Coiled-coil serine-rich protein 1 (CCSER 1) gene is a regulatory protein gene. This gene has been reported to be associated with various economic traits in large mammals in recent years. The aim of this study was to investigate the association between CCSER1 gene single nucleotide polymorphisms (SNPs) and Gannan yaks and to identify potential molecular marker loci for breeding milk quality in Gannan yaks. We genotyped 172 Gannan yaks using Illumina Yak cGPS 7K liquid microarrays and analyzed the correlation between the three SNPs loci of the CCSER1 gene and the milk qualities of Gannan yaks, including milk fat, protein and casein. It was found that mutations at the g.183,843A>G, g.222,717C>G and g.388,723G>T loci all affected the fat, protein, casein and lactose traits of Gannan yak milk to varying extents, and that the milk quality of individuals with mutant phenotypes was significantly improved. Among them, the milk fat content of AG heterozygous genotype population at g.183,843A>G locus was significantly higher than that of AA and GG genotype populations (p < 0.05); the casein and protein content of mutant GG and CG genotype populations at g.222,717C>G locus was significantly higher than that of wild-type CC genotype population (p < 0.05); and the g.388,723G>T locus of the casein and protein contents of the mutant TT genotype population were significantly higher (p < 0.05) than those of the wild-type GG genotype population. These results provide potential molecular marker sites for Gannan yak breeding.

Copy number variation (CNV) is a fundamental type of structural variation of the genome affecting the economic traits of livestock. The SOX6 gene (sex-determining region Y-box 6), as a transcription factor, has multiple functions with regard to sex determination, embryonic growth, the nervous system development, as well as bone, and various organ formation. This study employed quantitative real-time fluorescence quota PCR (qPCR) for detecting the SOX6-CNV of the 311 Ashidan yaks and analyzed the correlation of the SOX6-CNV with four phenotypes (including body weight, withers height, body length, and chest girth) of the yaks aged 6, 12, 18, and 30 months using ANOVA and multiple comparisons. Furthermore, the SOX6 gene expression was identified in seven different tissues of the yaks. The experiment results demonstrated the expression of SOX6 in each tissue, and the kidney and muscle tissue were found to have higher relative expression levels. Based on the processing by IBM SPSS software, SOX6-CNV was significantly correlated with the chest girth of the 6-months old yaks (p < 0.05) and 30-months yaks (p < 0.05), and withers height of 6 months yaks (p < 0.05) and 18-months yaks (p < 0.05), as well as the normal type of CNV, was chosen for yak breeding. In conclusion, SOX6 might be prominently involved in promoting growth and development of yaks, suggesting that the SOX6 gene can be used in breeding yaks by molecular marker-assisted selection (MAS). The study also offered some important insights into the references and clues for the genetic breeding of yaks.

Copy number variations (CNVs) are a result of genomic rearrangement affecting DNA regions over 1 kb in length, and can include inversions, translocations, deletions, and duplications. The molecule interacting with CasL-like protein 2 (MICALL2) gene is primarily associated with mitochondrial protein targeting and exhibits predicted stress fiber colocalization. The monoacylglycerol O-acyltransferase 2 (MOGAT2) gene encodes an enzyme responsible for catalyzing diacylglycerol synthesis from 2-monoacylglycerol and fatty acyl-CoA. For this study, blood samples were obtained from 315 yaks, and the body weight, body length, withers height, and chest girth of these animals were measured at 6, 12, 18, and 30 months of age. Genomic DNA was harvested from the collected blood samples, and CNVs in these samples were detected by qPCR. The resultant data were compared using ANOVAs, revealing significant associations between MICALL2 gene CNVs and body weight at 6 months of age (p < 0.05), body length and chest girth at 30 months of age (p < 0.05), and withers height at 18 months of age (p < 0.01) in Ashidan yaks. Similarly, MOGAT2 CNVs were significantly associated with body weight at 6 and 30 months of age (p < 0.05), and with withers height at 18 months of age (p < 0.01) in these Ashidan yaks. MICALL2 and MOGAT2 gene expression was further analyzed in yak tissue samples, revealing that MICALL2 was most highly expressed in the adipose tissue, whereas MOGAT2 was most highly expressed in the lung. These results thus confirmed the relationship between CNVs in the MICALL2 and MOGAT2 genes and Ashidan yak growth traits, providing a valuable gene locus that can be leveraged for future marker-assisted yak breeding efforts.