Short tandem repeats (STRs) are abundant and have high mutation rates across cattle genomes; however, comprehensive exploration of cattle STRs is needed. Here, we constructed a comprehensive map of 467 553 polymorphic STRs (pSTRs) constructed from 423 cattle genomes representing 59 breeds worldwide. We observed that pSTRs in coding sequences and 5'UTRs (Untranslated Regions) were under strong selective constraints and exhibited a relatively low level of diversity. Furthermore, we found that these pSTRs underwent more contraction than expansion. Population analysis showed a strong positive correlation (R = 1) between pSTR diversity and single nucleotide polymorphic heterozygosity. We also investigated STR differences between taurine and indicine cattle and detected 2301 highly divergent STRs, which might relate to immune, endocrine and neurodevelopmental pathways. In summary, our large-scale study characterizes the spectrum of STRs in cattle, expands the scale of known cattle STR variation and provides novel insights into differences among various cattle subspecies.

Structural variations (SVs) play crucial roles in the evolutionary adaptation of domesticated animals to natural and human-controlled environments, but SVs have not been explored in Tibetan cattle, which recently migrated and rapidly adapted to the high altitudes of the Qinghai-Tibetan Plateau (QTP). In this study, a de novo chromosome-level genome assembly for Tibetan cattle is constructed. It is found that using a lineage-specific reference genome significantly increased variant detection accuracy and completeness. Analysis of long-read sequencing data from 36 high-altitude QTP and 48 low-altitude cattle identified 222 528 SVs and 259 SV hotspot regions. Positively selected SVs in high-altitude cattle are related to energy metabolism erythropoiesis and angiogenesis, and peroxisomal metabolism. A 102-bp intronic deletion in GNPAT likely upregulated its expression. It is distinguished 7293 SVs that may be introgressed from yak, including variants upstream of the hypoxia-inducing gene EGLN1. Finally, a ≈2-Mb heterozygous inversion and two translocations on chromosome 6 are likely associated with the cattle gray coat via regulatory effects on the KIT gene. The results confirm the importance of SVs in evolutionary adaptation and the contribution yak-introgressed SVs to the rapid acclimatization of QTP cattle.

Keratins are the main structural protein components of wool fibres, and variation in them and their genes (KRTs) is thought to influence wool structure and characteristics. The PCR–single strand conformation polymorphism technique has been used previously to investigate genetic variation in selected coding and intron regions of the type II sheep keratin gene KRT81, but no variation was identified. In this study, we used the same technique to explore the 5′ untranslated region of KRT81 and detected three sequence variants (A, B and C) that contain four single nucleotide polymorphisms. Among the 389 Merino × Southdown cross sheep investigated, variant B was linked to a reduction in clean fleece weight, while C was associated with an increase in both greasy fleece weight and clean fleece weight. No discernible effects on staple length or mean-fibre-diameter-related traits were observed. These findings suggest that variation in ovine KRT81 might influence wool growth by changing the density of wool follicles in the skin, the density of individual fibres, or the area of the skin producing fibre, as opposed to changing the rate of extrusion of fibres or their diameter.

Qaidam cattle are a typical Chinese native breed inhabiting northwest China. They bear the characteristics of high cold and roughage tolerance, low-oxygen adaptability and good meat quality. To analyze the genetic diversity of Qaidam cattle, 60 samples were sequenced using whole-genome resequencing technology, along with 192 published sets of whole-genome sequencing data of Indian indicine cattle, Chinese indicine cattle, North Chinese cattle breeds, East Asian taurine cattle, Eurasian taurine cattle and European taurine cattle as controls. It was found that Qaidam cattle have rich genetic diversity in Bos taurus, but the degree of inbreeding is also high, which needs further protection. The phylogenetic analysis, principal component analysis and ancestral component analysis showed that Qaidam cattle mainly originated from East Asian taurine cattle. Qaidam cattle had a closer genetic relationship with the North Chinese cattle breeds and the least differentiation from Mongolian cattle. Annotating the selection signals obtained by composite likelihood ratio, nucleotide diversity analysis, integrated haplotype score, genetic differentiation index, genetic diversity ratio and cross-population extended haplotype homozygosity methods, several genes associated with immunity, reproduction, meat, milk, growth and adaptation showed strong selection signals. In general, this study provides genetic evidence for understanding the germplasm characteristics of Qaidam cattle. At the same time, it lays a foundation for the scientific and reasonable protection and utilization of genetic resources of Chinese local cattle breeds, which has great theoretical and practical significance.

