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Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle

BACKGROUND: Signatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional li...

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Autores principales: Pérez O’Brien, Ana M, Utsunomiya, Yuri T, Mészáros, Gábor, Bickhart, Derek M, Liu, George E, Van Tassell, Curtis P, Sonstegard, Tad S, Da Silva, Marcos VB, Garcia, José Fernando, Sölkner, Johann
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014805/
https://www.ncbi.nlm.nih.gov/pubmed/24592996
http://dx.doi.org/10.1186/1297-9686-46-19
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author Pérez O’Brien, Ana M
Utsunomiya, Yuri T
Mészáros, Gábor
Bickhart, Derek M
Liu, George E
Van Tassell, Curtis P
Sonstegard, Tad S
Da Silva, Marcos VB
Garcia, José Fernando
Sölkner, Johann
author_facet Pérez O’Brien, Ana M
Utsunomiya, Yuri T
Mészáros, Gábor
Bickhart, Derek M
Liu, George E
Van Tassell, Curtis P
Sonstegard, Tad S
Da Silva, Marcos VB
Garcia, José Fernando
Sölkner, Johann
author_sort Pérez O’Brien, Ana M
collection PubMed
description BACKGROUND: Signatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium (LD) patterns. METHODS: By comparing the differences in regional LD variation between dairy and beef cattle types, and between indicine and taurine subspecies, we aim at finding signatures of selection for production and adaptation in cattle breeds. The VarLD method was applied to compare the LD variation in the autosomal genome between breeds, including Angus and Brown Swiss, representing taurine breeds, and Nelore and Gir, representing indicine breeds. Genomic regions containing the top 0.01 and 0.1 percentile of signals were characterized using the UMD3.1 Bos taurus genome assembly to identify genes in those regions and compared with previously reported selection signatures and regions with copy number variation. RESULTS: For all comparisons, the top 0.01 and 0.1 percentile included 26 and 165 signals and 17 and 125 genes, respectively, including TECRL, BT.23182 or FPPS, CAST, MYOM1, UVRAG and DNAJA1. CONCLUSIONS: The VarLD method is a powerful tool to identify differences in linkage disequilibrium between cattle populations and putative signatures of selection with potential adaptive and productive importance.
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spelling pubmed-40148052014-05-10 Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle Pérez O’Brien, Ana M Utsunomiya, Yuri T Mészáros, Gábor Bickhart, Derek M Liu, George E Van Tassell, Curtis P Sonstegard, Tad S Da Silva, Marcos VB Garcia, José Fernando Sölkner, Johann Genet Sel Evol Research BACKGROUND: Signatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium (LD) patterns. METHODS: By comparing the differences in regional LD variation between dairy and beef cattle types, and between indicine and taurine subspecies, we aim at finding signatures of selection for production and adaptation in cattle breeds. The VarLD method was applied to compare the LD variation in the autosomal genome between breeds, including Angus and Brown Swiss, representing taurine breeds, and Nelore and Gir, representing indicine breeds. Genomic regions containing the top 0.01 and 0.1 percentile of signals were characterized using the UMD3.1 Bos taurus genome assembly to identify genes in those regions and compared with previously reported selection signatures and regions with copy number variation. RESULTS: For all comparisons, the top 0.01 and 0.1 percentile included 26 and 165 signals and 17 and 125 genes, respectively, including TECRL, BT.23182 or FPPS, CAST, MYOM1, UVRAG and DNAJA1. CONCLUSIONS: The VarLD method is a powerful tool to identify differences in linkage disequilibrium between cattle populations and putative signatures of selection with potential adaptive and productive importance. BioMed Central 2014-03-04 /pmc/articles/PMC4014805/ /pubmed/24592996 http://dx.doi.org/10.1186/1297-9686-46-19 Text en Copyright © 2014 Pérez O’Brien 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 credited.
spellingShingle Research
Pérez O’Brien, Ana M
Utsunomiya, Yuri T
Mészáros, Gábor
Bickhart, Derek M
Liu, George E
Van Tassell, Curtis P
Sonstegard, Tad S
Da Silva, Marcos VB
Garcia, José Fernando
Sölkner, Johann
Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle
title Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle
title_full Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle
title_fullStr Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle
title_full_unstemmed Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle
title_short Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle
title_sort assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014805/
https://www.ncbi.nlm.nih.gov/pubmed/24592996
http://dx.doi.org/10.1186/1297-9686-46-19
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