The Wadi sheep (WAD) is a unique Chinese indigenous breed previously reported to show adaptation to humid and saline–alkali lowlands, disease resistance, high fecundity, and favorable meat quality. However, the recent widespread introduction of commercial sheep breeds has led to a sharp decline in the purebred WAD population, posing serious threats to the preservation of its unique genetic resources. Therefore, there is an urgent need to assess the current population structure and genetic diversity of WAD to support its conservation and sustainable utilization. In this study, we systematically analyzed genomic variation, population structure, and selection signatures using whole-genome resequencing data from 30 WAD sheep and 80 publicly available genomes representing five other breeds obtained from the NCBI database. Population genomic analyses revealed that WAD retains substantial genetic diversity and exhibits a distinct population structure, shaped by its unique breeding history. Selection signature analyses using FST, π ratio, and XP-EHH identified 457 candidate genes under positive selection, which are associated with key biological processes including environmental adaptation, immune defense, muscle traits, growth, and reproduction. These findings identify genomic regions potentially related to reported WAD traits and provide a theoretical basis for its conservation, molecular breeding, and sustainable utilization in lowland environments.

A complete goat (Capra hircus) reference genome enhances analyses of genetic variation, thus providing insights into domestication and selection in goats and related species. Here, we assemble a telomere-to-telomere (T2T) gap-free genome (2.86 Gb) from a cashmere goat (T2T-goat1.0), including a Y chromosome of 20.96 Mb. With a base accuracy of >99.999%, T2T-goat1.0 corrects numerous genome-wide structural and base errors in previous assemblies and adds 288.5 Mb of previously unresolved regions and 446 newly assembled genes to the reference genome. We sequence the genomes of five representative goat breeds for PacBio reads, and use T2T-goat1.0 as a reference to identify a total of 63,417 structural variations (SVs) with up to 4711 (7.42%) in the previously unresolved regions. T2T-goat1.0 was applied in population analyses of global wild and domestic goats, which revealed 32,419 SVs and 25,397,794 SNPs, including 870 SVs and 545,026 SNPs in the previously unresolved regions. Also, our analyses reveal a set of selective variants and genes associated with domestication (e.g., NKG2D and ABCC4) and cashmere traits (e.g., ABCC4 and ASIP).

The authors declare no conflict of interest. Sequence data have been deposited in GenBank (BioProject accession no. PRJNA940187). Figure S1. Table S1. Table S2. Table S3. Table S4. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

The rumen undergoes developmental changes during maturation. To characterize this understudied dynamic process, we profiled single-cell transcriptomes of about 308,000 cells from the rumen tissues of sheep and goats at 17 time points. We built comprehensive transcriptome and metagenome atlases from early embryonic to rumination stages, and recapitulated histomorphometric and transcriptional features of the rumen, revealing key transitional signatures associated with the development of ruminal cells, microbiota, and core transcriptional regulatory networks. In addition, we identified and validated potential cross-talk between host cells and microbiomes and revealed their roles in modulating the spatiotemporal expression of key genes in ruminal cells. Cross-species analyses revealed convergent developmental patterns of cellular heterogeneity, gene expression, and cell-cell and microbiome-cell interactions. Finally, we uncovered how the interactions can act upon the symbiotic rumen system to modify the processes of fermentation, fiber digestion, and immune defense. These results significantly enhance understanding of the genetic basis of the unique roles of rumen.

