Comparative transcriptome analysis reveals potentially novel roles of Homeobox genes in adipose deposition in fat-tailed sheep

Kang, Dan-Ju; Zhou, Guangxian; Zhou, Shiwei; Zeng, Jie; Wang, Xiaolong; Jiang, Yu; Yang, Yuxin; Chen, Yulin

doi:10.1038/s41598-017-14967-9

Cited by 44 publications

(48 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Moreover, there are no SNPs located within the HOX and HOX‐related genes ( HOXA6 , HOXA9 , HOXA10 , HOXB2 , HOXB5 , HOXB7 , HOXC4 , HOXC6 , HOXC8 , HOXC9 , HOXC10 , HOXC11 , HOXC12 and HOXC13 ), which are differentially expressed between subcutaneous‐, visceral‐ and tail‐fat tissues (Kang et al . ). Current evidence suggests that the CREB1 gene may have a significant role in tail type formation in sheep.…”

Section: Number Of Snps Identified From Three Sheep Breeds Using Rna‐mentioning

confidence: 97%

“…Additionally, Kang et al . () identified that HOX and HOX‐related genes might play key roles in regulating regional fat distribution and diverse tail types in the Tan sheep, which is a fat‐tailed sheep breed. However, until now, a full understanding of the molecular determinants of fat and thin tails is still lacking.…”

Section: Number Of Snps Identified From Three Sheep Breeds Using Rna‐mentioning

confidence: 99%

See 1 more Smart Citation

Genetic variants in fat‐ and short‐tailed sheep from high‐throughput RNA‐sequencing data

Cai

et al. 2018

Animal Genetics

View full text Add to dashboard Cite

The identification of genetic variations underlying desired phenotypes is one of the main challenges of current livestock genetic research. High-throughput transcriptome sequencing has been recognized as an efficient way to unravel the rich genetic variants across various species. The Lanzhou Fat-Tail sheep is an endangered sheep breed in China with a notable feature of an exaggerated fat tail that also independently occurs in other sheep breeds. However, the genetic mechanism underlying this particular trait has not been fully elucidated yet. In this study, we used RNA-seq on tissue samples (longissimus dorsi muscle, perinephric fat and tail fat) from three sheep breeds with either fat or thin tails and characterized the genetic variation in Lanzhou Fat-Tail sheep with the ultimate goal of identifying the causal genes and genetic networks responsible for the fat tail in this rare sheep breed. In total, 7 122 920 SNPs and 901 518 indels were detected in the nine individual sheep investigated, of which 606 952 SNPs (8.5%) and 77 633 indels (8.6%) overlapped with QTL associated with fat traits in sheep. Furthermore, we detected 26 613 specific SNPs in Lanzhou Fat-Tail sheep and 44 SNPs located in the same genomic position reported in another sheep breed with fat tails. Interestingly, 33 SNPs are selectively distributed on a chromosome 3 region (39.58-40.91 Mb) that was reported as a strong candidate genomic region for fat deposition in tails of sheep. Our research has also suggested that three genes (CREB1, WDR92 and ETAA1) may be associated with fat tail development. In summary, the resultant genetic variants data in this study provide a valuable resource for marker-assisted selection of the trait in Lanzhou Fat-Tail sheep populations.

show abstract

Section: Number Of Snps Identified From Three Sheep Breeds Using Rna‐mentioning

confidence: 97%

Section: Number Of Snps Identified From Three Sheep Breeds Using Rna‐mentioning

confidence: 99%

Genetic variants in fat‐ and short‐tailed sheep from high‐throughput RNA‐sequencing data

Cai

et al. 2018

Animal Genetics

View full text Add to dashboard Cite

show abstract

“…The region containing the HOXC@ could be under selection in the Lezgin, Edilbai, and Karakul breeds while the HOXA@-containing region, in the Karachaev, Kulundin, Russian Longhaired, Buubei, and Karakul breeds. The HOX genes are involved in regulation of limb development in mammals [65,66], with the HOXA@ also being associated with body composition and structure in pigs [67] and HOXC@ being associated with tail fat deposition in sheep [68]. The region containing LAP3, NCAPG, LCORL, and HERC6 genes on OAR6 is known to be related to growth traits, carcass composition, body size, weight and height in sheep [1], horses [69], and cattle [70,71].…”

Section: Growth and Feed Intakementioning

confidence: 99%

High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia

et al. 2019

View full text Add to dashboard Cite

Background: Domestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs. The genomes of local breeds, therefore, are valuable sources of genomic variants to be used to understand mechanisms of response to adaptation and artificial selection. As a step toward this we performed a high-density genotyping and comprehensive scans for signatures of selection in the genomes from 15 local sheep breeds reared across Russia. Results: Results demonstrated that the genomes of Russian sheep breeds contain multiple regions under putative selection. More than 50% of these regions matched with intervals identified in previous scans for selective sweeps in sheep genomes. These regions contain well-known candidate genes related to morphology, adaptation, and domestication (e.g., KITLG, KIT, MITF, and MC1R), wool quality and quantity (e.g., DSG@, DSC@, and KRT@), growth and feed intake (e.g., HOXA@, HOXC@, LCORL, NCAPG, LAP3, and CCSER1), reproduction (e.g., CMTM6, HTRA1, GNAQ, UBQLN1, and IFT88), and milk-related traits (e.g., ABCG2, SPP1, ACSS1, and ACSS2). In addition, multiple genes that are putatively related to environmental adaptations were top-ranked in selected intervals (e.g., EGFR, HSPH1, NMUR1, EDNRB, PRL, TSHR, and ADAMTS5). Moreover, we observed that multiple key genes involved in human hereditary sensory and autonomic neuropathies, and genetic disorders accompanied with an inability to feel pain and environmental temperatures, were top-ranked in multiple or individual sheep breeds from Russia pointing to a possible mechanism of adaptation to harsh climatic conditions.

show abstract

“…Comparative transcriptome analysis is another efficient way used for identifying candidate causative genes that associated with distinct phenotypic differences between thin-and fat-tailed sheep breeds [56][57][58]. However, it presented little power to identify genetic factors that contribute to these phenotypic differences because the identified DEGs always reflect both cisand trans-acting regulatory variations [59].…”

Section: Discussionmentioning

confidence: 99%

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

Shao¹,

He²,

Pan³

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

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

show abstract

Comparative transcriptome analysis reveals potentially novel roles of Homeobox genes in adipose deposition in fat-tailed sheep

Cited by 44 publications

References 55 publications

Genetic variants in fat‐ and short‐tailed sheep from high‐throughput RNA‐sequencing data

Genetic variants in fat‐ and short‐tailed sheep from high‐throughput RNA‐sequencing data

High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia

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

Contact Info

Product

Resources

About