Cargando…

Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle

BACKGROUND: Our aim was to identify genomic regions via genome-wide association studies (GWAS) to improve the predictability of genetic merit in Holsteins for 10 calving and 28 body conformation traits. Animals were genotyped using the Illumina Bovine 50 K BeadChip and imputed to the Illumina Bovine...

Descripción completa

Detalles Bibliográficos
Autores principales: Abo-Ismail, Mohammed K., Brito, Luiz F., Miller, Stephen P., Sargolzaei, Mehdi, Grossi, Daniela A., Moore, Steve S., Plastow, Graham, Stothard, Paul, Nayeri, Shadi, Schenkel, Flavio S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6389134/
https://www.ncbi.nlm.nih.gov/pubmed/29115939
http://dx.doi.org/10.1186/s12711-017-0356-8
_version_ 1783397894504579072
author Abo-Ismail, Mohammed K.
Brito, Luiz F.
Miller, Stephen P.
Sargolzaei, Mehdi
Grossi, Daniela A.
Moore, Steve S.
Plastow, Graham
Stothard, Paul
Nayeri, Shadi
Schenkel, Flavio S.
author_facet Abo-Ismail, Mohammed K.
Brito, Luiz F.
Miller, Stephen P.
Sargolzaei, Mehdi
Grossi, Daniela A.
Moore, Steve S.
Plastow, Graham
Stothard, Paul
Nayeri, Shadi
Schenkel, Flavio S.
author_sort Abo-Ismail, Mohammed K.
collection PubMed
description BACKGROUND: Our aim was to identify genomic regions via genome-wide association studies (GWAS) to improve the predictability of genetic merit in Holsteins for 10 calving and 28 body conformation traits. Animals were genotyped using the Illumina Bovine 50 K BeadChip and imputed to the Illumina BovineHD BeadChip (HD). GWAS were performed on 601,717 real and imputed single nucleotide polymorphism (SNP) genotypes using a single-SNP mixed linear model on 4841 Holstein bulls with breeding value predictions and followed by gene identification and in silico functional analyses. The association results were further validated using five scenarios with different numbers of SNPs. RESULTS: Seven hundred and eighty-two SNPs were significantly associated with calving performance at a genome-wise false discovery rate (FDR) of 5%. Most of these significant SNPs were on chromosomes 18 (71.9%), 17 (7.4%), 5 (6.8%) and 7 (2.4%) and mapped to 675 genes, among which 142 included at least one significant SNP and 532 were nearby one (100 kbp). For body conformation traits, 607 SNPs were significant at a genome-wise FDR of 5% and most of them were located on chromosomes 5 (30%), 18 (27%), 20 (13%), 6 (6%), 7 (5%), 14 (5%) and 13 (3%). SNP enrichment functional analyses for calving traits at a FDR of 1% suggested potential biological processes including musculoskeletal movement, meiotic cell cycle, oocyte maturation and skeletal muscle contraction. Furthermore, pathway analyses suggested potential pathways associated with calving performance traits including tight junction, oxytocin signaling, and MAPK signaling (P < 0.10). The prediction ability of the 1206 significant SNPs was between 78 and 83% of the prediction ability of the BovineSNP50 SNPs for calving performance traits and between 35 and 79% for body conformation traits. CONCLUSIONS: Various SNPs that are significantly associated with calving performance are located within or nearby genes with potential roles in tight junction, oxytocin signaling, and MAPK signaling. Combining the significant SNPs or SNPs within or nearby gene(s) from the HD panel with the BovineSNP50 panel yielded a marginal increase in the accuracy of prediction of genomic estimated breeding values for all traits compared to the use of the BovineSNP50 panel alone. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12711-017-0356-8) contains supplementary material, which is available to authorized users.
format Online
Article
Text
id pubmed-6389134
institution National Center for Biotechnology Information
language English
publishDate 2017
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-63891342019-03-19 Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle Abo-Ismail, Mohammed K. Brito, Luiz F. Miller, Stephen P. Sargolzaei, Mehdi Grossi, Daniela A. Moore, Steve S. Plastow, Graham Stothard, Paul Nayeri, Shadi Schenkel, Flavio S. Genet Sel Evol Research Article BACKGROUND: Our aim was to identify genomic regions via genome-wide association studies (GWAS) to improve the predictability of genetic merit in Holsteins for 10 calving and 28 body conformation traits. Animals were genotyped using the Illumina Bovine 50 K BeadChip and imputed to the Illumina BovineHD BeadChip (HD). GWAS were performed on 601,717 real and imputed single