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Yaks are crucial to local herders' economy and agriculture. However, several diseases pose a significant threat to the health of yaks and cause substantial economic losses for herders. Therefore, studying the immune indicators and breeding of yaks has become an important task. This study aimed to investigate the association between single nucleotide polymorphisms (SNPs) of the G protein-activated inwardly rectifying K+ channel 2 (KCNJ6, GIRK2) gene and yak immune indicators, with the goal of identifying potential candidate molecular markers for yak breeding. In this study, we genotyped 192 healthy adult yaks and detected three SNPs (g163684421 C > T, g163688148 C > T, and g163690745 T > C) in the yak KCNJ6 gene. These SNPs were found to be distributed in the yak population. Subsequently, we performed a linkage disequilibrium analysis and found that the linkage disequilibrium levels of g163684421 C > T and g163690745 T > C were relatively high. Through a correlation analysis of yak KCNJ6 gene SNPs and immune indicators, we found that g163684421 C > T and g163690745 T > C were significantly associated with IgA, IgG, IgM, CRP, HP, IL-2, IL-4, IFN-γ, and TNF-α (p < 0.05), and the mutation of these SNPs leads to a decrease in yak immune indicators. On the other hand, g163688148 C > T was significantly associated with IgG, IL-4, IFN-γ, TNF-α, IgA, CRP, and HP (p < 0.05), and the mutation of this SNP leads to an increase in yak immune indicators. In conclusion, we identified SNPs associated with yak immune indicators and found that KCNJ6 gene polymorphisms can serve as candidate molecular markers for yak immune indicators. This study provides valuable genetic resources for marker-assisted selection in yak breeding. The results of this study are of great importance for the research on yak immune indicators and marker-assisted selection in yak breeding. [ABSTRACT FROM AUTHOR]

Simple Summary: Yaks are indispensable economic animals in pastoral areas, providing local herdsmen with abundant necessities of life. Their meat is of excellent quality and highly favored by the market. As a newly cultivated breed, the Ashidan yak has been under continuous selection and breeding to improve its production performance, which is a long-term goal. The growth traits of yaks are crucial indicators of their economic benefits. Therefore, through the use of SNP molecular marker-assisted selection technology, the early and precise selection of yak growth traits can be achieved. This technology effectively accelerates the pace of genetic improvement and enhances breeding efficiency. The tyrosine protein kinase (TXK) gene, as a member of the non-receptor tyrosine kinase Tec family, plays a vital role in signal transduction mediation. Phospholipase C epsilon 1 (PLCE1), a membrane-associated enzyme, is of paramount importance for the differentiation of myoblasts and the normal functioning of muscle tissue. In recent years, both of these genes have been reported to be associated with the economic traits of animals. This study aimed to investigate the relationship between single nucleotide polymorphisms (SNPs) in the TXK and PLCE1 genes and growth traits in Ashidan yaks and to search for potential molecular marker loci that can influence Ashidan yak breeding. A cGPS liquid microarray was utilized to genotype 232 Ashidan yaks and to analyze correlations between two SNP loci in the TXK and PLCE1 genes and yak body weight, body height, body length, and chest circumference at different periods. The results indicated that the g.55,999,531C>T locus of the TXK gene and the g.342,350T>G locus of the PLCE1 gene were significantly correlated with the growth traits of Ashidan yaks. Among these, individuals with the CC genotype at the g.55,999,531C>T locus showed a significantly higher body length at 6 months old compared to TT individuals, and those with the CT genotype at 12 months old had a significantly higher chest circumference than TT individuals. At the g.342,350T>G locus, the body height of GG genotype individuals at 18 months of age was significantly higher than that of TT genotype individuals and TG genotype individuals. The above findings can be used as theoretical support for the subsequent improvement of Ashidan yak breeding. [ABSTRACT FROM AUTHOR]

