Pangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks

Background The genetic diversity of yak,a key domestic animal on the Qinghai-Tibetan Plateau(QTP),is a vital resource for domestication and breeding efforts.This study presents the first yak pangenome obtained through the de novo assembly of 16 yak genomes.Results We discovered 290 Mb of nonreference sequences and 504 new genes.Our pangenome-wide presence and absence variation(PAV)analysis revealed 5,120 PAV-related genes,highlighting a wide range of variety-specific genes and genes with varying frequencies across yak populations.Principal component analysis(PCA)based on binary gene PAV data classified yaks into three new groups:wild,domestic,and Jinchuan.Moreover,we pro-posed a‘two-haplotype genomic hybridization model'for understanding the hybridization patterns among breeds by integrating gene frequency,heterozygosity,and gene PAV data.A gene PAV-GWAS identified a novel gene(Bos-Gru3G009179)that may be associated with the multirib trait in Jinchuan yaks.Furthermore,an integrated transcrip-tome and pangenome analysis highlighted the significant differences in the expression of core genes and the muta-tional burden of differentially expressed genes between yaks from high and low altitudes.Transcriptome analysis across multiple species revealed that yaks have the most unique differentially expressed m RNAs and lnc RNAs(between high-and low-altitude regions),especially in the heart and lungs,when comparing high-and low-altitude adaptations.Conclusions The yak pangenome offers a comprehensive resource and new insights for functional genomic studies,supporting future biological research and breeding strategies.

Effect of Nitrogenous Fertilizer Treatment on Mineral Metabolism in Grazing Yaks

To assess the impact of N fertilization on contents of mineral elements in herbage and the effect of increased forage S on the copper metabolism of grazing yaks, study was conducted during the summer grazing season （2005, 2006, and 2007）. Pasture replicates （20 ha; n=3 per treatment） received the same fertilizer treatment in each growing season, consisting of i） 90 kg N ha^-1 from quickly available nitrogen, ii） 90 kg N ha^-1 from ammonium nitrate, iii） 90 kg N ha^-1 from ammonium sulfate, and iv） control （no fertilizer）. Forage sampling was collected at 60 days intervals following fertilization （10 samples per pasture） for Cu, Mo, Mn, Se, Fe, Zn, Ca, and P. To determine the effect of fertilizer treatment on mineral metabolism in grazing yaks, liver and blood samples were collected at the start and end of the study period in 2005, 2006, and 2007. Ammonium sulfate fertilization increased （P 〈 0.01） forage S concentration. Plant tissue N concentrations were increased by N fertilization, regardless of source in 2005, 2006, and 2007. Yaks grazing S fertilization pastures had lower （P〈0.05） liver and blood Cu concentrations at the end of the study period in 2005, 2006, and 2007, compared with urea, ammonium nitrate, and control. Nominal increases in forage in vitro organic matter digestibility were realized by fertilization, regardless of N source in each year.

Study on the Correlation between Blood Enzyme Activity and Production Performance in Tibetan Yaks

Yak ( Bos grunniens ) is classified as Bovine genus,they live in Qingzang Plateau with elevation more than 3500m and it's neighbor highland,where the weather is high chilly,short of oxygen and large difference of temperature between day and night.But yak have adapted that circumstance after thousands of years' artificial and natural selection and has great anti adversity capacity.Yak is an important sustenance and means of production to Tibetan.China is a country with the largest number of yak,whose amount of livestock on hand accounts for 95% of the world and Tibet region takes the second place next to Qinghai in the number of yak.Tibetan yak has formed some groups for Tibetan's large area,complicated geological ecosystem conditions,geological isolation.The typical better groups are Yadong yak,Jiali yak and Sibu yak. Study about yak fell behind other animals due to the restriction of inconvenient transportation,difficult sampling and poor experimental technology.Study about the relationship between yak blood enzyme activities and milk production was little,only Jing (1992) studied correlation of milk production with serum amylase,esterase in Gansu Jiulong yak,Maiwa yak and no report was found in other groups.This study discussed six Jiali yak blood enzyme activities lactate dehydrogenase (LDH),alkaline phosphatases (AKP),acid phosphatase (ACP),catalase (CAT),amylase (Amy) and superoxide dismutase (SOD),and explored their relationship with milk production in Jiali yak,so as to supply with theoretical evidence by using blood enzyme activity as biochemical assisted selection marker in the breeding of Tibetan yak milk yield. This experiment investigated activity of six blood enzymes from 28 Tibetan yaks and explored its relationship to production performance.The results showed a extremely positive significant difference ( P <0.01) between activity of LDH and milk yield,CAT activity and length of belly hair respectively,while a positive significant difference ( P <0.05) was observed between AKP activity and body weight,Amy activity and body weight and a negative significant difference ( P <0.05) for SOD activity and body weight.Stepwise Regression Analysis showed that activity of LDH could be used for the prediction of milk yield,AKP,CAT,Amy for body weight,CAT,Amy for length of belly hair.So it is expected to use activity of LDH,AKP,CAT,Amy as biochemical genetic marker in the selection of milk yield,body weight and length of belly hair.