Yak (Bos grunniens) is a unique livestock animal originating from the Qinghai-Tibet Plateau in China. In the current study, we investigated the maternal genetic diversity, differentiation and phylogeny of wild yak population and four domestic yak breeds (Qinghai-Gaoyuan, Huanhu, Xueduo, and Yushu) in Qinghai, China by analyzing 166 mitochondrial cytochrome b (Cytb) gene sequence variations. Our results indicated that the haplotype and nucleotide diversities of wild yak were 0.883±0.044 and 0.004±0.002, while the total haplotype and nucleotide diversities of four Qinghai domestic yak breeds were 0.646±0.040 and 0.003±0.001, respectively. Among the four Qinghai domestic yak breeds, the haplotype diversity was found to be highest in Yushu yak breed (Hd = 0.770±0.053), while the lowest was recorded in Huanhu yak breed (Hd = 0.501±0.088). Estimates of FST values showed a moderate genetic differentiation between wild yak and Huanhu yak (FST = 0.058) as well as that between Huanhu yak and Yushu yak breeds (FST = 0.052), but a weak genetic differentiation was observed between the other yak breeds/populations (-0.021＜FST＜0.037). Additionally, the clustering analysis based on RST values showed that Xueduo yak and Huanhu yak were clustered into one group, and each of the other three yak breeds/populations was separated into one group, respectively. Overall, the clustering relationship between wild yak and Yushu yak was closer. Maternal phylogenetic analysis showed that wild yak and four local yak breeds/populations in Qinghai represented in three maternal lineages (Mt-Ⅰ, Mt-Ⅱ, and Mt-Ⅲ), indicating three maternal origins in yak. Our study would provide valuable information for the conservation and utilization of wild yak and Qinghai domestic yak breeds.

The Qinghai Province of China is located in the northeast region of the Qinghai-Tibetan Plateau (QTP) and carries abundant yak genetic resources. Previous investigations of archaeological records, mitochondrial DNA, and Y chromosomal markers have suggested that Qinghai was the major center of yak domestication. In the present study, we examined the genomic diversity, differentiation, and selection signatures of 113 Qinghai yak, including 42 newly sequenced Qinghai yak and 71 publicly available individuals, from nine yak breeds/populations (wild, Datong, Huanhu, Xueduo, Yushu, Qilian, Geermu, Tongde, and Huzhu white) using high-depth whole-genome resequencing data. We observed that most of Qinghai yak breeds/populations have abundant genomic diversity based on four genomic parameters (nucleotide diversity, inbreeding coefficients, linkage disequilibrium decay, and runs of homozygosity). Population genetic structure analysis showed that Qinghai yak have two lineages with two ancestral origins and that nine yak breeds/populations are clustered into three distinct groups of wild yak, Geermu yak, and seven other domestic yak breeds/populations. F (ST) values showed moderate genetic differentiation between wild yak, Geermu yak, and the other Qinghai yak breeds/populations. Positive selection signals were detected in candidate genes associated with disease resistance (CDK2AP2, PLEC, and CYB5B), heat stress (NFAT5, HSF1, and SLC25A48), pigmentation (MCAM, RNF26, and BOP1), vision (C1QTNF5, MFRP, and TAX1BP3), milk quality (OPLAH and GRINA), neurodevelopment (SUSD4, INSYN1, and PPP1CA), and meat quality (ZRANB1), using the integrated PI, composite likelihood ratio (CLR), and F (ST) methods. These findings offer new insights into the genetic mechanisms underlying target traits in yak and provide important information for understanding the genomic characteristics of yak breeds/populations in Qinghai.

