Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Cao Y

PROVIDER: S-EPMC6411798 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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

Cao Yanhong Y Xu Han H Li Ran R Gao Shan S Chen Ningbo N Luo Jun J Jiang Yu Y

Frontiers in genetics 20190305

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 ...[more]

PMID: 30891061

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Project description:Hybrid incompatibility, such as sterility and inviability, prevents gene flow between closely-related populations as a reproductive isolation barrier. F1 hybrids between chickens and Japanese quail (hereafter, referred to as quail), exhibit a high frequency of developmental arrest at the preprimitive streak stage. To investigate the molecular basis of the developmental arrest at the preprimitive streak stage in chicken-quail F1 hybrid embryos, we investigated chromosomal abnormalities in the hybrid embryos using molecular cytogenetic analysis. In addition, we quantified gene expression in parental species and chicken- and quail-derived allele-specific expression in the hybrids at the early blastoderm and preprimitive streak stages by mRNA sequencing. Subsequently, we compared the directions of change in gene expression, including upregulation, downregulation, or no change, from the early blastoderm stage to the preprimitive streak stage between parental species and their hybrids. Chromosome analysis revealed that the cells of the hybrid embryos contained a fifty-fifty mixture of parental chromosomes, and numerical chromosomal abnormalities were hardly observed in the hybrid cells. Gene expression analysis revealed that a part of the genes that were upregulated from the early blastoderm stage to the preprimitive streak stage in both parental species exhibited no upregulation of both chicken- and quail-derived alleles in the hybrids. GO term enrichment analysis revealed that these misregulated genes are involved in various biological processes, including ribosome-mediated protein synthesis and cell proliferation. Furthermore, the misregulated genes included genes involved in early embryonic development, such as primitive streak formation and gastrulation. These results suggest that numerical chromosomal abnormalities due to a segregation failure does not cause the lethality of chicken-quail hybrid embryos, and that the downregulated expression of the genes that are involved in various biological processes, including translation and primitive streak formation, mainly causes the developmental arrest at the preprimitive streak stage in the hybrids.

Dataset Information

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

Publications

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

Similar Datasets

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