Confinement and Semi-confinement Raising Fattening Technology of Yaks in Agricultural Areas of Tibet

In the study, confinement and semi-confinement raising fattening technology of yaks in agricultural areas of tibet were analyzed. And several suggestions for improving the efficiency of yak raising were put forward. Aiming at providing the reference of healthy raising and sustainable development of yaks in the agricul- tural areas of tibet.

Meat Production from Crossbred and Domestic Yaks in China

Female domesticated yaks were artificially inseminated with semen taken from wild yaks and the offspring used to form a nucleus breeding herd of crossbred animals. The meat production of the first generation(F1 × F2)from breedtng within the nucleus herd was assessed by slaughter and carcass dissection of males. One group(no. =14)was slaughtered at 6 months of age and the second(no. = 12)at 18months. Crossbred yaks were significantly heavier(P＜0.01)at 6 months(74.7(s. e. 10.41)kg v. 59.8(s.e. 10.23)kg)and at 18 months(150.5(s. e. 56.1)kg v. 117.7(s. e. 17.4)kg)than domesticated ones,The killing-out proportion(0.47)was similar at both ages and for both groups of animals. Carcass weight,meat weight and the yield of prime cuts were higher for crossbred animals than for domestic yak at both ages.

The Milking Performance of dual-purpose Crossbred Yaks

Wild yak males were crossed with domesticated female yaks to produce a breeding herd of crossbred animals. The milk production of the progeny of this herd was measured in the present study. Yaks were milked once daily after prior suckling of the calf. yaks were allowed to graze for 15 h/day on high-altitude(3200 to 3500 m) pastures. No supplementary food was given. Average daily milk yield of 1.77(s. e. 0. 16)kg and milk yield over 120 days,212.2(s. e. 20.2)kg were significantly higher(P＜0.01)than the corresponding figures for uninlproved domestic yaks(1.53(s. e. 0. 10)kg and 164. 6(s. e. 10.5)kg respectively). The fat content of milk from crossbred yaks, 52(s. e. 2. 9)g/kg, was not significantly dlfferent from that of unimproved animals, 53.5(s. e. 4. 1), g/kg.

YAKS710-4 6300kW 6kV高压增安型三相异步电动机的研制

介绍了YAKS71 0 - 4 630 0kW 6kV高压增安型三相异步电动机的研制过程、性能指标及防爆安全性等 ,对该电动机的技术经济性进行了分析 ,并提出了非防爆型避雷器、电容器在防爆危险区域内应用所采取的措施。

Domestication process of yaks revealed

In his monumental work “Origin of Species,” Charles Darwin suggested that all domestic animals originated from their wild an-

Improving the Breed of Yaks

Yaks live in high frigid areas some 3,000-5,000 meters above sea level.In China there are 13 million yaks,making up 90 percent of the world total.They provide with transport means,meat and hide for 4.6 Tibe-tans in Tibet as well as Qinghai,Sichuan,Yunnan and Gansu prov-inces.

Potential antibacterial activity of berberine against multi drug resistant enterovirulent Escherichia coli isolated from yaks(Poephagus grunniens) with haemorrhagic diarrhoea

Objective:To evaluate the antimicrobial efficacy of berberine,a plant alkaloid.Methods:Five multi-drug resistant（MDR） STEC/EPEC and five MDR ETEC isolates from yaks with haemorrhagic diarrhoea were selected for the study.Antibacterial activity of berberine was evaluated by broth dilution and disc diffusion methods.The binding kinetics of berberine to DNA and protein was also enumerated.Results:For both categories of enterovirulent Escherichia coli（E.roli） isolates, berberine displayed the antibaclerial effect in a dose dependent manner.The MIC50 of berberine chloride for STEC/EPEC isolates varied from 2.07μM to 3.6μM with a mean of（2.95±0.33）μM where as for ETEC strains it varied from 1.75 to 1.96μM with a mean of（1.87±0.03）μM. Berberine bind more tightly with double helix DNA with Bmax and Kd of（24.68±2.62） and（357.8±57.8）,respectively.Berberine reacted with protein in comparatively loose manner with Bmax and Kd of（18.9±3.83） and 【286.2±113.6),respectively.Conclusions:The results indicate clearly that berberine may serve as a good antibacterial against multi drug resistant E.coli.