Nangqian grey yak (Bos grunniens) is a unique yak population in Qinghai Province, China. In this study, the whole mitogenome sequences of 18 Nangqian grey yaks were sequenced based on the next-generation sequencing (NGS) technology and annotated. The total length of whole mitogenome sequence is between 16.323 bp and 16.325 bp, including a non-coding control region (D-loop region), 22 tRNA genes, 13 protein-coding genes and two rRNA genes (12S rRNA and 16S rRNA). Maternal genetic diversity based on the mitogenome variations was analyzed. A total of 12 haplotypes were identified among 18 complete mitogenome sequences, the haplotype diversity and nucleotide diversity of Nangqian grey yak were 0.948±0.033 and 0.001±0.001, respectively. Compared with the wild yak population and six other domestic yak breeds/populations in China, the haplotype diversity of Nangqian grey yak population was higher, indicating abundant maternal genetic diversity in Nangqian grey yak. The phylogenetic tree showed that Nangqian grey yak was most closely related to Tibet alpine, Xueduo, Changtai, Sibu, Zhongdian, Tianzhu white, Ashdan, Jinchuan, Jiulong, Pamir, Pali, Qinghai plateau, Huanhu, Datong, Bazhou and wild yak breeds/populations, closer to Chawula, Muli, Gannan, Niangya and Yushu yak breeds, but far away from other yak breeds (i.e. Leiwuqi and Maiwa yak).

Yaks are tough animals living in Tibet's hypoxic stress environment. However, the metabolite composition of yak milk and its role in hypoxic stress tolerance remains largely unexplored. The similarities and differences between yak and human milk in hypoxic stress tolerance are also unclear. This study explored yak colostrum (YC) and yak mature milk (YMM) using GC-MS, and 354 metabolites were identified in yak milk. A comparative metabolomic analysis of yak and human milk metabolites showed that over 70% of metabolites were species-specific. Yak milk relies mainly on essential amino acids- arginine and essential branched-chain amino acids (BCAAs): L-isoleucine, L-leucine, and L-valine tolerate hypoxic stress. To slow hypoxic stress, human breast milk relies primarily on the neuroprotective effects of non-essential amino acids or derivates, such as citrulline, sarcosine, and creatine. In addition, metabolites related to hypoxic stress were significantly enriched in YC than in YMM. These results reveal the unique metabolite composition of yak and human milk and provide practical information for applying yak and human milk to hypoxic stress tolerance.

BackgroundStructural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine and indicine origins that have evolved to adapt to cold and hot environments, respectively. However, few studies have investigated SVs in East Asian cattle genomes and their roles in environmental adaptation, and little is known about adaptively introgressed SVs in East Asian cattle.ResultsIn this study, we examine the roles of SVs in the climate adaptation of these two cattle lineages by generating highly contiguous chromosome-scale genome assemblies. Comparison of the two assemblies along with 18 Mongolian and Hainan cattle genomes obtained by long-read sequencing data provides a catalog of 123,898 nonredundant SVs. Several SVs detected from long reads are in exons of genes associated with epidermal differentiation, skin barrier, and bovine tuberculosis resistance. Functional investigations show that a 108-bp exonic insertion in SPN may affect the uptake of Mycobacterium tuberculosis by macrophages, which might contribute to the low susceptibility of Hainan cattle to bovine tuberculosis. Genotyping of 373 whole genomes from 39 breeds identifies 2610 SVs that are differentiated along a "north-south" gradient in China and overlap with 862 related genes that are enriched in pathways related to environmental adaptation. We identify 1457 Chinese indicine-stratified SVs that possibly originate from banteng and are frequent in Chinese indicine cattle.ConclusionsOur findings highlight the unique contribution of SVs in East Asian cattle to environmental adaptation and disease resistance.

