The Bos taurus-Bos indicus balance in fertility and milk related genes.
Numerical approaches to high-density single nucleotide polymorphism (SNP) data are often employed independently to address individual questions. We linked independent approaches in a bioinformatics pipeline for further insight. The pipeline driven by heterozygosity and Hardy-Weinberg equilibrium (HW...
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doaj-05e21fb5d6804f11b747d032d9a91b062020-11-25T01:31:19ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01128e018193010.1371/journal.pone.0181930The Bos taurus-Bos indicus balance in fertility and milk related genes.Parthan KasarapuLaercio R Porto-NetoMarina R S FortesSigrid A LehnertMauricio A MudaduLuiz CoutinhoLuciana RegitanoAndrew GeorgeAntonio ReverterNumerical approaches to high-density single nucleotide polymorphism (SNP) data are often employed independently to address individual questions. We linked independent approaches in a bioinformatics pipeline for further insight. The pipeline driven by heterozygosity and Hardy-Weinberg equilibrium (HWE) analyses was applied to characterize Bos taurus and Bos indicus ancestry. We infer a gene co-heterozygosity network that regulates bovine fertility, from data on 18,363 cattle with genotypes for 729,068 SNP. Hierarchical clustering separated populations according to Bos taurus and Bos indicus ancestry. The weights of the first principal component were subjected to Normal mixture modelling allowing the estimation of a gene's contribution to the Bos taurus-Bos indicus axis. We used deviation from HWE, contribution to Bos indicus content and association to fertility traits to select 1,284 genes. With this set, we developed a co-heterozygosity network where the group of genes annotated as fertility-related had significantly higher Bos indicus content compared to other functional classes of genes, while the group of genes associated with milk production had significantly higher Bos taurus content. The network analysis resulted in capturing novel gene associations of relevance to bovine domestication events. We report transcription factors that are likely to regulate genes associated with cattle domestication and tropical adaptation. Our pipeline can be generalized to any scenarios where population structure requires scrutiny at the molecular level, particularly in the presence of a priori set of genes known to impact a phenotype of evolutionary interest such as fertility.http://europepmc.org/articles/PMC5538644?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Parthan Kasarapu Laercio R Porto-Neto Marina R S Fortes Sigrid A Lehnert Mauricio A Mudadu Luiz Coutinho Luciana Regitano Andrew George Antonio Reverter |
spellingShingle |
Parthan Kasarapu Laercio R Porto-Neto Marina R S Fortes Sigrid A Lehnert Mauricio A Mudadu Luiz Coutinho Luciana Regitano Andrew George Antonio Reverter The Bos taurus-Bos indicus balance in fertility and milk related genes. PLoS ONE |
author_facet |
Parthan Kasarapu Laercio R Porto-Neto Marina R S Fortes Sigrid A Lehnert Mauricio A Mudadu Luiz Coutinho Luciana Regitano Andrew George Antonio Reverter |
author_sort |
Parthan Kasarapu |
title |
The Bos taurus-Bos indicus balance in fertility and milk related genes. |
title_short |
The Bos taurus-Bos indicus balance in fertility and milk related genes. |
title_full |
The Bos taurus-Bos indicus balance in fertility and milk related genes. |
title_fullStr |
The Bos taurus-Bos indicus balance in fertility and milk related genes. |
title_full_unstemmed |
The Bos taurus-Bos indicus balance in fertility and milk related genes. |
title_sort |
bos taurus-bos indicus balance in fertility and milk related genes. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2017-01-01 |
description |
Numerical approaches to high-density single nucleotide polymorphism (SNP) data are often employed independently to address individual questions. We linked independent approaches in a bioinformatics pipeline for further insight. The pipeline driven by heterozygosity and Hardy-Weinberg equilibrium (HWE) analyses was applied to characterize Bos taurus and Bos indicus ancestry. We infer a gene co-heterozygosity network that regulates bovine fertility, from data on 18,363 cattle with genotypes for 729,068 SNP. Hierarchical clustering separated populations according to Bos taurus and Bos indicus ancestry. The weights of the first principal component were subjected to Normal mixture modelling allowing the estimation of a gene's contribution to the Bos taurus-Bos indicus axis. We used deviation from HWE, contribution to Bos indicus content and association to fertility traits to select 1,284 genes. With this set, we developed a co-heterozygosity network where the group of genes annotated as fertility-related had significantly higher Bos indicus content compared to other functional classes of genes, while the group of genes associated with milk production had significantly higher Bos taurus content. The network analysis resulted in capturing novel gene associations of relevance to bovine domestication events. We report transcription factors that are likely to regulate genes associated with cattle domestication and tropical adaptation. Our pipeline can be generalized to any scenarios where population structure requires scrutiny at the molecular level, particularly in the presence of a priori set of genes known to impact a phenotype of evolutionary interest such as fertility. |
url |
http://europepmc.org/articles/PMC5538644?pdf=render |
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