Comparison of rumen archaeal diversity in adult and elderly yaks(Bos grunniens)using 16S rRNA gene high-throughput sequencing

This study was conducted to investigate the phylogenetic diversity of archaea in the rumen of adult and elderly yaks. Six domesticated female yaks, 3 adult yaks （（5.3±0.6） years old）, and 3 elderly yaks （（10.7±0.6） years old）, were used for the rumen contents collection. Illumina MiSeq high-throughput sequencing technology was applied to examine the archaeal composition of rumen contents. A total of 92 901 high-quality archaeal sequences were analyzed, and these were assigned to 2 033 operational taxonomic units （OTUs）. Among these, 974 OTUs were unique to adult yaks while 846 OTUs were unique to elderly yaks; 213 OTUs were shared by both groups. At the phylum level, more than 99% of the obtained OTUs belonged to the Euryarchaeota phylum. At the genus level, the archaea could be divided into 7 archaeal genera. The 7 genera （i.e., Methanobrevibacter, Methanobacterium, Methanosphaera, Thermogymnomonas, Methanomicrobiu, Meth- animicrococcus and the unclassified genus） were shared by all yaks, and their total abundance accounted for 99% of the rumen archaea. The most abundant archaea in elderly and adult yaks were Methanobrevibacterand Thermogymnomonas, respectively. The abundance of Methanobacteria （class）, Methanobacteriales （order）, Methanobacteriaceae （family）, and Methanobrevibacter （genus） in elderly yaks was significantly higher than in adult yaks. In contrast, the abundance of Ther-mogymnomonas in elderly yaks was 34% lower than in adult yaks, though the difference was not statistically significant. The difference in abundance of other archaea was not significant between the two groups. These results suggested that the structure of archaea in the rumen of yaks changed with age. This is the first study to compare the phytogenetic differences of rumen archaeal structure and composition using the yak model.

Sulfur-Induced Copper Deficiency in the Yaks

Since the 1990s, yak in the Haizi area in China has been affected by an ailment characterized by pica, emaciation, dyskinesia, and anemia. To determine the cause of disease, the mineral composition of soil and forages, and samples of blood, hair, and liver of yaks from the Haizi area in China were determined. The concentrations of copper in soil and forage from affected ranches and unaffected areas are within the normal ranges. The mean concentration of copper in blood and liver from the affected yaks was （0.31±0.03） and （13.7±3.1）μg·g^-1 respectively, compared with （0.98±0.16） and （95.6±11.2）μg·g^-1 for unaffected yaks. The concentrations of sulfur in soil and forage from affected ranches were （1.91±0.26） and （1.37±0.17）%, respectively, compared with （1.11±0.31） and （0.52±0.18）% （dry matter） for normal areas. The contents of sulfur in blood and liver affected animals were （7.32±1.8） and （2.54±3.1）%, respectively, compared with （4.22±0.73） and （1.31±0.33）% （in fresh and soft tissues） for healthy animals, respectively. Oral administration of tribasic copper chloride prevented and cured the disease. Thus it is reasonable to conclude that ailments of yaks in the Haizi area are probably caused by a secondary copper deficiency, mainly due to high sulfur content in soil and forage.

Morphological Observation on the Test and Epididymis in Hybrid of Wild and Domestic Yaks During the Growth Periods

This paper was carried out on the morphological character of the test and epididymis of three types of yak bull age 6,12,18,24 months old (1/2 wild yak, cross 1/2 wild yak and domestic yak). The results showed that the weight and size of testes and epidiymis was increased with the age which was hardly affected by imbalance of food supply during the cold and warm seasons. The development were similar for three kinds of yak at the same age(P＞0.05).