Qaidam cattle (CDM) are indigenous breed inhabiting Northwest China. In the present study, we newly sequenced 20 Qaidam cattle to investigate the copy number variants (CNVs) based on the ARS-UMD1.2 reference genome. We generated the CNV region (CNVR) datasets to explore the genomic CNV diversity and population stratification. The other four cattle breeds (Xizang cattle, XZ; Kazakh cattle, HSK; Mongolian cattle, MG; and Yanbian cattle, YB) from the regions of North China embracing 43 genomic sequences were collected and are distinguished from each of the other diverse populations by deletions and duplications. We also observed that the number of duplications was significantly more than deletions in the genome, which may be less harmful to gene formation and function. At the same time, only 1.15% of CNVRs overlapped with the exon region. Population differential CNVRs and functional annotations between the Qaidam cattle population and other cattle breeds revealed the functional genes related to immunity (MUC6), growth (ADAMTSL3), and adaptability (EBF2). Our analysis has provided numerous genomic characteristics of some Chinese cattle breeds, which are valuable as customized biological molecular markers in cattle breeding and production.

The study aimed to investigate the genetic diversity and evolutionary relationships of the sires from Qaidam cattle and Mongolian cattle at genomic level. In this study, the whole genome resequencing was used to scan the Y-chromosome single copy gene regions of a total of 22 individuals from 5 different geographical populations of the Qaidam cattle and 23 individuals from Mongolian cattle, and their paternal genetic diversity and phylogenetic relationship were analyzed using bioinformatics methods. The results showed that a total of 4 haplotypes were defined in 22 Qaidam cattle, with a haplotype diversity of 0.610±0.093 and a nucleotide diversity of 0.074±0.015, whereas a total of 10 haplotypes were identified in 23 Mongolian cattle, with a haplotype diversity of 0.925±0.025 and a nucleotide diversity of 0.137±0.013, indicating that Qaidam cattle had lower paternal genetic diversity compared to Mongolian cattle. The phylogenetic tree and haplotype network diagrams constructed showed that the 22 Qaidam cattle were clearly divided into two haplogroups, namely Y1（18.2%） and Y2（81.8%）, of which Y2 was the dominant haplogroup, and the Y2 haplogroup included two sub-haplogroups, namely Y2a（18.2%） and Y2b（63.6%）, of which the Y2b sub-haplogroup was dominant, indicating that the Qaidam cattle had both Y1 and Y2 paternal origins. Mongolian cattle also had both Y1（17.4%） and Y2（82.6%） paternal origins, but the Y2 haplogroup was dominated by the Y2a sub-haplogroup（47.8%）. The above results suggest that Qaidam and Mongolian cattle have similar paternal genetic composition. However, considering the lower paternal genetic diversity of Qaidam cattle, it is suggested to increase the gene exchange of bulls from different populations within this breed for improving their genetic diversity. This study provides a theoretical basis for clarifying the paternal genetic differences between Qaidam cattle and Mongolian cattle, and for the conservation and exploitation of their germplasm resources.

As a calcium-binding protein,calcyphosine(CAPS)plays an important role in maintaining the balance of calcium and phosphorus in vivo.In this study,the CDS region of yak CAPS gene was cloned,its nucleo-tide sequence was analyzed,and bioinformatics analysis was carried out.Results showed that the CDS region of CAPS gene was 570 bp long and encoded 189 amino acids.The formula,molecular weight,theoretical pI,aliphat-ic index,instability index of the encoded protein was C905 H1434 N266 O297 S8,21 049.43 Da,4.69,75.29 and 37.52,respectively,which suggested it was a stable fat-soluble protein.Phylogenetic analysis showed that the CDS region of CAPS gene in yak had the highest similarity with that of common cattle and Zebu,with higher simi-larity with buffalo,sheep and pig.This study provided reference datafor further study on the physiological function of CAPS in yak.