The IQ motif containing GTPase activating protein 2 (IQGAP2) gene functions as a tumor suppressor, reducing the malignant properties of breast cancer cells. The circulating cartilage acidic protein 1 (CRTAC1) gene, present in the whey protein fraction of dairy cows throughout lactation, is significantly correlated with fatty acids in milk. In this study, we investigated the correlation between single nucleotide polymorphisms (SNPs) in the IQGAP2 and CRTAC1 genes and milk quality traits in Gannan yaks, aiming to identify potential molecular marker loci for enhancing milk quality. Using the Illumina Yak cGPS 7K liquid chip, we genotyped 162 yaks and identified five SNPs in the IQGAP2 (g.232,769C>G, g.232,922G>C) and CRTAC1 (g.4,203T>C, g.5,348T>G, g.122,451T>C) genes. Genetic polymorphism analysis revealed that these five SNPs were moderately polymorphic and in Hardy–Weinberg equilibrium. An association analysis results showed that, at the g.232,769C>G locus of the IQGAP2 gene, the heterozygous CG genotype had significantly higher lactose content than the CC and GG homozygous genotypes (p < 0.05). Similarly, at the g.232,922G>C locus, the heterozygous GC and mutant CC genotypes significantly increased the contents of milk fat, lactose, and total solids (TS) (p < 0.05). In the CRTAC1 gene (g.4,203T>C, g.5,348T>G, g.122,451T>C), the mutant CC genotype significantly increased milk fat content, while the heterozygous TG genotype significantly increased lactose content (p < 0.05). In summary, mutations at the loci of g.232,769C>G, g.232,922G>C, g.4,203T>C, g.5,348T>G, and g.122,451T>C significantly elevated the lactose, milk fat, and TS content in Gannan yak milk, providing potential molecular marker candidates for improving Gannan yak milk quality. [ABSTRACT FROM AUTHOR]

This study explored the polymorphism of the leucine aminopeptidase (LAP3) gene and its relationship with milk quality characteristics in Gannan yak. A cohort of 162 Gannan yak was genotyped utilizing the Illumina Yak cGPS 7K BeadChip, and the identified single nucleotide polymorphisms (SNPs) were evaluated for their association with milk protein, casein, lactose, and fat concentrations. The results showed that four SNPs (g.4494G > A, g.5919A > G, g.8033G > C, and g.15,615A > G) in the LAP3 gene exhibited polymorphism with information content values of 0.267, 0.267, 0.293, and 0.114, respectively. All four SNPs were in Hardy–Weinberg equilibrium (p > 0.05). The g.4494G > A and g.5919A > G SNPs were significantly associated with protein content (p < 0.05), with homozygous genotypes showing significantly higher protein content than heterozygous genotypes (p < 0.05). The g.8033G > C SNP was significantly associated with casein content, protein content, non-fat solids, and acidity (p < 0.05), with the CC genotype having significantly higher casein, protein, and non-fat solids content than the GG and GC genotypes (p < 0.05). The g.15,615A > G SNP was significantly associated with average fat globule diameter (p < 0.05). In general, the mutations within the LAP3 gene demonstrated a positive impact on milk quality traits in Gannan yak, with mutated genotypes correlating with enhanced milk quality. These results indicate that the LAP3 gene could be a significant or candidate gene affecting milk quality traits in Gannan yak and offer potential genetic markers for molecular breeding programs in this species. [ABSTRACT FROM AUTHOR]

