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 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.

中国云岭黑山羊和非洲努比亚山羊是不同的品种，在体型、产奶量和环境适应性方面存在显著差异。然而，这些表型差异背后的遗传机制仍有待阐明。在本研究中，我们通过对这两个品种杂交产生的9只F1代杂种后代的6种组织进行54次RNA - Seq分析，并结合两个品种的13个基因组，详细描述了等位基因特异性表达（ASE）情况。我们共鉴定出524个具有等位基因特异性表达的基因，它们参与骨骼发育、肌肉细胞分化以及脂质代谢过程的调控。通过比较两个品种的13个基因组，我们进一步发现38个具有等位基因特异性表达的基因也受到定向选择；这38个基因在代谢、免疫反应以及对炎热潮湿环境的适应中发挥重要作用。总之，我们的研究表明，对F1代杂种中等位基因特异性表达基因的探索为理解两个不同山羊品种表型差异的遗传基础提供了一种有效的途径。