The fat tail of sheep is an important organ that has evolved to adapt to extreme environments. However, the genetic mechanisms underlying the fat tail phenotype remain poorly understood. Here, we characterize transcriptome and lipidome profiles and morphological changes in 250 adipose tissues from two thin-tailed and three fat-tailed sheep populations in summer and winter. We implement whole-genome selective sweep tests to identify genetic variants related to fat-tails. We identify a set of functional genes that show differential expression in the tail fat of fat-tailed and thin-tailed sheep in summer and winter. These genes are significantly enriched in pathways, such as lipid metabolism, extracellular matrix (ECM) remodeling, molecular transport, and inflammatory response. In contrast to thin-tailed sheep, tail fat from fat-tailed sheep show slighter changes in adipocyte size, ECM remodeling, and lipid metabolism, and had less inflammation in response to seasonal changes, indicating improved homeostasis. Whole-genome selective sweep tests identify genes involved in preadipocyte commitment (e.g., BMP2, PDGFD ) and terminal adipogenic differentiation (e.g., VEGFA ), which could contribute to enhanced adipocyte hyperplasia. Altogether, we establish a model of regulatory networks regulating adipose homeostasis in sheep tails. These findings improve our understanding of how adipose homeostasis is maintained, in response to extreme environments in animals.

试验旨在研究埋植和饲喂褪黑素对绵羊断奶后生长性能、氧化应激和免疫功能的影响.选用65～75日龄、体重19 kg左右的绵羊30只,随机分为5组,每组6个重复,对照组正常饲喂,埋植组分别颈部皮下埋植60 mg和90 mg褪黑素1次,饲喂组按绵羊体重饲喂1、3 mg/(kg·d)褪黑素,预试验30 d,正试期60 d.结果表明:与对照组相比,埋植60 mg和90 mg褪黑素可提高平均日增重(P<0.05),饲喂1 mg/kg褪黑素也可提高平均日增重(P<0.01);埋植90 mg褪黑素组的生长速率、饲喂1 mg/kg褪黑素组生长速率、体高、胸围、胸宽、胸深平均日增长均提高(P<0.01);埋植90 mg褪黑素组体高平均日增长(P<0.01)、胸深平均日增长(P<0.05)也均得到提高;饲喂3 mg/kg褪黑素组体高、胸围平均日增长提高(P<0.05);埋植90 mg褪黑素组和饲喂1 mg/kg褪黑素组皮质醇(COR)浓度降低(P<0.01),饲喂1 mg/kg褪黑素组超氧化物歧化酶(SOD)含量升高(P<0.05)、丙二醛(MDA)降低(P<0.01);饲喂1 mg/kg褪黑素免疫球蛋白A(IgA)、免疫球蛋白M(IgM)含量升高(P<0.05).本试验条件下,褪黑素能够缓解绵羊断奶氧化应激,提高血清抗氧化能力,增强机体免疫能力,提高绵羊的生长性能.

Abstract Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms, ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3′-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep.

东弗里升绵羊是优秀的乳肉兼用品种,探究东弗里升绵羊和地方特色品种洼地绵羊杂交改良,有利于挖掘种质资源,培育新品种.本研究利用程序化冷冻方法制备东弗里升细管冻精,分析精子冷冻前后的活力和运动能力.同时对28只洼地绵羊进行同期发情内窥镜输精处理,记录受胎率及后代生长发育数据.结果表明:冷冻降低精子的运动能力,精液冷冻后曲线速度(VCL)、精子头侧摆幅度(ALH)和快速运动精子比例与鲜精相比降低(P<0.05);28只洼地绵羊内窥镜输精妊娠率为71.43％(20/28),产羔率为128.57％(36/28),窝产2～3羔比例为72.22％(13/18);随窝产羔数增加,羔羊平均出生重降低;东洼杂交F1代同时期体重均高于洼地绵羊,其中18月龄东洼杂交F1代母羊体重高于洼地绵羊母羊(P<0.05);东洼F1代育肥期平均日增重(305 VS 264 g)、耗料增重比(4.1 VS 3.5)均高于洼地绵羊(P>0.05).因此,通过细管冻精腹腔内窥镜技术进行东弗里升与洼地绵羊杂交能够提高洼地绵羊的生产性能.