Yak milk, known as the "liquid gold", is a nutritious food with extensive consumption. Compared with cow milk, yak milk contains higher levels of nutrients such as dry matter, milk fat, and milk protein, which demonstrates great potential for exploitation and utilization. Protein kinase cGMP-dependent 1 (PRKG1) is an important functional molecule in the cGMP signaling pathway, and its significant influence on milk fatty acids has been discovered. The aim of this study is to explore the correlation between single nucleotide polymorphisms (SNPs) in the PRKG1 gene and the quality traits of Gannan yak milk in order to identify candidate molecular markers for Gannan yak breeding. In this study, genotyping was performed on 172 healthy, 4–5-year-old lactating Gannan yaks with similar body types, naturally grazed, and two to three parity. Three SNPs (g.404195C>T, g.404213C>T, and g.760138T>C) were detected in the PRKG1 gene of Gannan yaks, which were uniformly distributed in the yak population. Linkage disequilibrium analysis was conducted, revealing complete linkage disequilibrium between g.404195C>T and g.404213C>T. After conducting a correlation analysis between SNPs in the PRKG1 gene and milk quality in Gannan yaks, we found that PRKG1 SNPs significantly increased the content of casein, protein, and SNFs in yak milk. Among them, the TT homozygous genotype at the PRKG1 g.404195C>T loci exhibited higher casein and protein contents compared to the CC and CT genotypes (p < 0.05). The SNP g.760138T>C locus was associated with casein, protein, SNFs, and TS traits (p < 0.05). The CC genotype had higher casein and protein contents than the TT and TA genotypes (p < 0.05). However, there were no significant differences in milk fat, lactose, and acidity among the three genotypes (p > 0.05). In summary, PRKG1 gene polymorphism can serve as a candidate molecular marker for improving milk quality in Gannan yaks. [ABSTRACT FROM AUTHOR]

A single-nucleotide polymorphism (SNP) is a genome-level trait that arises from a variation in a single nucleotide, leading to diversity in DNA sequences. SNP screening is commonly used to provide candidate genes for yak breeding efforts. Integrin Subunit Alpha 9 (ITGA9) is an integrin protein. It plays an important role in cell adhesion, signalling, and other processes. The aim of this study was to discuss the association between genetic polymorphisms in the ITGA9 gene and milk quality traits and to identify potential molecular marker loci for yak breeding quality. We genotyped 162 yaks using an Illumina Yak cGPS 7K liquid chip and identified the presence of polymorphisms at nine SNP loci in the ITGA9 gene of yaks. The results showed that the mutant genotypes in the loci g.285,808T>A, g.306,600T>C, and g.315,413C>T were positively correlated with the contents of casein, protein, total solids (TS), and solid nonfat (SNF) in yak milk. In other loci, heterozygous genotypes had a positive correlation with nutrient content in yak milk. Then, two ITGA9 haplotype blocks were constructed based on linkage disequilibrium, which facilitated a more accurate screening of ITGA9 as a candidate gene for yak milk quality improvement. In conclusion, we identified SNPs and haplotype blocks related to yak milk quality traits and provided genetic resources for marker-assisted selection in yak breeding. [ABSTRACT FROM AUTHOR]