为探究柴达木黄牛的母系遗传多样性及遗传背景,本研究随机选取柴达木黄牛5个主产区268个个体,通过PCR方法和直接测序技术得到其mtDNA Cyt b基因全序列,使用生物信息学软件分析其遗传多样性、分化及母系起源,进而在分子水平上揭示其母系遗传多样性水平、分化程度及母系遗传背景.结果表明:柴达木黄牛Cyt b基因核苷酸序列长度为1140 bp,比对分析共检测到29个核苷酸多态位点,其中单一多态位点4个,简约信息位点25个;依据序列间核苷酸变异共确定了12种单倍型,其中优势单倍型为H2,品种单倍型多样度为0.5882±0.0300,核苷酸多样度为0.0040±0.0022,表明柴达木黄牛具有较丰富的母系遗传多样性.柴达木黄牛品种内5个群体间分化指数Fst值在-0.0104～0.1618,提示品种内群体间分化程度存在差异,其中格尔木群体与乌兰群体间分化程度最大(Fst=0.1618),大柴旦群体和茫崖群体间的分化程度最小(Fst=-0.0104).基于UPGMA法的品种内群体间聚类关系表明,柴达木黄牛品种内5个群体可聚为2类,其中格尔木群体与都兰群体最先聚在一起,大柴旦群体与茫崖群体也最先聚为一起,随后它们再聚为1类,而乌兰群体单独为另一类,2类最后聚为一大类.系统发育分析表明,柴达木黄牛由普通牛和瘤牛2个母系遗传支系组成,表明柴达木黄牛有普通牛和瘤牛2个母系起源且以普通牛起源为主.此外,研究发现,茫崖、乌兰、都兰各群体均有1个个体为牦牛mtDNA Cyt b单倍型序列类型,占总头数的1.12％,提示柴达木黄牛品种中存在一定程度的牦牛基因渗入.

微卫星或简单序列重复(SSRs)广泛分布于真核生物基因组中,其在物种基因组结构组成和功能中发挥着重要作用.本研究以 2021 年报道的牦牛(Bos grunniens)Y染色体基因组序列为研究对象,利用生物信息学方法系统分析了其单纯型微卫星的丰度状况.结果表明,在牦牛Y染色体基因组(26.36 Mb)中共发现 12699 个 1～6 个碱基重复的单纯型SSRs,总长为 0.33 Mb,平均长度为 25.68 bp,相对频率和相对密度分别为 481.77 loci/Mb和 12371.73 bp/Mb,提示牦牛Y染色体基因组包含约 1.25％的单纯型SSRs.6 类单纯型SSRs在牦牛Y染色体上分布不均匀,其中二碱基重复的SSRs最为丰富,总数为 5835 个(45.95％),平均长度为27.82 bp,而单碱基和三、四、五、六碱基重复的SSRs所占比例分别为29.79％、9.66％、8.81％、5.57％和 0.22％.不同类别的单纯型SSRs其不同重复单元的重复次数存在差异,其中以A、AC、AAC等为重复单元的单纯型SSRs在牦牛Y染色体上所含比例相对较高;各重复单元重复次数的范围分别集中在12～20次(单碱基)、7～21 次(二碱基)、5～10 次(三碱基)、4～8 次(四碱基)、4～5 次(五碱基)和 4～8 次(六碱基).本研究结果为深入了解牦牛Y染色体基因组重复DNA序列组成和特征特别是单纯型SSRs的丰度状况提供了参考,为后续探明牦牛Y染色体基因组结构组成和发掘牦牛Y染色体特异性SSRs标记、构建Y染色体遗传图谱等奠定了基础.

抗缪勒管激素(AMH)是一种主要由睾丸支持细胞和卵巢颗粒细胞分泌的生殖激素,在胎儿生殖器官发育、精子生成、卵泡发生等生物学过程中起着重要作用.本文从牛AMH的结构与生理功能、母牛血液AMH浓度的影响因素以及AMH在母牛繁殖中的应用等方面进行了综述.

