Genome-wide DNA methylation analysis reveals different methylation patterns in Chinese indigenous sheep with different type of tail.

Background: The study was aimed to analyze the difference of genome-wide DNA differential methylation in Lanzhou Large-tailed sheep, Altay sheep and Tibetan sheep, which the typical breeds with different type tails, as to screen the differentially methylated genes (DMGs) that affect the type of tails. Methods: In this study, three Lanzhou Large-tailed sheep, three Altay sheep and three Tibetan sheep were detected by whole genome bisulfite sequencing (WGBS). The degree of genome-wide DNA methylation, differentially methylated regions (DMRs) and DMGs were analyzed. The candidate genes affecting the tail type of sheep were identified by GO and KEGG pathway enrichment analysis of DMGs. Results: we identified 68,603 different methylated regions (DMCs) and 75 differentially methylated genes (DMGs) associated with these DMCs. Functional analysis showed that these DMGs were mainly enriched in biological process, cellular component and molecular function, Some of the genes in these pathways are involved in fat metabolism: NFATC4, LPIN2, MGAT2 and MAT2B. Conclusion: Our results may help to further understand the epigenetic regulation mechanisms of deposition of fat in the tail of sheep and provide new basic data for the study of local sheep.

Detection of copy number variation and selection signatures on the X chromosome in Chinese indigenous sheep with different types of tail.

OBJECTIVE: Chinese indigenous sheep breeds can be classified into the following three categories by their tail morphology: fat-tailed, fat-rumped and thin-tailed sheep. The typical sheep breeds corresponding to fat-tailed, fat-rumped, and thin-tailed sheep are large-tailed Han, Altay, and Tibetan sheep, respectively. Detection of copy number variation (CNV) and selection signatures provides information on the genetic mechanisms underlying the phenotypic differences of the different sheep types. METHODS: In this study, PennCNV software and F-statistics (FST) were implemented to detect CNV and selection signatures, respectively, on the X chromosome in three Chinese indigenous sheep breeds using ovine high-density 600K single nucleotide polymorphism arrays. RESULTS: In large-tailed Han, Altay, and Tibetan sheep, respectively, a total of six, four and 22 CNV regions (CNVRs) with lengths of 1.23, 0.93, and 7.02 Mb were identified on the X chromosome. In addition, 49, 34, and 55 candidate selection regions with respective lengths of 27.49, 16.47, and 25.42 Mb were identified in large-tailed Han, Altay, and Tibetan sheep, respectively. The bioinformatics analysis results indicated several genes in these regions were associated with fat, including dehydrogenase/reductase X-linked, calcium voltage-gated channel subunit alpha1 F, and patatin like phospholipase domain containing 4. In addition, three other genes were identified from this analysis: the family with sequence similarity 58 member A gene was associated with energy metabolism, the serine/arginine-rich protein specific kinase 3 gene was associated with skeletal muscle development, and the interleukin 2 receptor subunit gamma gene was associated with the immune system. CONCLUSION: The results of this study indicated CNVRs and selection regions on the X chromosome of Chinese indigenous sheep contained several genes associated with various heritable traits.

Determination of 15 sedative residues in mutton by rapid resolution liquid chromatography-tandem mass spectrometry.

BACKGROUND: The use of xenobiotic compounds in animal husbandry has given rise to consumer anxieties regarding residual risk and food safety. Thus, animal tissues have become main samples for residue analysis and food safety for sedatives. In this study, a rapid resolution liquid chromatography-tandem mass spectrometry (RRLC-MS/MS) method was established for the determination of 15 sedatives residues in mutton. RESULTS: After enzymolysis, sedatives residues in mutton were extracted by ammonium hydroxide-acetonitrile (10:90, v/v) and determined by RRLC-MS/MS with quantification by standard curve method. The calibration curves showed good linearity within the concentrations of 0.5-50 µg kg(-1) with the correlation coefficients (r(2)) ranged from 0.9639 to 0.9984. The limits of detection (LODs) and quantification (LOQs) were 0.25-2.5 and 0.5-5 µg kg(-1), respectively. The average recoveries of spikes samples were in the ranges of 74.1-116.8% with relative standard deviations of intra- and inter-day ranged from 2.6% to 11.2% and from 2.1% to 11.4%, respectively. CONCLUSION: This method is simple, sensitive and accurate in the determination of sedative residues.

Mutations in MC1R gene determine black coat color phenotype in Chinese sheep.

The melanocortin receptor 1 (MC1R) plays a central role in regulation of animal coat color formation. In this study, we sequenced the complete coding region and parts of the 5'- and 3'-untranslated regions of the MC1R gene in Chinese sheep with completely white (Large-tailed Han sheep), black (Minxian Black-fur sheep), and brown coat colors (Kazakh Fat-Rumped sheep). The results showed five single nucleotide polymorphisms (SNPs): two non-synonymous mutations previously associated with coat color (c.218 T>A, p.73 Met>Lys. c.361 G>A, p.121 Asp>Asn) and three synonymous mutations (c.429 C>T, p.143 Tyr>Tyr; c.600 T>G, p.200 Leu>Leu. c.735 C>T, p.245 Ile>Ile). Meanwhile, all mutations were detected in Minxian Black-fur sheep. However, the two nonsynonymous mutation sites were not in all studied breeds (Large-tailed Han, Small-tailed Han, Gansu Alpine Merino, and China Merino breeds), all of which are in white coat. A single haplotype AATGT (haplotype3) was uniquely associated with black coat color in Minxian Black-fur breed (P = 9.72E - 72, chi-square test). The first and second A alleles in this haplotype 3 represent location at 218 and 361 positions, respectively. Our results suggest that the mutations of MC1R gene are associated with black coat color phenotype in Chinese sheep.