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

Abstract

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.

RNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep

“…However, under the hypothesis that the important genes/genomic regions related to fat-tail formation are evolutionarily conserved among different sheep breeds, we took into account the common SNPs/genes or genomic regions with previous similar studies. In total, 300 SNPs (78 SNPs in Lori-Bakhtiari and 222 SNPs in Zel) were concordant with previous studies on sheep breeds 6 , 8 , 44 . These SNPs were located within 91 genes (Supplementary File S1 ).…”

“…In a recent study, transcriptome of samples from longissimus dorsi muscle, perinephric fat and fat-tail of Lanzhou sheep, were subjected to RNA-Seq and 606,952 SNPs were identified overlapping with QTLs of fat traits. The latter study also suggested three potential genes (CREB1, WDR92 and ETAA1) related to fat-tail development 8 . Also, whole genome sequencing identified T gene as an important candidate gene influencing tail size in Hulunbuir short-tailed sheep 9 .…”

Comparative Transcriptome Profiling of mRNA and lncRNA Related to Tail Adipose Tissues of Sheep

“…LFTS is an endangered breed that needs protection. Compared with LFTS, STHS have smaller tails and fat accumulation ( Xu et al, 2017 ; Ma et al, 2018 ). STHS have a high reproductive capacity and show polyembryony; they grow fast and could be in oestrum at all seasons ( Kashan et al, 2005 ).…”

Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages

“…In recent years, with the evolution of sequencing technology, increasing sequencing is used in the identification of differential expression. A few transcriptome studies had been done to review gene expression or genetic variation profiling in livestock [4][5][6][7]. There are many studies on mRNA and long non-coding RNAs (lncRNAs) levels in the muscle from different pig breeds [8][9][10][11].…”