Identifying signatures of recent selection in Holstein cattle in the tropic

Background: Holstein cattle have undergone strong selection processes in the world. These selection signatures can be recognized and utilized to identify regions of the genome that are important for milk yield. Objective: To identify recent selection signatures in Holstein from the Province of Antio...

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Autores principales:	Juan C. Rincón, Albeiro López, Julián Echeverri
Formato:	article
Lenguaje:	EN
Publicado:	Universidad de Antioquia 2018
Materias:	dairy cattle genetic mapping qtls selection pressure single nucleotide polymorphism Animal culture SF1-1100
Acceso en línea:	https://doaj.org/article/3d47d86b47634397bc825a82bfd08c1b
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spelling	oai:doaj.org-article:3d47d86b47634397bc825a82bfd08c1b2021-12-01T19:43:12ZIdentifying signatures of recent selection in Holstein cattle in the tropic2256-295810.17533/udea.rccp.v31n1a06https://doaj.org/article/3d47d86b47634397bc825a82bfd08c1b2018-03-01T00:00:00Zhttps://revistas.udea.edu.co/index.php/rccp/article/view/329310https://doaj.org/toc/2256-2958Background: Holstein cattle have undergone strong selection processes in the world. These selection signatures can be recognized and utilized to identify regions of the genome that are important for milk yield. Objective: To identify recent selection signatures in Holstein from the Province of Antioquia (Colombia), using the integrated haplotype score (iHS) methodology. Methods: Blood or semen was extracted from 150 animals with a commercial kit. The animals were genotyped with the BovineLD chip (6909 SNPs). The editing process was carried out while preserving the loci whose minor allele frequency (MAF) was greater than 0.05. In addition, genotypes with Mendelian errors were discarded using R and PLINK v1.07 software programs. Furthermore, the extended haplotype homozygosity (EHH), iHS and the p-value were determined with the “rehh” package of R language. Results: The minor allele frequencies showed a tendency toward intermediate frequency alleles. In total, 144 focal markers were significant (p < 0.001) for selection signatures. Some chromosomes showed a greater number of signatures than others. Many of the variants were found inside genes, although they were in intronic regions. Some important regions were associated with genes TRAPPC12, PANK3, ZNF16, OPLA and DPYSL4, which are related with cellular transport, excretion or metabolism. Conclusion: Identifying signatures of selection using the iHS method made it possible to determine some important regions for selection in Holstein cattle in the high tropics, some of which had been previously reported to be associated with quantitative traits loci (QTLs).Juan C. RincónAlbeiro LópezJulián EcheverriUniversidad de Antioquiaarticledairy cattlegenetic mappingqtlsselection pressuresingle nucleotide polymorphismAnimal cultureSF1-1100ENRevista Colombiana de Ciencias Pecuarias, Vol 31, Iss 1, Pp 45-58 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	dairy cattle genetic mapping qtls selection pressure single nucleotide polymorphism Animal culture SF1-1100
spellingShingle	dairy cattle genetic mapping qtls selection pressure single nucleotide polymorphism Animal culture SF1-1100 Juan C. Rincón Albeiro López Julián Echeverri Identifying signatures of recent selection in Holstein cattle in the tropic
description	Background: Holstein cattle have undergone strong selection processes in the world. These selection signatures can be recognized and utilized to identify regions of the genome that are important for milk yield. Objective: To identify recent selection signatures in Holstein from the Province of Antioquia (Colombia), using the integrated haplotype score (iHS) methodology. Methods: Blood or semen was extracted from 150 animals with a commercial kit. The animals were genotyped with the BovineLD chip (6909 SNPs). The editing process was carried out while preserving the loci whose minor allele frequency (MAF) was greater than 0.05. In addition, genotypes with Mendelian errors were discarded using R and PLINK v1.07 software programs. Furthermore, the extended haplotype homozygosity (EHH), iHS and the p-value were determined with the “rehh” package of R language. Results: The minor allele frequencies showed a tendency toward intermediate frequency alleles. In total, 144 focal markers were significant (p < 0.001) for selection signatures. Some chromosomes showed a greater number of signatures than others. Many of the variants were found inside genes, although they were in intronic regions. Some important regions were associated with genes TRAPPC12, PANK3, ZNF16, OPLA and DPYSL4, which are related with cellular transport, excretion or metabolism. Conclusion: Identifying signatures of selection using the iHS method made it possible to determine some important regions for selection in Holstein cattle in the high tropics, some of which had been previously reported to be associated with quantitative traits loci (QTLs).
format	article
author	Juan C. Rincón Albeiro López Julián Echeverri
author_facet	Juan C. Rincón Albeiro López Julián Echeverri
author_sort	Juan C. Rincón
title	Identifying signatures of recent selection in Holstein cattle in the tropic
title_short	Identifying signatures of recent selection in Holstein cattle in the tropic
title_full	Identifying signatures of recent selection in Holstein cattle in the tropic
title_fullStr	Identifying signatures of recent selection in Holstein cattle in the tropic
title_full_unstemmed	Identifying signatures of recent selection in Holstein cattle in the tropic
title_sort	identifying signatures of recent selection in holstein cattle in the tropic
publisher	Universidad de Antioquia
publishDate	2018
url	https://doaj.org/article/3d47d86b47634397bc825a82bfd08c1b
work_keys_str_mv	AT juancrincon identifyingsignaturesofrecentselectioninholsteincattleinthetropic AT albeirolopez identifyingsignaturesofrecentselectioninholsteincattleinthetropic AT julianecheverri identifyingsignaturesofrecentselectioninholsteincattleinthetropic
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Identifying signatures of recent selection in Holstein cattle in the tropic

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