A comparison of average daily gain,apparent digestibilities,energy balance,rumen fermentation parameters,and serum metabolites between yaks(Bos grunniens)and Qaidam cattle(Bos taurus)consuming diets differing in energy level

Yaks(Bos grunniens),indigenous to the harsh Qinghai-Tibetan Plateau,are well adapted to the severe conditions,and graze natural pasture without supplements all year round.Qaidam cattle(Bos taurus),introduced to the Qinghai-Tibetan Plateau 1,700 years ago,are raised at a lower altitude than yaks,provided with shelter at night and offered supplements in winter.Based on their different backgrounds,we hypothesized that yaks have lower energy requirements for maintenance than cattle.To test this hypothesis,we measured average daily gain(ADG),apparent digestibilities,energy balance,rumen fermentation parameters,and serum metabolites in growing yaks and cattle offered diets differing in metabolizable energy(ME)levels(6.62,8.02,9.42 and 10.80 MJ/kg),but with the same crude protein concentration.Six castrated yaks(155±5.8 kg)and 6 castrated Qaidam cattle(154±8.0 kg),all 2.5 years old,were used in 2 concurrent 4×4 Latin square designs.Neutral and acid detergent fiber digestibilities were greater(P<0.05)in yaks than in cattle,and decreased linearly(P<0.05)with increasing dietary energy level;whereas,digestibilities of dry matter,organic matter,crude protein and ether extract increased(P<0.05)linearly with increasing energy level.The ADG was greater(P<0.001)in yaks than in cattle,and increased(P<0.05)linearly with increasing energy levels.From the regressions of ADG on ME intake,the estimated ME requirement for maintenance was lower(P<0.05)in yaks than in cattle(0.43 vs.0.57 MJ/kg BW0.75).The ratios of digestible energy(DE):gross energy and ME:DE were higher(P<0.05)in yaks than in cattle,and increased(P<0.05)linearly with increasing dietary energy level.Ruminal pH decreased(P<0.05),whereas concentrations of total volatile fatty acids(VFAs)and ammonia increased(P<0.01)with increasing dietary energy level,and all were greater(P<0.05)in yaks than in cattle.Concentrations of ruminal acetate and iso-VFAs were greater(P<0.05),whereas propionate was lower(P<0.05)in yaks than in cattle;acetate decreased(P<0.001),whereas butyrate and propionate increased(P<0.001)linearly with increasing dietary energy level.Serum concentrations ofβ-hydroxybutyrate were lower(interaction,P<0.001)in yaks than in cattle fed diets of 9.42 and 10.80 MJ/kg,whereas non-esterified fatty acids were greater(interaction,P<0.01)in yaks than in cattle fed diets of 6.62 and 8.02 MJ/kg.Concentrations of serum leptin and growth hormone were greater in yaks than in cattle and serum insulin and growth hormone increased(P<0.01)linearly with increasing dietary energy level.Our hypothesis that yaks have lower energy requirements for maintenance than cattle was supported.This lower requirement confers an advantage to yaks over Qaidam cattle in consuming low energy diets during the long winter on the Qinghai-Tibetan Plateau.

The adaptive strategies of yaks to live in the Asian highlands

The yak(Bos grunniens),an indigenous herbivore raised at altitudes between 3,000 and 5,000 m above sea level,is closely linked to more than 40 ethnic communities and plays a vital role in the ecological stability,livelihood security,socio-economic development,and ethnic cultural traditions in the Asian highlands.They provide the highlanders with meat,milk,fibres,leather and dung(fuel).They are also used as pack animals to transport goods,for travel and ploughing,and are important in many religious and traditional ceremonies.The Asian highlands are known for an extremely,harsh environment,namely low air temperature and oxygen content and high ultraviolet light and winds.Pasture availability fluctuates greatly,with sparse pasture of poor quality over the long seven-month cold winter.After longterm natural and artificial selections,yaks have adapted excellently to the harsh conditions:1)by genomics,with positively selected genes involved in hypoxia response and energy metabolism;2)anatomically,including a short tongue with a weak sense of taste,and large lung and heart;3)physiologically,by insensitivity to hypoxic pulmonary vasoconstriction,maintaining foetal haemoglobin throughout life,and low heart rate and heat production in the cold season;4)behaviourlly,by efficient grazing and selecting forbs with high nutritional contents;5)by low nitrogen and energy requirements for maintenance and low methane emission and nitrogen excretion,namely,‘Low-Carbon’and‘Nitrogen-Saving’traits;6)by harboring unique rumen microbiota with a distinct maturation pattern,that has coevolved with host metabolism.This review aims to provide an overview of the comprehensive adaptive strategies of the yak to the severe conditions of the highlands.A better understanding of these strategies that yaks employ to adapt to the harsh environment could be used in improving their production,breeding and management,and gaining benefits in ecosystem service and a more resilient livelihood to climate change in the Asian highlands.

