Genetic Basis of Phenotypic Differences Between Chinese Yunling Black Goats and Nubian Goats Revealed by Allele-Specific Expression in Their F1 Hybrids

Chinese Yunling black goats and African Nubian goats are divergent breeds showing significant differences in body size, milk production, and environmental adaptation. However, the genetic mechanisms underlying these phenotypic differences remain to be elucidated. In this report, we provide a detaile...

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Autores principales: Cao, Yanhong, Xu, Han, Li, Ran, Gao, Shan, Chen, Ningbo, Luo, Jun, Jiang, Yu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6411798/
https://www.ncbi.nlm.nih.gov/pubmed/30891061
http://dx.doi.org/10.3389/fgene.2019.00145
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author Cao, Yanhong
Xu, Han
Li, Ran
Gao, Shan
Chen, Ningbo
Luo, Jun
Jiang, Yu
author_facet Cao, Yanhong
Xu, Han
Li, Ran
Gao, Shan
Chen, Ningbo
Luo, Jun
Jiang, Yu
author_sort Cao, Yanhong
collection PubMed
description Chinese Yunling black goats and African Nubian goats are divergent breeds showing significant differences in body size, milk production, and environmental adaptation. However, the genetic mechanisms underlying these phenotypic differences remain to be elucidated. In this report, we provide a detailed portrait of allele-specific expression (ASE) from 54 RNA-Seq analyses across six tissues from nine F1 hybrid offspring generated by crossing the two breeds combined with 13 genomes of the two breeds. We identified a total of 524 genes with ASE, which are involved in bone development, muscle cell differentiation, and the regulation of lipid metabolic processes. We further found that 38 genes with ASE were also under directional selection by comparing 13 genomes of the two breeds; these 38 genes play important roles in metabolism, immune responses, and the adaptation to hot and humid environments. In conclusion, our study shows that the exploration of genes with ASE in F1 hybrids provides an efficient way to understand the genetic basis underlying the phenotypic differences of two diverse goat breeds.
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spelling pubmed-64117982019-03-19 Genetic Basis of Phenotypic Differences Between Chinese Yunling Black Goats and Nubian Goats Revealed by Allele-Specific Expression in Their F1 Hybrids Cao, Yanhong Xu, Han Li, Ran Gao, Shan Chen, Ningbo Luo, Jun Jiang, Yu Front Genet Genetics Chinese Yunling black goats and African Nubian goats are divergent breeds showing significant differences in body size, milk production, and environmental adaptation. However, the genetic mechanisms underlying these phenotypic differences remain to be elucidated. In this report, we provide a detailed portrait of allele-specific expression (ASE) from 54 RNA-Seq analyses across six tissues from nine F1 hybrid offspring generated by crossing the two breeds combined with 13 genomes of the two breeds. We identified a total of 524 genes with ASE, which are involved in bone development, muscle cell differentiation, and the regulation of lipid metabolic processes. We further found that 38 genes with ASE were also under directional selection by comparing 13 genomes of the two breeds; these 38 genes play important roles in metabolism, immune responses, and the adaptation to hot and humid environments. In conclusion, our study shows that the exploration of genes with ASE in F1 hybrids provides an efficient way to understand the genetic basis underlying the phenotypic differences of two diverse goat breeds. Frontiers Media S.A. 2019-03-05 /pmc/articles/PMC6411798/ /pubmed/30891061 http://dx.doi.org/10.3389/fgene.2019.00145 Text en Copyright © 2019 Cao, Xu, Li, Gao, Chen, Luo and Jiang. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Cao, Yanhong
Xu, Han
Li, Ran
Gao, Shan
Chen, Ningbo
Luo, Jun
Jiang, Yu
Genetic Basis of Phenotypic Differences Between Chinese Yunling Black Goats and Nubian Goats Revealed by Allele-Specific Expression in Their F1 Hybrids
title Genetic Basis of Phenotypic Differences Between Chinese Yunling Black Goats and Nubian Goats Revealed by Allele-Specific Expression in Their F1 Hybrids
title_full Genetic Basis of Phenotypic Differences Between Chinese Yunling Black Goats and Nubian Goats Revealed by Allele-Specific Expression in Their F1 Hybrids
title_fullStr Genetic Basis of Phenotypic Differences Between Chinese Yunling Black Goats and Nubian Goats Revealed by Allele-Specific Expression in Their F1 Hybrids
title_full_unstemmed Genetic Basis of Phenotypic Differences Between Chinese Yunling Black Goats and Nubian Goats Revealed by Allele-Specific Expression in Their F1 Hybrids
title_short Genetic Basis of Phenotypic Differences Between Chinese Yunling Black Goats and Nubian Goats Revealed by Allele-Specific Expression in Their F1 Hybrids
title_sort genetic basis of phenotypic differences between chinese yunling black goats and nubian goats revealed by allele-specific expression in their f1 hybrids
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6411798/
https://www.ncbi.nlm.nih.gov/pubmed/30891061
http://dx.doi.org/10.3389/fgene.2019.00145
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