Transcriptomic analyses revealed common tailed and perirenal adipose differentially expressed genes in four Chinese indigenous sheep breeds
Graphical abstract
Introduction
Fat depositions in different body sites are of significant interest to select desirable livestock for breeding and production. In some sheep breeds, fat is excessively accumulated around the tail region, which is regarded as the fat-tail phenotype. According to the length and shape of the tail, fat-tailed sheep can be further divided into short fat-tailed, long fat-tailed, and fat-rumped types (Mohapatra and Shinde, 2018). Different from other mammals, the unique distribution of sheep fat, i.e. the fat-tail phenotype, has attracted increasing interest. On one hand, fat tail has lost its commercial value because customers preferred lower-fat meat. On the other hand, protecting this special trait may have a potential role for the future breeding for adaptation to a harsh environment. Hence, it is important for sheep industry to identify the candidate genes associated with tail fat deposition and further understand the genetic mechanism underlying this process.
Previously, some candidate genes or genomic regions associated with the fat tail characteristic were identified by contrasting divergent phenotypes or via association with tailed phenotype (Moradi et al., 2012; Moioli et al., 2015; Wei et al., 2015; Zhu et al., 2016; Xu et al., 2017; Yuan et al., 2017; Li et al., 2018; Ma et al., 2018b; Mastrangelo et al., 2018; Zhi et al., 2018; Ahbara et al., 2019). These studies laid the foundation for studying the formation of sheep tail fat. However, the causal genes for such a phenotype remains unclear. Exploring differentially expressed genes (DEGs) in different tissues is a way to identify important candidate genes because the variation in the gene expression across tissues is attributable to their functionality. Recently, researchers identified some DEGs or specifically expressed genes by comparing adipose tissues from several body sites in Tan sheep, Guangling large-tailed sheep, and small-tailed Han sheep (Kang et al., 2017; Li et al., 2018). Animal species and breeds can differ in their characteristics related to adipose tissue deposition (Hausman et al., 2014). The short fat-tailed Hu sheep is one of the most widely raised indigenous sheep breeds in China known for its high fecundity (Yue, 1996). Its gene expression pattern in different adipose tissue types has not been thoroughly investigated.
The evidence from previous studies suggest some common genes associated with the tail fat phenotype are shared across different breeds (Moioli et al., 2015; Yuan et al., 2017; Mastrangelo et al., 2018). Our hypothesis for this study was that an integrative study combining the results of RNA-seq in different breeds could reveal strong candidate genes for the complex fat tailed phenotype. In the current study, we used RNA-seq technology to identify DEGs in three different tissues, namely tail adipose tissue (TAT), perirenal adipose tissue (PAT) and longissimus dorsi muscle tissue (MUT) from Hu Sheep. In addition, we incorporated published RNA-seq data (Guangling large-tailed sheep and small-tailed Han sheep, Table 1) and summary data (mean reads per kilobase per million mapped reads, RPKM) of DEGs’ in Tan sheep to investigate the common DEGs across different breeds (Kang et al., 2017; Li et al., 2018). Further, we also investigated the expression pattern of 42 candidate genes in Hu sheep, small-tailed Han sheep and Guangling large-tailed sheep, which were identified by selection signature analysis or genome wide association analysis from the published literature.