The uniqueness and superiority of energy utilization in yaks compared with cattle in the highlands:A review

Yaks living on the Qinghai-Tibetan Plateau for a long time have evolved a series of mechanisms to adapt to the unique geographical environment and climate characteristics of the plateau.Compared with other ruminants,yaks have higher energy utilization and metabolic efficiency.This paper presents possible mechanisms responsible for the efficient energy utilization,absorption and metabolism resulting from the unique evolutionary process of yaks.It is hoped that the information discussed in this review will give a better insight into the uniqueness and superiority of yaks in regards to energy metabolism and utilization compared with cattle and open new avenues for the targeted regulation of energy utilization pathways of other ruminants.

Composition Analysis on Intermuscular Fatty Acid of Qinghai Datong Yak

[ Objective] The study aimed to provide a theoretical basis for rational utilization of Datong yak resource. [ Method] By qualitative and quantitative determination with gas chromatograph, the composition and content of intermuscular fatty acid of Datong yak were compared with those of Datong yellow cattle. [ Result] Comparing with Datong yellow cattle, Datong yak had lower saturated fatty acid （SFA） content and higher polyunsaturated fatty acid （PUFA） content at extremely significant level （P 〈0.01 ）, while the difference of monounsaturated fatty acid （MUFA） contents between them was not significant （P〉0.05）. The PUFA/SFA and n-6/n-3 PUFA of Datong yak were in accordance with the recommended proportions. [ Conclusion] The intermuscular fatty acid composition of Datong yak is superior to that of local yellow cattle, which indicates that Datong yak meat has high nutritive value and wide development prospect.

Cloning and Bioinformatics Analysis of Lfcin Gene of Datong Yak

[Objective] This study was to clone Lfcin gene from Datong yak, so as to provide reference for applying this gene in feed industry and breeding industry. [Method] Using PCR technology, the lactoferricin(Lfcin)-encoding gene was obtained from genome of Datong yak; then it was cloned into pGEM-T easy vector, and then sequenced; the sequencing results were subsequently aligned with the sequences of dairy cow accessed in GenBank. Moreover, amino acid sequences of Lfcin gene from various species including yak, dairy cow, human and mouse were used for sequence alignment and phylogenesis analysis. [Result] The second exon of lactoferrin(LF) from Datong yak, which is 778 bp in length, was obtained, within which the coding region of Lfcin gene is 75 bp (25 amino acid residues); sequence analysis showed that there is discrepancy of eleven bases between Datong yak and dairy cow; Lfcin proteins from various species shared high homeology, of which that from Datong yak and dairy cow were completely identical; phylogenesis analysis showed that cladogram based on Lfcin was consistent with species evolutionary law. [Conclusion] This study laid a foundation for the prokaryotic or eukaryotic expression of Lfcin gene and further understanding the activity of Lfcin protein.

Study on Carcass Traits of Changtai Yak

For studying the germplasm charactedsUcs and carcass traits of Changtai yak, 8 adult yaks （5 male, 3 female） were selected and tested. The results showed that the pre-slaughter weight of the adult male and female Changtai yak was 364.32 and 266.83 kg, respectively, which presented extremely significant difference （P〈0.01）. The carcass weight, net bone weight net meat weight, and the ratio of bone to meat also showed extremely significant difference （P〈O.01）, which were 186.60 and 125.67 kg, 39.74 and 25.00 kg, 147.84 and 100.83 kg, 1：3.73 and 1： 4.03, respectively. The dressing percentage had significant difference which was 51.15% and 49.34%, respectively （P〈0.05）. The neat meat percentage and carcass meat production rate showed no significant difference which were 40.54% and 37.66%, 79.29% and 80.24%, respectively （P〉0.05）. It indicated that Changtai yak has better growth performance and meat performance potential, and worth of further studying and breeding.

牦牛高原低氧适应性生理及分子机制

在高原地区主要环境表现为低氧,高原上的物种主要朝着适应当地环境而不断进化。目前人们对于高原物种的研究方向主要为高原物种如何适应低氧环境,人们通过比较高原物种与平原近亲之间的生理以及基因上的差异如牦牛,逐步找到了一些与高原适应有关的生理特点和基因。本文主要从牦牛的生理指标和相关基因等方面分析牦牛能够适应高原环境的优势,为后续对牦牛或其他高原物种的研究及高原引种提供了理论基础。