Genetic polymorphisms within the ETAA1 gene associated with growth traits in Chinese sheep breeds.

Ewing tumor-associated antigen 1 (ETAA1) is an important candidate gene for fat deposition in sheep. This study aimed to investigate the indel variations in the ETAA1 gene and their associations with growth traits in the 1619 sheep. The polymorphism information content of this indel ranged from 0.308 to 0.375, with medium genetic diversity (0.25 ≤ polymorphism information content ≤ 0.5). The correlation analysis showed that an 8-bp insertion within the ETAA1 gene was significantly associated with growth traits in Luxi Blackhead sheep (LXBH), Lanzhou fat-tailed sheep, Hu sheep, Tong sheep, and Tan sheep (p < 0.05). Furthermore, the ETAA1 gene was significantly associated with several growth traits (p < 0.01), such as chest width and paunch girth of LXBH, Tong, and Tan rams. It was significantly related to the body morphometric traits of LXBH, Lanzhou fat-tailed sheep, Hu, Tong, and Tan ewes. In conclusion, the detected 8-bp indel within the ETAA1 gene was confirmed in sheep, significantly affecting the growth traits, and might be a potential DNA marker for the selection of high-quality individuals in marker-assisted selection for sheep breeding.

An insertion/deletion within the CREB1 gene identified using the RNA-sequencing is associated with sheep body morphometric traits.

In a previous study, the cyclic AMP response element-binding protein 1 (CREB1) gene, which is likely involved in the regulation of fat metabolism in sheep adipose tissue, was identified using RNA sequencing. CREB1 is a transcription factor that participates in the regulation of cell proliferation, differentiation, and survival as well as energy metabolism. Therefore, based on preliminary studies, this study aimed to reveal the correlation between the insertion/deletion (indel) polymorphism of the CREB1 gene and sheep growth traits. One insertion variation of the ovine CREB1 gene, C3-ins-26 bp, was investigated in 1847 Chinese and Mongolian sheep breeds. The minor allele frequencies in the CREB1 gene varied from 0.021 to 0.938. Further, statistical analyses indicated that the C3-ins-26 bp indel in the CREB1 gene was significantly related to various body measurements (body length, height, and index; chest width, depth, and width index; cannon circumference index; and height at the hip cross) in a Tan sheep population (p < 0.05). Collectively, these findings may provide important insights into marker-assisted selection of sheep.

Sheep zinc finger proteins 395 (ZNF395): insertion/deletion variations, associations with growth traits, and mRNA expression.

Zinc finger protein 395 (ZNF395), belonging to the Krüppel C2H2-type zinc-finger protein family, is a common transcription factor, which is involved in several cellular responses such as cell proliferation, differentiation, metabolism, and immunity, especially in the process of adipogenesis. In order to explore the insertion/deletion (indel) genetic variations of ZNF395 and evaluate their effects on sheep growth traits, a total of 1934 samples from five Chinese and two Mongolian sheep breeds were investigated. Genetic variation analysis of ZNF395 revealed a novel 23 bp indel at the intron 3 with three genotypes. Association analysis results showed that this locus was significantly associated with 10 different growth traits, especially chest width (p = 0.003) and chest circumference (p = 0.003) of Small Tail Han sheep and cannon circumference (p = 0.007) of Hu sheep. In addition, the mRNA expression of ZNF395 was investigated in two sheep breeds of different tail types. The result indicated that the expression was significantly different between the tail fat of Lanzhou Fat-Tail sheep and Small Tail Han sheep (p < 0.05). This study showed that the 23 bp indel locus in the ZNF395 gene were associated with sheep growth traits, which could be beneficial for animal breeding.