旨在从分子水平上探究野牦牛及青海地方牦牛品种的母系遗传多样性、群体遗传结构、亲缘关系和遗传背景.本研究在测定青海省4个地方牦牛品种(即青海高原、环湖、雪多和玉树牦牛)22条全线粒体基因组(Mitoge-nome)序列的基础上,从GenBank下载了已公布的野牦牛及上述4个地方牦牛品种的142条相应序列,使用BioEdit 7.2.5、Arlequin 3.11和Network 10.1等软件对共计164条线粒体基因组序列进行综合分析.结果显示:1)根据序列间核苷酸变异共确定了 115种单倍型,其中野牦牛和青海地方牦牛品种分别拥有22种和93种单倍型;在野牦牛和青海高原、环湖、雪多、玉树牦牛中分别检测到22、26、18、23、19种特有的单倍型.遗传多样性分析显示,野牦牛单倍型多样度最高(0.992 8±0.014 4),且高于4个青海地方牦牛品种的单倍型多样度(0.973 1±0.007 7);4个青海地方牦牛品种单倍型多样度大小依次为:雪多牦牛(0.988 5士0.012 6)、玉树牦牛(0.975 8士0.018 7)、青海高原牦牛(0.973 0±0.016 6)和环湖牦牛(0.939 3±0.027 8).2)野牦牛与环湖牦牛之间的固定分化指数值(FsT值)最大(0.041 2),分化程度最高,而与玉树牦牛间的FST值最小(-0.008 8),分化程度最低.青海4个地方牦牛品种中,雪多牦牛与青海高原牦牛之间F ST值最大(0.035 8),分化程度最高,而雪多牦牛与环湖牦牛间FST值最小(0.011 2),分化程度最低.3)聚类分析显示,4个青海地方牦牛品种各自为1类,存在明显的母系遗传差异.相比而言,环湖牦牛和雪多牦牛聚类较近,青海高原牦牛和玉树牦牛聚类较近,而野牦牛与玉树牦牛聚类关系更近,各品种(群体)间的聚类结果与其分化程度、地理分布一致.4)系统发育分析表明,115种单倍型分布在3个大的母系遗传分支(即Mt-Ⅰ、Mt-Ⅱ和Mt-Ⅲ),其中Mt-Ⅰ支系所占比例为72.17％,由A、B、E和F 4种单倍型组构成;Mt-Ⅱ支系包括C、D和H 3种单倍型组,占26.09％;而Mt-Ⅲ支系只包含G单倍型组,由雪多牦牛和野牦牛所拥有,所占比例为1.74％,提示牦牛有3个母系起源.综上所述,野牦牛和青海4个地方牦牛品种均具有丰富的母系遗传多样性,其多样性水平由高到低依次为野牦牛、雪多牦牛、玉树牦牛、青海高原牦牛和环湖牦牛.青海4个地方牦牛品种间及与野牦牛间的遗传分化程度均较弱,但各自拥有特有的母系遗传信息,存在明显的母系遗传差异.野牦牛和青海家牦牛品种由3个母系支系组成,推测牦牛有3个母系起源.

High-altitude stress threatens the survival rate of Tibetan sheep and reduces their fertility. However, the molecular basis of this phenomenon remains elusive. Here, we used RNA-seq to elucidate the transcriptome dynamics of high-altitude stress in Tibetan sheep ovaries. In total, 104 genes were characterized as high-altitude stress-related differentially expressed genes (DEGs). In addition, 36 DEGs contributed to ovarian follicle development, and 28 of them were downregulated under high-altitude stress. In particular, high-altitude stress significantly suppressed the expression of two ovarian lymphatic system marker genes: LYVE1 and ADAMTS-1. Network analysis revealed that luteinizing hormone (LH)/follicle-stimulating hormone (FSH) signaling-related genes, such as EGR1, FKBP5, DUSP1, and FOS, were central regulators in the DEG network, and these genes were also suppressed under high-altitude stress. As a post-transcriptional regulation mechanism, alternative splicing (AS) is ubiquitous in Tibetan sheep. High-altitude stress induced 917 differentially alternative splicing (DAS) events. High-altitude stress modulated DAS in an AS-type-specific manner: suppressing skipped exon events but increasing retained intron events. C2H2-type zinc finger transcription factors and RNA processing factors were mainly enriched in DAS. These findings revealed high-altitude stress repressed ovarian development by suppressing the gene expression of LH/FSH hormone signaling genes and inducing intron retention of C2H2-type zinc finger transcription factors.