Protein kinase D1 (PRKD1) functions primarily in normal mammary cells, and the potassium voltage-gated channel subfamily Q member 3 (KCNQ3) gene plays an important role in controlling membrane potential and neuronal excitability, it has been found that this particular gene is linked to the percentage of milk fat in dairy cows. The purpose of this study was to investigate the relationship between nucleotide polymorphisms (SNPs) of PRKD1 and KCNQ3 genes and the milk quality of Gannan yak and to find molecular marker sites that may be used for milk quality breeding of Gannan yak. Three new SNPs were detected in the PRKD1 (g.283,619T>C, g.283,659C>A) and KCNQ3 gene (g.133,741T>C) of 172 Gannan lactating female yaks by Illumina yak cGPS 7K liquid-phase microarray technology. Milk composition was analyzed using a MilkoScanTM milk composition analyzer. We found that the mutations of these three loci significantly improved the lactose, milk fat, casein, protein, non-fat milk solid (SNF) content and acidity of Gannan yaks. The lactose content of the TC heterozygous genotype population at g.283,619T>C locus was significantly higher than that of the TT wild-type population (p < 0.05); the milk fat content of the CA heterozygous genotype population at g.283,659C>A locus was significantly higher than that of the CC wild-type and AA mutant populations (p < 0.05); the casein, protein and acidity of the CC mutant and TC heterozygous groups at the g.133,741T>C locus were significantly higher than those of the wild type (p < 0.05), and the SNF of the TC heterozygous group was significantly higher than that of the mutant group (p < 0.05). The results showed that PRKD1 and KCNQ3 genes could be used as candidate genes affecting the milk traits of Gannan yak. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Simple Summary: The domesticated yak is among the most important livestock species on the Qinghai-Tibet Plateau. Breeders have the task of developing varieties that provide growth performance and disease resistance. Traditional breeding processes rely on complete family pedigree information and large numbers of data records. However, there are inevitably records that are missing, including incomplete pedigrees and long-term data tracking, resulting in prolonged breeding cycles, reduced breeding efficiency, and the lack of economic benefit. Genome selection (GS), also known as whole genomic selection (WGS), can significantly reduce the selection cycle of quantitative traits and accelerate genetic progression while displaying appropriate prediction accuracy (PA). It combines a reference population and single nucleotide polymorphism (SNP) loci rather than pedigrees to estimate the effect of all SNPs. Then breeding values of target traits are predicted. The key for GS is genomic prediction (GP) and an assessment of PA. The aim of this study was to explore the possibility of applying GP to important economic traits in the domesticated yak, thus providing theoretical support for its molecular breeding. A reference population was constructed consisting of 354 polled yaks, measuring four growth traits and eight hematological traits related to resistance to disease (involved in immune response and phagocytosis). The Illumina bovine HD 770k chip was used to obtain SNP information of all the individuals. With these genotypes and phenotypes, GBLUP, Bayes B and Bayes Cπ methods were used to predict genomic estimated breeding values (GEBV) and assess prediction capability. The correlation coefficient of the association of GEBV with estimated breeding value (EBV) was used as PA for each trait. The prediction accuracy varied from 0.043 to 0.281 for different traits. Each trait displayed similar PAs when using the three methods. Lymphocyte counts (LYM) exhibited the highest predictive accuracy (0.319) during all GP, while chest girth (CG) provided the lowest predictive accuracy (0.043). Our results showed moderate PA in most traits such as body length (0.212) and hematocrit (0.23). Those traits with lower PA could be improved by using SNP chips designed specifically for yak, a better optimized reference group structure, and more efficient statistical algorithms and tools. [ABSTRACT FROM AUTHOR]

• The CNV of the AHR gene was verified by the real-time quantitative PCR (qRT-PCR). • Copy number variations have greater effects on animal performance than single nucleotide polymorphisms. • AHR gene may be used as a new molecular marker in yak breeding. Copy number variation (CNV) is a principal genomic structure variation affecting the gene expression through the dose-effect and change of gene regulatory region. It plays an important role in regulating the various complex traits of vertebrates. The aromatic hydrocarbon receptor (AHR) is a member of ligand-dependent transcription factors which belong to the alkaline helix-loop-helix PASS family. It is used as a conservative environmental sensor during biological evolution. This study, tracked the growth data (body weight, withers height, body length, chest girth) of 332 yaks in four stages (6, 12, 18, and 30 months) were tracked. The CNV of the yaks was analyzed using real-time quantitative PCR, and the correlation between CNV of AHR and yak growth traits was analyzed using the SPSS and R software. The AHR gene expression profiles were assessed in different tissues of the 18-month-old yak. The statistical analysis indicated the AHR -CNV of the Ashidan yak to significantly correlate with the body length (P < 0.05), and was found to be correlated with the withers height at 18 months old (P < 0.01) with extreme significance. To sum up, this study for the first time discussed the relationship between AHR -CNV and the growth traits of the Ashidan yak. The results indicated that the AHR gene might become a new molecular marker in the breeding yak. [ABSTRACT FROM AUTHOR]