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

The Lanzhou Fat-Tail sheep (LFTS, long fat-tailed sheep) is an endangered sheep breed in China with a fat tail compared to the traditional local varieties, Small Tail Han sheep (STHS, thin-tailed sheep) with a small tail, and Tibetan sheep (TS, short thin-tailed sheep) with a little tail. However, little is known regarding how tail fat deposition is regulated by long noncoding RNA (lncRNA). To evaluate the lncRNA and mRNA associated with tail fat deposition and development among these breeds, high-throughput RNA sequencing of three individuals each of LFTS, STHS, and TS were performed and analyzed in this study. RNA sequencing data from these three groups revealed 10 differentially expressed genes (DEGs) and 37 differentially expressed lncRNAs between the LFTS and STHS groups, 390 DEGs and 59 differentially expressed lncRNAs between the LFTS and TS groups, and 80 DEGs and 16 differentially expressed lncRNAs between the STHS and TS groups (p-value < 0.05 and fold change ≥ 2), respectively. Gene Ontology and pathway analysis of DEGs and target genes of differentially expressed lncRNAs revealed enrichment in fatty acid metabolism and fatty acid elongation-related pathways that contribute to fat deposition. Subsequently, the expression of 14 DEGs and 6 differentially expressed lncRNAs was validated by quantitative real-time PCR. Finally, two co-expression networks of differentially expressed mRNA and lncRNAs were constructed. The results suggested that some differentially expressed lncRNAs (TCONS_00372767, TCONS_00171926, TCONS_00054953, and TCONS_00373007) may play crucial roles as core lncRNAs in tail fat deposition processes. In summary, the present study extends the sheep tail fat lncRNA database and these differentially expressed mRNA and lncRNAs may provide novel candidate regulators for future genetic and molecular studies on tail fat deposition of sheep.

Nucleotide variants in prion-related protein (testis-specific) gene (PRNT) and effects on Chinese and Mongolian sheep phenotypes.

Studies of the ovine prion-related protein (testis-specific) gene (PRNT), including studies of genetic diversity, have highlighted its potential relationship to scrapie infection and economically important ovine traits. PRNT was previously reported to be highly polymorphic in Portuguese sheep. To characterize genetic polymorphisms in this gene in Asian sheep, a direct sequencing method was used to detect polymorphic loci in PRNT in 285 individual sheep from four Chinese and one Mongolian breeds. Seven SNP variants in PRNT were identified, including three novel variants (g.93G>A, g.162G>T, and g.190A>G) and four previously reported variants (g.17 C>T, g.112G>C, g.129C>T, and g.144A>G). In the five breeds that we analyzed, the mutation frequencies of g.190A>G in Lanzhou Fat-tail sheep (LFTS) and g.129C>T in the other four varieties were high (F>0.5). Moreover, thirteen different haplotypes that had a comparable distribution in the tested breeds were also identified; 'C-G-G-C-A-G-A' occurred at the highest frequency in the five sheep breeds. Additionally, we previously explored the significance of relationships between polymorphisms in PRNP or PRND and ovine growth performance. Here, we also performed correlation analysis in all tested loci. These loci polymorphisms were significantly associated with ten different growth traits (P<0.05), except for g.93G>A. Meanwhile, in contrast to a previous study, there was no significant association between the seven SNP loci analyzed and our previously reported sheep PRND or PRNP insertion/deletion mutations. Our findings may provide new insights into polymorphic variation in ovine PRNT, which may contribute to genetic improvements in economic traits that are important for sheep breeding.

Genetic effects of PRNP gene insertion/deletion (indel) on phenotypic traits in sheep.

Prion protein (PRNP) gene is well known for affecting mammal transmissible spongiform encephalopathies (TSE), and is also reported to regulate phenotypic traits (e.g. growth traits) in healthy ruminants. To identify the insertion/deletion (indel) variations of the PRNP gene and evaluate their effects on growth traits, 768 healthy individuals from five sheep breeds located in China and Mongolia were identified and analyzed. Herein, four novel indel polymorphisms, namely, Intron-1-insertion-7bp (I1-7bp), Intron-2-insertion-15bp (I2-15bp), Intron-2-insertion-19bp (I2-19bp), and 3' UTR-insertion-7bp (3' UTR-7bp), were found in the sheep PRNP gene. In five analyzed breeds, the minor allelic frequencies (MAF) of the above indels were in the range of 0.008 to 0.986 (I1-7bp), 0.113 to 0.336 (I2-15bp), 0.281 to 0.510 (I2-19bp), and 0.040 to 0.238 (3' UTR-7bp). Additionally, there were 15 haplotypes and the haplotype 'II2-15bp-D3'UTR-7bp-DI2-19bp-DI1-7bp' had the highest frequency, which varied from 0.464 to 0.629 in five breeds. Moreover, association analysis revealed that all novel indel polymorphisms were significantly associated with 13 different growth traits (P < 0.05). Particularly, the influences of I2-15bp on chest width (P = 0.001) in Small Tail Han sheep (ewe), 3' UTR-7bp on chest circumference (P = 0.003) in Hu sheep, and I2-19bp on tail length (P = 0.001) in Tong sheep, were highly significant (P < 0.01). These findings may be a further step toward the detection of indel-based typing within and across sheep breeds, and of promising target loci for accelerating the progress of marker-assisted selection in sheep breeding.