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Genetic variants in fat‐ and short‐tailed sheep from high‐throughput RNA ‐sequencing data
Author(s) -
Ma L.,
Li Z.,
Cai Y.,
Xu H.,
Yang R.,
Lan X.
Publication year - 2018
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12699
Subject(s) - biology , single nucleotide polymorphism , genetics , indel , candidate gene , breed , quantitative trait locus , genetic variation , gene , genotype
Summary 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 SNP s and 901 518 indels were detected in the nine individual sheep investigated, of which 606 952 SNP s (8.5%) and 77 633 indels (8.6%) overlapped with QTL associated with fat traits in sheep. Furthermore, we detected 26 613 specific SNP s in Lanzhou Fat‐Tail sheep and 44 SNP s located in the same genomic position reported in another sheep breed with fat tails. Interestingly, 33 SNP s 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 ( CREB 1 , WDR 92 and ETAA 1 ) 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.