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

Cao, Yukun; Xu, Han; Li, Ran; Gao, Shan; Chen, Ningbo; Luo, Jun; Jiang, Yu

doi:10.3389/fgene.2019.00145

Cited by 13 publications

(15 citation statements)

References 35 publications

(39 reference statements)

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“…These genomic characteristics are important as a genomic basis for coping with future threats to the species arising from environmental change (Benjelloun et al, 2015), but are rapidly disappearing due to extensive crossbreeding and substitution with imported breeds. Therefore, to reveal their unique genomic characteristics, many genomic studies have been carried out in various indigenous livestock: cattle (Browett et al, 2018; Weldenegodguad et al, 2018); chicken (Johansson and Nelson, 2015; Walugembe et al, 2018); sheep (Yang et al, 2016; Edea et al, 2017); and goat (Benjelloun et al, 2015; Cao et al, 2019). In this context, our study focused on identifying KNG and revealed their distinct genomic characteristics.…”

Section: Discussionmentioning

confidence: 99%

Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds

et al. 2019

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Indigenous breeds develop their own genomic characteristics by adapting to local environments or cultures over long periods of time. Most of them are not particularly productive in commercial terms, but they have abilities to survive in harsh environments or tolerate to specific diseases. Their adaptive characteristics play an important role as genetic materials for improving commercial breeds. As a step toward this goal, we analyzed the genome of Korean indigenous goats within 10 goat breeds. We collected 136 goat individuals by sequencing 46 new goats and employing 90 publicly available goats. Our whole-genome data was comprised of three indigenous breeds (Korean indigenous goat, Iranian indigenous goat, and Moroccan indigenous goat; n = 29, 18, 20), six commercial breeds (Saanen, Boer, Anglo-Nubian, British Alpine, Alpine, and Korean crossbred; n = 16, 11, 5, 5, 2, 13), and their ancestral species ( Capra aegagrus ; n = 17). We identified that the Iranian indigenous goat and the Moroccan indigenous goat have relatively similar genomic characteristics within a large category of genomic diversity but found that the Korean indigenous goat has unique genomic characteristics distinguished from the other nine breeds. Through population analysis, we confirmed that these characteristics have resulted from a near-isolated environment with strong genetic drift. The Korean indigenous goat experienced a severe genetic bottleneck upon entering the Korean Peninsula about 2,000 years ago, and has subsequently rarely experienced genetic interactions with other goat breeds. From selection analysis and gene-set enrichment analysis, we revealed selection signals for Salmonella infection and cardiomyopathy in the genome of the Korean indigenous goat. These adaptive characteristics were further identified with genomic-based evidence. We uncovered genomic regions of selective sweeps in the LBP and BPI genes ( Salmonella infection) and the TTN and ITGB6 genes (cardiomyopathy), among several candidate genes. Our research presents unique genomic characteristics and distinctive selection signals of the Korean indigenous goat based on the extensive comparison. Although the adaptive traits require further validation through biological experiments, our findings are expected to provide a direction for future biodiversity conservation strategies and to contribute another option to genomic-based breeding programmes for improving the viability of Capra hircus .

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Section: Discussionmentioning

confidence: 99%

Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds

et al. 2019

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“…The great variations in different phenotypic traits of two selected sheep breeds provide an opportunity for studying molecular mechanisms underlying gene expression related to phenotypic difference between thin-and fat-tailed sheep breeds. In this study, the candidate causative genes were detected by ASE analysis, which avoid the effect of trans-acting and has become research focus in recent years [24][25][26][27][28]. We divided all sheep individuals into 15 family trios.…”

Section: Discussionmentioning

confidence: 99%

“…Loci with both alleles < 100 reads and each allele in heterozygous sites with < 3 reads were filtered, which can remove loci exhibiting MAE and a relative lower expression [38][39][40]. Allelic read ratios were counted by a Python Script [27], significant allelic imbalances were identified using the cut-off criteria of allele ratio ≥ 0.65 or ≤ 0.35 [29], and statistical tests were conducted by…”