Section snippets
Animal tissues collection and RNA extraction
Three Hu male lambs at six-month old with similar body weight were selected to slaughter for sample collection, which were fed in the same environment from weaning to six-month old at Minqin Zhongtian Sheep Industry Co., Ltd (Minqin, Gansu, P.R.China). The PAT, TAT and MUT tissues for each Hu sheep (Supplemental Fig. S1) was sampled in triplicate within 30 minutes after slaughter, immediately frozen in liquid nitrogen, and stored at −80°C until RNA extraction. The RNAprep Pure Tissue Kit
RNA-seq quality
After filtering the low-quality raw reads, we obtained about 180.18 million clean paired-end reads from 9 libraries (Supplemental Table S1). Sample clustering analysis shows that there were two outlier samples (PAT1 and TAT1, Supplemental Fig. S2) and these two samples were removed for further analyses. In total, 7 samples (3 MUTs, 2 TATs, 2 PATs) were used for further analysis (Fig. 1A). Approximately 82.86-88.27% of clean reads uniquely mapped to the sheep reference genome (Fig. 1B). The
Conclusion
In conclusion, this study identified a total of 1336, 427, 665 DEGs in MUT, PAT, TAT of Hu sheep, respectively. Of which, 600 and 336 were expressed uniquely in TAT and PAT, respectively. Integrative study combining the results of RNA-seq in small-tailed Han, Guangling large-tailed sheep and Tan sheep revealed 9 and 13 common candidate genes for the perirenal adipose specific deposition and fat tail phenotype, respectively. Of those, WT1, TCF21, PPFIBP1 and WNT10B were highly expressed in PAT
Declaration of Competing Interest
None.
Acknowledgments
We thank Dr. Hans D. Daetwyler of AgriBio, the Centre for AgriBioscience for providing data analytic platform. This work was supported by the National Natural Science Foundation of China (31872319), China Agriculture Research System (CARS-38) and Fundamental Research Funds for the Central Universities (561219029).
References (50)
- et al.
Ablation of PRDM16 and beige adipose causes metabolic dysfunction and a subcutaneous to visceral fat switch
Cell
(2014) - et al.
Chemerin: at the crossroads of inflammation and obesity
Trends Endocrinol. Metab.
(2010) - et al.
Chemerin, a novel adipokine that regulates adipogenesis and adipocyte metabolism
J. Biol. Chem.
(2007) - et al.
Growth performance and carcass quality of fattening lambs from fat-tailed and tailed sheep breeds
Small Ruminant Res
(2005) - et al.
Wnt10b inhibits development of white and brown adipose tissues
J. Biol. Chem.
(2004) - et al.
A C/T mutation in microRNA target sites in BMP5 gene is potentially associated with fatness in pigs
Meat Sci
(2011) - et al.
A secreted slit2 fragment regulates adipose tissue thermogenesis and metabolic function
Cell Metab
(2016) - et al.
Identification and characterization of microRNA from chicken adipose tissue and skeletal muscle
Poult. Sci.
(2012) Reproductive characteristics of Chinese Hu sheep
Anim. Reprod. Sci.
(1996)- et al.
Effect of docking and sex of lambs on carcass characteristics of fat-tailed Najdi sheep
J. Appl. Anim. Res.
(1992)
Genome-wide variation, candidate regions and genes associated with fat deposition and tail morphology in Ethiopian indigenous sheep
Front. Genet.
Global gene expression profiling of brown to white adipose tissue transformation in sheep reveals novel transcriptional components linked to adipose remodeling
BMC Genomics
Trimmomatic: a flexible trimmer for Illumina sequence data
Bioinformatics
Signaling properties of chemerin receptors CMKLR1
GPR1 and CCRL2
STAR: ultrafast universal RNA-seq aligner
Bioinformatics
Preadipocyte and adipose tissue differentiation in meat animals: influence of species and anatomical location
Annu. Rev. Anim. Biosci.
Comparative transcriptome analysis reveals potentially novel roles of Homeobox genes in adipose deposition in fat-tailed sheep
Sci. Rep.
Effects of Wnt signaling on brown adipocyte differentiation and metabolism mediated by PGC-1alpha
Mol. Cell Biol.
Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition
BMC Genomics
The sequence alignment/map format and SAMtools
Bioinformatics
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Bioinformatics
Genetic variants in fat- and short-tailed sheep from high-throughput RNA-sequencing data
Anim. Genet.
Comparative transcriptome profiling of mRNA and lncRNA related to tail adipose tissues of sheep
Front. Genet.
Genome-wide scan of fat-tail sheep identifies signals of selection for fat deposition and adaptation
Anim. Prod. Sci.
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