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An integrated genetic linkage map for white clover (Trifolium repens L.) with alignment to Medicago

BACKGROUND: White clover (Trifolium repens L.) is a temperate forage legume with an allotetraploid genome (2n=4×=32) estimated at 1093 Mb. Several linkage maps of various sizes, marker sources and completeness are available, however, no integrated map and marker set has explored consistency of linka...

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Autores principales: Griffiths, Andrew G, Barrett, Brent A, Simon, Deborah, Khan, Anar K, Bickerstaff, Paul, Anderson, Craig B, Franzmayr, Benjamin K, Hancock, Kerry R, Jones, Chris S
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3693905/
https://www.ncbi.nlm.nih.gov/pubmed/23758831
http://dx.doi.org/10.1186/1471-2164-14-388
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author Griffiths, Andrew G
Barrett, Brent A
Simon, Deborah
Khan, Anar K
Bickerstaff, Paul
Anderson, Craig B
Franzmayr, Benjamin K
Hancock, Kerry R
Jones, Chris S
author_facet Griffiths, Andrew G
Barrett, Brent A
Simon, Deborah
Khan, Anar K
Bickerstaff, Paul
Anderson, Craig B
Franzmayr, Benjamin K
Hancock, Kerry R
Jones, Chris S
author_sort Griffiths, Andrew G
collection PubMed
description BACKGROUND: White clover (Trifolium repens L.) is a temperate forage legume with an allotetraploid genome (2n=4×=32) estimated at 1093 Mb. Several linkage maps of various sizes, marker sources and completeness are available, however, no integrated map and marker set has explored consistency of linkage analysis among unrelated mapping populations. Such integrative analysis requires tools for homoeologue matching among populations. Development of these tools provides for a consistent framework map of the white clover genome, and facilitates in silico alignment with the model forage legume, Medicago truncatula. RESULTS: This is the first report of integration of independent linkage maps in white clover, and adds to the literature on methyl filtered GeneThresher®-derived microsatellite (simple sequence repeat; SSR) markers for linkage mapping. Gene-targeted SSR markers were discovered in a GeneThresher® (TrGT) methyl-filtered database of 364,539 sequences, which yielded 15,647 SSR arrays. Primers were designed for 4,038 arrays and of these, 465 TrGT-SSR markers were used for parental consensus genetic linkage analysis in an F(1) mapping population (MP2). This was merged with an EST-SSR consensus genetic map of an independent population (MP1), using markers to match homoeologues and develop a multi-population integrated map of the white clover genome. This integrated map (IM) includes 1109 loci based on 804 SSRs over 1274 cM, covering 97% of the genome at a moderate density of one locus per 1.2 cM. Eighteen candidate genes and one morphological marker were also placed on the IM. Despite being derived from disparate populations and marker sources, the component maps and the derived IM had consistent representations of the white clover genome for marker order and genetic length. In silico analysis at an E-value threshold of 1e(-20) revealed substantial co-linearity with the Medicago truncatula genome, and indicates a translocation between T. repens groups 2 and 6 relative to M. truncatula. CONCLUSIONS: This integrated genetic linkage analysis provides a consistent and comprehensive linkage analysis of the white clover genome, with alignment to a model forage legume. Associated marker locus information, particularly the homoeologue-specific markers, offers a new resource for forage legume research to enable genetic analysis and improvement of this forage and grassland species.
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spelling pubmed-36939052013-06-27 An integrated genetic linkage map for white clover (Trifolium repens L.) with alignment to Medicago Griffiths, Andrew G Barrett, Brent A Simon, Deborah Khan, Anar K Bickerstaff, Paul Anderson, Craig B Franzmayr, Benjamin K Hancock, Kerry R Jones, Chris S BMC Genomics Research Article BACKGROUND: White clover (Trifolium repens L.) is a temperate forage legume with an allotetraploid genome (2n=4×=32) estimated at 1093 Mb. Several linkage maps of various sizes, marker sources and completeness are available, however, no integrated map and marker set has explored consistency of linkage analysis among unrelated mapping populations. Such integrative analysis requires tools for homoeologue matching among populations. Development of these tools provides for a consistent framework map of the white clover genome, and facilitates in silico alignment with the model forage legume, Medicago truncatula. RESULTS: This is the first report of integration of independent linkage maps in white clover, and adds to the literature on methyl filtered GeneThresher®-derived microsatellite (simple sequence repeat; SSR) markers for linkage mapping. Gene-targeted SSR markers were discovered in a GeneThresher® (TrGT) methyl-filtered database of 364,539 sequences, which yielded 15,647 SSR arrays. Primers were designed for 4,038 arrays and of these, 465 TrGT-SSR markers were used for parental consensus genetic linkage analysis in an F(1) mapping population (MP2). This was merged with an EST-SSR consensus genetic map of an independent population (MP1), using markers to match homoeologues and develop a multi-population integrated map of the white clover genome. This integrated map (IM) includes 1109 loci based on 804 SSRs over 1274 cM, covering 97% of the genome at a moderate density of one locus per 1.2 cM. Eighteen candidate genes and one morphological marker were also placed on the IM. Despite being derived from disparate populations and marker sources, the component maps and the derived IM had consistent representations of the white clover genome for marker order and genetic length. In silico analysis at an E-value threshold of 1e(-20) revealed substantial co-linearity with the Medicago truncatula genome, and indicates a translocation between T. repens groups 2 and 6 relative to M. truncatula. CONCLUSIONS: This integrated genetic linkage analysis provides a consistent and comprehensive linkage analysis of the white clover genome, with alignment to a model forage legume. Associated marker locus information, particularly the homoeologue-specific markers, offers a new resource for forage legume research to enable genetic analysis and improvement of this forage and grassland species. BioMed Central 2013-06-10 /pmc/articles/PMC3693905/ /pubmed/23758831 http://dx.doi.org/10.1186/1471-2164-14-388 Text en Copyright © 2013 Griffiths et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Griffiths, Andrew G
Barrett, Brent A
Simon, Deborah
Khan, Anar K
Bickerstaff, Paul
Anderson, Craig B
Franzmayr, Benjamin K
Hancock, Kerry R
Jones, Chris S
An integrated genetic linkage map for white clover (Trifolium repens L.) with alignment to Medicago
title An integrated genetic linkage map for white clover (Trifolium repens L.) with alignment to Medicago
title_full An integrated genetic linkage map for white clover (Trifolium repens L.) with alignment to Medicago
title_fullStr An integrated genetic linkage map for white clover (Trifolium repens L.) with alignment to Medicago
title_full_unstemmed An integrated genetic linkage map for white clover (Trifolium repens L.) with alignment to Medicago
title_short An integrated genetic linkage map for white clover (Trifolium repens L.) with alignment to Medicago
title_sort integrated genetic linkage map for white clover (trifolium repens l.) with alignment to medicago
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3693905/
https://www.ncbi.nlm.nih.gov/pubmed/23758831
http://dx.doi.org/10.1186/1471-2164-14-388
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