Genetic diversity analysis of DRB3.2 in domestic yak (Bos grunniens) in Qinghai-Tibetan Plateau

DRB3 gene has been extensively evaluated as a candidate marker for association with many bovine disease and immunological traits. A hemi-nested polymerase chain reaction-sequencing method was used to investigate the polymorphisms of DRB3.2 gene from 209 individuals in three different domestic yak (Bos grunniens) populations (62 Tianzhu white yaks, 78 Gannan yaks and 69 Datong yaks) from the Qinghai-Tibetan Plateau. Sixty-three polymorphic sites and 143 haplotypes were detected. The percentage of polymorphic sites in Gannan Yak (GNY), Tianzhu white Yak (TWY) and Datong Yak (DTY) were 21.80, 29.95 and 12.95%, while the haplotype diversity were 0.9987, 0.9984 and 0.9855, respectively. At the amino acid level, Glu had the highest content; the percentage was 12.326%, followed by Arg (10.315%), Phe (10.804%), Val (8.346%), Gly (8.315%), Leu (6.606%) and Ala (5.851%), whereas Met and Ile were below than 1%. Only 19 amino acids were found in DTY, Met was lost. Among the synonymous codons, whose third base was G and/or C had a higher usage frequency. Most variability were found in amino acid residues 11, 13, 26, 28, 30, 32, 37, 56, 57, 59, 60, 61, 67, 70, 71, 72, 73 and 74. In GNY, the residues at positions 71, 11 and 72 were highly polymorphic with 8, 7 and 7, at 50, 58, 70, 74 and 78, the residues were selectively polymorphic than other yak populations; the other polymorphic sites were common in the populations. The results of this study indicated that the Chinese domestic yak populations in the Qinghai-Tibetan Plateau have abundant polymorphism in DRB3.2, and the GNY was the highest, followed by TWY and DTY.Key words: Domestic Yak, Hemi-nested PCR, BoLA-DRB3.2, polymorphism

Evaluation of 17 microsatellite markers for parentage testing and individual identification of domestic yak (Bos grunniens)

Background Yak (Bos grunniens) is the most important domestic animal for people living at high altitudes. Yak ordinarily feed by grazing, and this behavior impacts the accuracy of the pedigree record because it is difficult to control mating in grazing yak. This study aimed to evaluate the pedigree system and individual identification in polled yak. Methods A total of 71 microsatellite loci were selected from the literature, mostly from the studies on cattle. A total of 35 microsatellite loci generated excellent PCR results and were evaluated for the parentage testing and individual identification of 236 unrelated polled yaks. A total of 17 of these 35 microsatellite loci had polymorphic information content (PIC) values greater than 0.5, and these loci were in Hardy–Weinberg equilibrium without linkage disequilibrium. Results Using multiplex PCR, capillary electrophoresis, and genotyping, very high exclusion probabilities were obtained for the combined core set of 17 loci. The exclusion probability (PE) for one candidate parent when the genotype of the other parent is not known was 0.99718116. PE for one candidate parent when the genotype of the other parent is known was 0.99997381. PE for a known candidate parent pair was 0.99999998. The combined PEI (PE for identity of two unrelated individuals) and PESI (PE for identity of two siblings) were >0.99999999 and 0.99999899, respectively. These findings indicated that the combination of 17 microsatellite markers could be useful for efficient and reliable parentage testing and individual identification in polled yak. Discussion Many microsatellite loci have been investigated for cattle paternity testing. Nevertheless, these loci cannot be directly applied to yak identification because the two bovid species have different genomic sequences and organization. A total of 17 loci were selected from 71 microsatellite loci based on efficient amplification, unambiguous genotyping, and high PIC values for polled yaks, and were suitable for parentage analysis in polled yak populations

Microbiome and Metabolomics Reveal the Effects of Different Feeding Systems on the Growth and Ruminal Development of Yaks

The change in the feeding system can greatly improve the growth performance of the yak (Bos grunniens), an important livestock species in the plateau region. Here, we comprehensively compared the effects of different feeding systems on the growth performance and ruminal development of yaks, and investigated the effects of ruminal microorganisms and metabolites using the 16S rRNA gene sequencing and liquid chromatograph–mass spectrometer (LC-MS) technologies. We found that compared to traditional grazing feeding, house feeding significantly improved the growth performance (such as average daily gain and net meat weight) and rumen development of the yaks. At the genus level, the abundance of Rikenellaceae RC9 Gut group, Christensenellaceae R-7 group, Lachnospiraceae NK3A20 group, Ruminococcaceae UCG-014, and Prevotellaceae UCG-003 showed significant differences and was closely related to rumen development in the two distinct feeding systems. Also, metabolomics revealed that the change in the feeding system significantly affected the concentration and metabolic pathways of the related rumen metabolites. The metabolites with significant differences were significantly enriched in purine metabolism (xanthine, adenine, inosine, etc.), tyrosine metabolism (L-tyrosine, dopaquinone, etc.), phenylalanine metabolism (dihydro-3-caumaric acid, hippuric acid, etc.), and cAMP signaling pathway [acetylcholine, (-)-epinephrine, etc.]. This study scientifically support the house fattening feeding system for yaks. Also, our results provide new insights into the composition and function of microbial communities that promote ruminal development and in general growth of the yaks

Evolutionary origin of genomic structural variations in domestic yaks

Yak has been subject to natural selection, human domestication and interspecific introgression during its evolution. However, genetic variants favored by each of these processes have not been distinguished previously. We constructed a graph-genome for 47 genomes of 7 cross-fertile bovine species. This allowed detection of 57,432 high-resolution structural variants (SVs) within and across the species, which were genotyped in 386 individuals. We distinguished the evolutionary origins of diverse SVs in domestic yaks by phylogenetic analyses. We further identified 334 genes overlapping with SVs in domestic yaks that bore potential signals of selection from wild yaks, plus an additional 686 genes introgressed from cattle. Nearly 90% of the domestic yaks were introgressed by cattle. Introgression of an SV spanning the KIT gene triggered the breeding of white domestic yaks. We validated a significant association of the selected stratified SVs with gene expression, which contributes to phenotypic variations. Our results highlight that SVs of different origins contribute to the phenotypic diversity of domestic yaks

Characterization of the complete mitochondrial genome of the Qiaoke sheep (Ovis aries)

Qiaoke sheep (Ovis aries) is a local sheep breed in Gansu province, China. It is a kind of Tibetan sheep that used for both meat and wool after long-term breeding. In this paper, the complete mitochondrial genome of Qiaoke sheep was sequenced. The total length of the mitochondrial genome is 16616 bp, and the base composition is 33.65% A, 13.14% G, 25.88% C and 27.33% T. The genome has a total of 37 genes, including 13 protein-coding genes, 22 tRNA genes, two ribosomal RNA genes and a control region (D-loop region). This complete sequence would enlarge useful genomic information for further studies