nucleotide polymorphism (SNP) genotypes using a single-SNP mixed linear model on 4841 Holstein bulls with breeding value predictions and followed by gene identification and in silico functional analyses. The association results were further validated using five scenarios with different numbers of SNPs. RESULTS: Seven hundred and eighty-two SNPs were significantly associated with calving performance at a genome-wise false discovery rate (FDR) of 5%. Most of these significant SNPs were on chromosomes 18 (71.9%), 17 (7.4%), 5 (6.8%) and 7 (2.4%) and mapped to 675 genes, among which 142 included at least one significant SNP and 532 were nearby one (100 kbp). For body conformation traits, 607 SNPs were significant at a genome-wise FDR of 5% and most of them were located on chromosomes 5 (30%), 18 (27%), 20 (13%), 6 (6%), 7 (5%), 14 (5%) and 13 (3%). SNP enrichment functional analyses for calving traits at a FDR of 1% suggested potential biological processes including musculoskeletal movement, meiotic cell cycle, oocyte maturation and skeletal muscle contraction. Furthermore, pathway analyses suggested potential pathways associated with calving performance traits including tight junction, oxytocin signaling, and MAPK signaling (P < 0.10). The prediction ability of the 1206 significant SNPs was between 78 and 83% of the prediction ability of the BovineSNP50 SNPs for calving performance traits and between 35 and 79% for body conformation traits. CONCLUSIONS: Various SNPs that are significantly associated with calving performance are located within or nearby genes with potential roles in tight junction, oxytocin signaling, and MAPK signaling. Combining the significant SNPs or SNPs within or nearby gene(s) from the HD panel with the BovineSNP50 panel yielded a marginal increase in the accuracy of prediction of genomic estimated breeding values for all traits compared to the use of the BovineSNP50 panel alone. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12711-017-0356-8) contains supplementary material, which is available to authorized users. BioMed Central 2017-11-07 /pmc/articles/PMC6389134/ /pubmed/29115939 http://dx.doi.org/10.1186/s12711-017-0356-8 Text en © The Author(s) 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Abo-Ismail, Mohammed K.
Brito, Luiz F.
Miller, Stephen P.
Sargolzaei, Mehdi
Grossi, Daniela A.
Moore, Steve S.
Plastow, Graham
Stothard, Paul
Nayeri, Shadi
Schenkel, Flavio S.
Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle
title Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle
title_full Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle
title_fullStr Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle
title_full_unstemmed Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle
title_short Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle
title_sort genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in holstein cattle
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6389134/
https://www.ncbi.nlm.nih.gov/pubmed/29115939
http://dx.doi.org/10.1186/s12711-017-0356-8
work_keys_str_mv AT aboismailmohammedk genomewideassociationstudiesandgenomicpredictionofbreedingvaluesforcalvingperformanceandbodyconformationtraitsinholsteincattle
AT britoluizf genomewideassociationstudiesandgenomicpredictionofbreedingvaluesforcalvingperformanceandbodyconformationtraitsinholsteincattle
AT millerstephenp genomewideassociationstudiesandgenomicpredictionofbreedingvaluesforcalvingperformanceandbodyconformationtraitsinholsteincattle
AT sargolzaeimehdi genomewideassociationstudiesandgenomicpredictionofbreedingvaluesforcalvingperformanceandbodyconformationtraitsinholsteincattle
AT grossidanielaa genomewideassociationstudiesandgenomicpredictionofbreedingvaluesforcalvingperformanceandbodyconformationtraitsinholsteincattle
AT mooresteves genomewideassociationstudiesandgenomicpredictionofbreedingvaluesforcalvingperformanceandbodyconformationtraitsinholsteincattle
AT plastowgraham genomewideassociationstudiesandgenomicpredictionofbreedingvaluesforcalvingperformanceandbodyconformationtraitsinholsteincattle
AT stothardpaul genomewideassociationstudiesandgenomicpredictionofbreedingvaluesforcalvingperformanceandbodyconformationtraitsinholsteincattle
AT nayerishadi genomewideassociationstudiesandgenomicpredictionofbreedingvaluesforcalvingperformanceandbodyconformationtraitsinholsteincattle
AT schenkelflavios genomewideassociationstudiesandgenomicpredictionofbreedingvaluesforcalvingperformanceandbodyconformationtraitsinholsteincattle