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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.00145

Genetic basis of phenotypic differences between Chinese Yunling black goats and Nubian goats revealed by allele-specific expression in their F1 hybrids

Yanhong Cao1,  Han Xu1, Ran Li1, Shan Gao1,  Ningbo Chen1, Jun Luo1* and  Yu Jiang1*
  • 1Northwest A&F University, China

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.

Keywords: Allele-specific expression(ASE), Chinese Yunling black goat,, Nubian goat, whole genome sequencing, RNA-Seq

Received: 25 Aug 2018; Accepted: 12 Feb 2019.

Edited by:

Robert J. Schaefer, University of Minnesota Twin Cities, United States

Reviewed by:

George E. Liu, Agricultural Research Service, United States Department of Agriculture, United States
Shikai Liu, Ocean University of China, China  

Copyright: © 2019 Cao, Xu, Li, Gao, Chen, Luo and Jiang. 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.

* Correspondence:
Prof. Jun Luo, Northwest A&F University, Yangling, China, luojun@nwafu.edu.cn
Prof. Yu Jiang, Northwest A&F University, Yangling, China, yu.jiang@nwafu.edu.cn