为从分子水平上揭示青海省囊谦青牦牛的母系遗传多样性、群体结构及遗传背景,对31头囊谦青牦牛mtDNA D-loop区序列进行PCR扩增、测序和序列比对分析,确定序列变异位点和单倍型数目,计算单倍型多样度和核苷酸多样度大小,并进行系统发育分析.结果表明,在囊谦青牦牛618 bp D-loop区序列分析中,共检测到34个多态位点,包括8个单一多态位点和26个简约信息位点.根据序列间核苷酸变异共确定了12种单倍型,单倍型多样度和核苷酸多样度分别为0.846±0.055和0.011±0.005.与野牦牛及我国其他18个家牦牛品种相比,囊谦青牦牛群体核苷酸多样度和单倍型多样度值均较低,表明囊谦青牦牛母系遗传多样性水平较低.以美洲野牛为外群构建的系统发育树结果显示,囊谦青牦牛群体的12种单倍型分布在3种单倍型组A、C、D中,且聚为2个大的分支,提示囊谦青牦牛由2个母系支系组成,拥有2个母系起源.综上,囊谦青牦牛群体母系遗传多样性较低,由2个母系支系组成,推测其有2个母系起源.

进入21世纪后,牦牛种质分子特性研究成为牦牛科学研究的热点,取得了许多新成果.该文以近年来的研究成果为主线,综合分析了牦牛种质资源的现状与特点、研究进展以及研究和开发利用中存在的问题,并探讨了其对策和措施,以便为今后合理开发利用牦牛种质资源提供理论依据.

The white yak, a type of unique and valuable farm animals on the Qinghai-Tibet Plateau, are mainly distributed in Tianzhu (County of Gansu Province), Menyuan, Huzhu and Ledu (three Counties of Qinghai Province) in China. In the present study, the Y-chromosomal genetic diversity, differentiation and phylogeny of three Chinese white yak breeds/populations (Tianzhu, Huzhu and Menyuan) were comprehensively explored using five Y-SNPs ( SRY4 , USP9Y , UTY19 , AMELY3 and OFD1Y10 ) and one Y-STR ( INRA189 ) markers. The results showed that six Y-haplotypes (H1Y1, H9Y1, H10Y1, H11Y2, H12Y2 and H13Y2) were identified in 97 male yak from three white yak breeds/populations. Among these haplotypes, H1Y1, H10Y1 and H11Y2 were shared by all of breeds/populations and H12Y2 was shared by Tianzhu and Huzhu populations. However, H9Y1 and H13Y2 haplotypes were only detected in Menyuan and Tianzhu white yak populations, respectively. The Y-haplotype diversity was maximum in Huzhu white yak (0.7500 ± 0.0349), the medium in Tianzhu white yak (0.6881 ± 0.0614) and the lowest in Menyuan white yak (0.5720 ± 0.0657). The total Y-haplotype diversity of three white yak breeds/populations was 0.7567 ± 0.0233, indicating rich paternal genetic diversity in white yak. The F ST values showed a moderate differentiation between Tianzhu and Menyuan ( F ST = 0.0763, P < 0.05) populations, but a weak differentiation between Huzhu and Tianzhu white yak breeds/populations ( F ST = 0.0186, P > 0.05) and Huzhu and Menyuan ( F ST = − 0.005, P > 0.05) populations. The clustering analysis revealed a close genetic relationship between Huzhu and Menyuan white yak, both were far from Tianzhu white yak breed. The phylogenetic analyses showed that white yak had two Y-haplogroups/lineages (Y1 and Y2) with two potential paternal origins. The findings of present study provide new insight into the basic information for the formulation of molecular breeding programs of white yak. Moreover, it also contributes to the conservation and utilization of this special animal genetic resource.