Population structure
topic Pine
Linkage mapping
Linkage disequilibrium
Population structure
description A consensus genetic map for Pinus taeda (loblolly pine) and Pinus elliottii (slash pine) was constructed by merging three previously published P. taeda maps with a map from a pseudo-backcross between P. elliottii and P. taeda. The consensus map positioned 3856 markers via genotyping of 1251 individuals from four pedigrees. It is the densest linkage map for a conifer to date. Average marker spacing was 0.6 cM and total map length was 2305 cM. Functional predictions of mapped genes were improved by aligning expressed sequence tags used for marker discovery to full-length P. taeda transcripts. Alignments to the P. taeda genome mapped 3305 scaffold sequences onto 12 linkage groups. The consensus genetic map was used to compare the genome-wide linkage disequilibrium in a population of distantly related P. taeda individuals (ADEPT2) used for association genetic studies and a multiple-family pedigree used for genomic selection (CCLONES). The prevalence and extent of LD was greater in CCLONES as compared to ADEPT2; however, extended LD with LGs or between LGs was rare in both populations. The average squared correlations, r2, between SNP alleles less than 1 cM apart were less than 0.05 in both populations and r2 did not decay substantially with genetic distance. The consensus map and analysis of linkage disequilibrium establish a foundation for comparative association mapping and genomic selection in P. taeda and P. elliottii.
publishDate 2015
dc.date.none.fl_str_mv 2015
2023
2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/338870
url http://hdl.handle.net/10261/338870
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv The underlying dataset has been published as a supplementary material of the article in the publisher platfrorm at doi:10.1534/g3.115.019588/-/DC1
https://doi.org/10.1534/g3.115.019588
No
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Oxford University Press
Genetics Society of America
publisher.none.fl_str_mv Oxford University Press
Genetics Society of America
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.812429

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