Section: Ase Analysis From Rna-seq Datamentioning

confidence: 99%

“…Recently, high-throughput sequencing technologies allowed us to identify ASE genes at a transcriptome-wide level. Several studies in different species such as mouse [24], pig [25], cow [26], goat [27], sheep [28], mule [29] and dzo [29] have shown that the different expression levels of alleles due to ASE may lead to variation in phenotypes.…”

Section: Introductionmentioning

confidence: 99%

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Allele-specific expression reveals the phenotypic differences between thin- and fat-tailed sheep

Shao¹,

He²,

Pan³

et al. 2020

Preprint

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Background: The thin-tailed sheep breeds from Europe and the fat-tailed sheep breeds from China exhibit distinct phenotypic differences in fat deposition and meat production traits. However, the molecular mechanisms underlying gene expression related to these phenotypic differences are not well understood. Allele-specific expression (ASE) refers to the significant imbalance of expression levels of two parental alleles. Characterization of such events in F1 hybrid offspring generated from these two groups of sheep breeds can minimize the external factors influencing gene expression and reveal the variants with a cis -regulatory effect on gene expression. The aim of the present study was to investigate the genetic factors that influence different fat-deposition and meat production traits between thin- and fat-tailed sheep.Results: Fifteen F1 hybrids were generated from crosses between Texel and Kazakh sheep as the representative phenotypes of thin- and fat-tailed breeds, respectively. Totally, 33 whole genomes from F1 individuals and their parents were sequenced with an average depth of ~17.21× coverage per sample. ASE analysis results from 70 RNA-seq samples of adipose and skeleton muscle tissues showed 128 ASE candidate genes were related to the function of fat deposition and meat production traits. A genome-wide scan of selective sweeps was also conducted between these two groups of sheep breeds in an effort to identify genomic regions related to fat deposition and meat production, respectively. We detected signatures of selection in ASE genes associated with fat deposition (e.g., PDGFD ) and meat production traits (e.g., LRCC2 ). Further analysis suggested that PDGFD and LRCC2 genes were speculated to be causative genes for fat deposition and meat production traits in sheep, respectively. Furthermore, AMPK signaling pathway was significantly enriched in ASE genes related to fatty acid biosynthesis in both adipose and skeleton muscle tissues, while PPAR signaling pathway was significantly enriched in ASE genes related to lipid metabolism in adipose tissue. Conclusions: Our finding illustrates that the expression of identified ASE genes could potentially lead to the differences in traits of fat deposition and meat production between thin- and fat-tailed sheep. Keywords: allele-specific expression, phenotypic difference, thin- and fat-tailed sheep, whole-genome sequencing, transcriptome

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“…offs are introduced such as ratio of allelic read counts > 0.9 (Chamberlain et al, 2015) or > 0.7 532 (Cao et al, 2019). We decided to exclude MAE from this study using read count bi-allelic 533 expression filtration because it is difficult to distinguish between sequencing error and MAE.…”

mentioning

confidence: 99%

Elimination of reference mapping bias reveals robust immune related allele-specific expression in crossbred sheep

Salavati

Bush

Palma-Vera

et al. 2019

Preprint

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24Pervasive allelic variation at both gene and single nucleotide level (SNV) between 25individuals is commonly associated with complex traits in humans and animals. Allele-specific 26 expression (ASE) analysis, using RNA-Seq, can provide a detailed annotation of allelic 27imbalance and infer the existence of cis-acting transcriptional regulation. However, variant 28 detection in RNA-Seq data is compromised by biased mapping of reads to the reference DNA 29sequence. In this manuscript we describe an unbiased standardised computational pipeline for 30 allele-specific expression analysis using RNA-Seq data, which we have adapted and developed 31 using tools available under open licence. The analysis pipeline we present is designed to 32 minimise reference bias while providing accurate profiling of allele-specific expression across 33 tissues and cell types. Using this methodology, we were able to profile pervasive allelic 34imbalance across tissues and cell types, at both the gene and SNV level,

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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

Cited by 13 publications

References 35 publications

Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds

Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds

Allele-specific expression reveals the phenotypic differences between thin- and fat-tailed sheep

Elimination of reference mapping bias reveals robust immune related allele-specific expression in crossbred sheep

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