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Simple Summary: Yak is the dominant animal species in China's plateau regions. The development of the yak industry is conducive to protecting the ecosystem of the Qinghai–Tibet Plateau and promoting local economic development. However, the slow growth and development of yak have seriously affected the development of the yak industry. Structural variation (SV) has been widely applied in livestock breeding for growth traits. Therefore, it is of great significance to use SV to improve yak growth traits in yak breeding. Meanwhile, the GHR gene plays an important role in the formation and normal development of bones. This study associated the correlation between the yak GHR SV gene and growth traits and confirmed that GHR-SV can be used as a molecular marker for the early reproduction of yaks. This study provides a theoretical basis for the early growth and development of yaks. The growth hormone receptor (GHR) is a member of the cytokine/hematopoietic factor receptor superfamily, which plays an important role in the growth and development, immunity, and metabolism of animals. This study identified a 246 bp deletion variant in the intronic region of the GHR gene, and three genotypes, including type II, type ID, and type DD, were observed. Genotype analysis of structural variation (SV) was performed on 585 individuals from 14 yak breeds, and it was found that 246 bp deletion was present in each breed. The II genotype was dominant in all yak breeds except for SB yak. The association analysis of gene polymorphisms and growth traits in the ASD yak population showed that the 246 bp SV was significantly associated with body length at 6 months (p < 0.05). GHR messenger RNA (mRNA) was expressed in all the tested tissues, with significantly higher levels in the liver, muscle, and fat than in other organs. The results of transcription activity showed that the luciferase activity of the pGL4.10-DD vector was significantly higher than that of the pGL4.10-II vector (p < 0.05). Additionally, the transcription-factor binding prediction results showed that the SV in the runt-related transcription factor 1 (Runx1) transcription-factor binding site may affect the transcriptional activity of the GHR gene, regulating yak growth and development. This study showed that the novel SV of the GHR gene could be used as a candidate molecular marker for the selection of the early growth trait in ASD yak. [ABSTRACT FROM AUTHOR]

Simple Summary: Kecai yaks are an important genetic resource in Gansu Province, China. These yaks, produced through the crossbreeding of Gannan yaks and wild yaks, exhibit excellent production performance and high fecundity. Despite these beneficial characteristics, the genetic characteristics, population structure, and other properties of Kecai yaks have not been effectively characterized to date. Accordingly, this study was developed to explore the genetic diversity and population structure of Kecai yaks through whole-genome resequencing. These analyses ultimately revealed the status of Kecai yaks as an independent group within the overall Chinese yak population. Kecai yaks are regarded as an important genetic resource in China owing to their high fecundity and flavorful meat. However, the genetic characteristics of Kecai yaks have not been effectively characterized to date, and the relationship between Kecai yaks and other yak breeds remains to be fully characterized. In this paper, the resequencing of the Kecai yak genome is performed leading to the identification of 11,491,383 high-quality single nucleotide polymorphisms (SNPs). Through principal component, phylogenetic, and population genetic structure analyses based on these SNPs, Kecai yaks were confirmed to represent an independent population of yaks within China. In this study, marker and functional enrichment analysis of genes related to positive selection in Kecai yak was carried out, and the results show that such selection in Kecai yaks is associated with the adaptation to alpine environments and the deposition of muscle fat. Overall, these results offer a theoretical foundation for the future utilization of Kecai yak genetic resources. [ABSTRACT FROM AUTHOR]

Maiwa yak is a unique local strain of yak breed resource in China. The complete mitochondrial genome was identified in this work. The mitochondrial DNA is a circular molecule with 16,324 bp in length, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a non-coding control region(D-loop). The overall nucleotide ratio is A (33.70%), G (13.22%), T (27.26%), C (25.82%) with a C + G content of 39.04%. Phylogenetic analysis of mitochondrial genomes of 17 close species using MEGA7.0 showed that Maiwa yak is most related to Pali yak and polled yak. [ABSTRACT FROM AUTHOR]

Datong horse processes a muscular physique with high tolerance to extensive management and adapts well to high altitude conditions in Qinghai, China. In this study, the whole mitochondrial genome sequence of E. caballus determined using next-generation sequencing data was 16,654 bp in length, consisting of 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a non-coding control region. Notably, there was one tandem repeat with 21 'CACCTGTG' located in the control region. The base composition of the genome was A (32.3%), C (28.6%), G (13.3%), and T (25.8%), with an A + T content of 58.1%. Molecular phylogeny demonstrated that E. caballus was more closely related to a breed from central Asia and processed distinct relationships with some Chinese breeds. This work characterized the mitogenome of E. caballus (Datong horse breed) and present significant genetic information for this valuable specimen. [ABSTRACT FROM AUTHOR]

Sunan yak is one of the unique and indigenous yak species in China. The complete mitochondrial genome sequence of the Sunan yak was first determined in this study. The mitochondrial DNA is a circular molecule with 16,322 bp in length, containing 12 protein-coding genes, two rRNA genes, 22 tRNA genes and a noncoding control region (D-loop), showed a typical mammal pattern. The overall nucleotide composition is A (33.71%), T(27.26%), C(25.82%), G(13.21%) with an A + T content of 60.97%. Phylogenetic analysis based on the mitochondrial genomes of 12 related species using MEGA 5.0 indicated that Sunan yak was most closely related to Qinghai Plateau yak and Maiwa yak. [ABSTRACT FROM AUTHOR]

The Meiren yak is an important genetic resource in Gansu Province, China. In this study, we aimed to explore the evolutionary history and population structure of the genetic resource of Meiren yak and to mine the characteristic genes of Meiren yak. We analysed a total of 93 yaks of eight yak breeds based on whole genome resequencing combined with population genomics and used θπ ratio and Fst method to screen the selected sites in the genome region. The results proved that Meiren yak can be used as a potential genetic resource in Gansu Province. The genes in Meiren yak with positive selection in selection signal analysis were subjected to the Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses, which indicated that the genes were related to the adaptability to high altitude and hypoxic environment. By analysing the genetic variation of Meiren yak at the genome-wide level, this study provided a theoretical basis for genetic improvement of Meiren yak and for the development of high-quality yak resources.

Datong yak is a famous artificially cultivated breed in China. In the present work, we report the complete mitochondrial genome sequence of Datong yak for the first time. The total length of the mitogenome is 16,323 bp long, containing 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one non-coding region (D-loop region). The gene order of Datong yak mitogenome is identical to that observed in most other vertebrates. The overall base composition is 33.71% A, 25.8.0% C, 13.21% G and 27.27% T, with an A + T content of 60.98%. The complete mitogenome sequence information of Datong yak can provide useful data for further studies on molecular breeding and taxonomic status.