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Genome and chromosome wide association studies for growth traits in Simmental and Simbrah cattle

OBJECTIVE: The objective of this study was to perform genome (genome wide association studies [GWAS]) and chromosome (CWAS) wide association analyses to identify single nucleotide polymorphisms (SNPs) associated with growth traits in registered Simmental and Simbrah cattle. METHODS: The phenotypes w...

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Autores principales: Calderón-Chagoya, René, Vega-Murillo, Vicente Eliezer, García-Ruiz, Adriana, Ríos-Utrera, Ángel, Martínez-Velázquez, Guillermo, Montaño-Bermúdez, Moisés
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Animal Bioscience 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9834659/
https://www.ncbi.nlm.nih.gov/pubmed/35798032
http://dx.doi.org/10.5713/ab.21.0517
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author Calderón-Chagoya, René
Vega-Murillo, Vicente Eliezer
García-Ruiz, Adriana
Ríos-Utrera, Ángel
Martínez-Velázquez, Guillermo
Montaño-Bermúdez, Moisés
author_facet Calderón-Chagoya, René
Vega-Murillo, Vicente Eliezer
García-Ruiz, Adriana
Ríos-Utrera, Ángel
Martínez-Velázquez, Guillermo
Montaño-Bermúdez, Moisés
author_sort Calderón-Chagoya, René
collection PubMed
description OBJECTIVE: The objective of this study was to perform genome (genome wide association studies [GWAS]) and chromosome (CWAS) wide association analyses to identify single nucleotide polymorphisms (SNPs) associated with growth traits in registered Simmental and Simbrah cattle. METHODS: The phenotypes were deregressed BLUP EBVs for birth weight, weaning weight direct, weaning weight maternal, and yearling weight. The genotyping was performed with the GGP Bovine 150k chip. After the quality control analysis, 105,129 autosomal SNP from 967 animals (473 Simmental and 494 Simbrah) were used to carry out genotype association tests. The two association analyses were performed per breed and using combined information of the two breeds. The SNP associated with growth traits were mapped to their corresponding genes at 100 kb on either side. RESULTS: A difference in magnitude of posterior probabilities was found across breeds between genome and chromosome wide association analyses. A total of 110, 143, and 302 SNP were associated with GWAS and CWAS for growth traits in the Simmental-, Simbrah- and joint-data analyses, respectively. It stands out from the enrichment analysis of the pathways for RNA polymerase (POLR2G, POLR3E) and GABAergic synapse (GABRR1, GABRR3) for Simmental cattle and p53 signaling pathway (BID, SERPINB5) for Simbrah cattle. CONCLUSION: Only 6,265% of the markers associated with growth traits were found using CWAS and GWAS. The associated markers using the CWAS analysis, which were not associated using the GWAS, represents information that due to the model and priors was not associated with the traits.
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spelling pubmed-98346592023-01-25 Genome and chromosome wide association studies for growth traits in Simmental and Simbrah cattle Calderón-Chagoya, René Vega-Murillo, Vicente Eliezer García-Ruiz, Adriana Ríos-Utrera, Ángel Martínez-Velázquez, Guillermo Montaño-Bermúdez, Moisés Anim Biosci Article OBJECTIVE: The objective of this study was to perform genome (genome wide association studies [GWAS]) and chromosome (CWAS) wide association analyses to identify single nucleotide polymorphisms (SNPs) associated with growth traits in registered Simmental and Simbrah cattle. METHODS: The phenotypes were deregressed BLUP EBVs for birth weight, weaning weight direct, weaning weight maternal, and yearling weight. The genotyping was performed with the GGP Bovine 150k chip. After the quality control analysis, 105,129 autosomal SNP from 967 animals (473 Simmental and 494 Simbrah) were used to carry out genotype association tests. The two association analyses were performed per breed and using combined information of the two breeds. The SNP associated with growth traits were mapped to their corresponding genes at 100 kb on either side. RESULTS: A difference in magnitude of posterior probabilities was found across breeds between genome and chromosome wide association analyses. A total of 110, 143, and 302 SNP were associated with GWAS and CWAS for growth traits in the Simmental-, Simbrah- and joint-data analyses, respectively. It stands out from the enrichment analysis of the pathways for RNA polymerase (POLR2G, POLR3E) and GABAergic synapse (GABRR1, GABRR3) for Simmental cattle and p53 signaling pathway (BID, SERPINB5) for Simbrah cattle. CONCLUSION: Only 6,265% of the markers associated with growth traits were found using CWAS and GWAS. The associated markers using the CWAS analysis, which were not associated using the GWAS, represents information that due to the model and priors was not associated with the traits. Animal Bioscience 2023-01 2022-06-30 /pmc/articles/PMC9834659/ /pubmed/35798032 http://dx.doi.org/10.5713/ab.21.0517 Text en Copyright © 2023 by Animal Bioscience https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Article
Calderón-Chagoya, René
Vega-Murillo, Vicente Eliezer
García-Ruiz, Adriana
Ríos-Utrera, Ángel
Martínez-Velázquez, Guillermo
Montaño-Bermúdez, Moisés
Genome and chromosome wide association studies for growth traits in Simmental and Simbrah cattle
title Genome and chromosome wide association studies for growth traits in Simmental and Simbrah cattle
title_full Genome and chromosome wide association studies for growth traits in Simmental and Simbrah cattle
title_fullStr Genome and chromosome wide association studies for growth traits in Simmental and Simbrah cattle
title_full_unstemmed Genome and chromosome wide association studies for growth traits in Simmental and Simbrah cattle
title_short Genome and chromosome wide association studies for growth traits in Simmental and Simbrah cattle
title_sort genome and chromosome wide association studies for growth traits in simmental and simbrah cattle
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9834659/
https://www.ncbi.nlm.nih.gov/pubmed/35798032
http://dx.doi.org/10.5713/ab.21.0517
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