Feng-Hua Lv, Yin-Hong Cao, Guang-Jian Liu, Ling-Yun Luo, Ran Lu, 7 Ming-Jun Liu, Wen-Rong Li, Ping Zhou, Xin-Hua Wang, Min Shen, Lei Gao, 8 Jing-Quan Yang, Hua Yang, Yong-Lin Yang, Chang-Bin Liu, Peng-Cheng 9 Wan, Yun-Sheng Zhang, Wen-Hui Pi, Yan-Ling Ren, Zhi-Qiang Shen, Feng 10 Wang, Yu-Tao Wang, Jin-Quan Li, Hosein Salehian-Dehkordi, Eer Hehua, 11 Yong-Gang Liu, Jian-Fei Chen, Jian-Kui Wang, Xue-Mei Deng, Ali 12 Esmailizadeh, Mostafa Dehghani-Qanatqestani, Hadi Charati, Maryam Nosrati, 13 Ondřej Štěpánek, Hossam E. Rushdi, Ingrid Olsaker, Ino Curik, Neena A. 14 Gorkhali, Samuel R. Paiva, Alexandre R. Caetano, Elena Ciani, Marcel 15 Amills, Christina Weimann, Georg Erhardt, Agraw Amane, Joram M 16 Mwacharo, Jian-Lin Han, Olivier Hanotte, Kathiravan Periasamy, Anna 17 M. Johansson, Jón H. Hallsson, Juha Kantanen, David W. Coltman, Michael W. 18 Bruford, Johannes A. Lenstra, Meng-Hua Li 19 College of Animal Science and Technology, China Agricultural University, Beijing, China 20 CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese 21

Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facilitate our efforts towards further improvement. Here, we report the deep resequencing of 248 sheep including the wild ancestor (O. orientalis), landraces, and improved breeds. We explored the sheep variome and selection signatures. We detected genomic regions harboring genes associated with distinct morphological and agronomic traits, which may be past and potential future targets of domestication, breeding, and selection. Furthermore, we found non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds. We identified PDGFD as a likely causal gene for fat deposition in the tails of sheep through transcriptome, RT-PCR, qPCR, and Western blot analyses. Our results provide insights into the demographic history of sheep and a valuable genomic resource for future genetic studies and improved genome-assisted breeding of sheep and other domestic animals.

The domestication and subsequent global dispersal of livestock are crucial events in human history, but the migratory episodes during the history of livestock remain poorly documented [1-3]. Here, we first developed a set of 493 novel ovine SNPs of the male-specific region of Y chromosome (MSY) by genome mapping. We then conducted a comprehensive genomic analysis of Y chromosome, mitochondrial DNA, and whole-genome sequence variations in a large number of 595 rams representing 118 domestic populations across the world. We detected four different paternal lineages of domestic sheep and resolved, at the global level, their paternal origins and differentiation. In Northern European breeds, several of which have retained primitive traits (e.g., a small body size and short or thin tails), and fat-tailed sheep, we found an overrepresentation of MSY lineages y-HC and y-HB, respectively. Using an approximate Bayesian computation approach, we reconstruct the demographic expansions associated with the segregation of primitive and fat-tailed phenotypes. These results together with archaeological evidence and historical data suggested the first expansion of early domestic hair sheep and the later expansion of fat-tailed sheep occurred similar to 11,800-9,000 years BP and similar to 5,300-1,700 years BP, respectively. These findings provide important insights into the history of migration and pastoralism of sheep across the Old World, which was associated with different breeding goals during the Neolithic agricultural revolution.

Reproduction is an important trait in sheep breeding as well as in other livestock. However, despite its importance the genetic mechanisms of litter size in domestic sheep (Ovis aries) are still poorly understood. To explore genetic mechanisms underlying the variation in litter size, we conducted multiple independent genome-wide association studies in five sheep breeds of high prolificacy (Wadi, Hu, Icelandic, Finnsheep, and Romanov) and one low prolificacy (Texel) using the Ovine Infinium HD BeadChip, respectively. We identified different sets of candidate genes associated with litter size in different breeds: BMPR1B, FBN1, and MMP2 in Wadi; GRIA2, SMAD1, and CTNNB1 in Hu; NCOA1 in Icelandic; INHBB, NF1, FLT1, PTGS2, and PLCB3 in Finnsheep; ESR2 in Romanov and ESR1, GHR, ETS1, MMP15, FLI1, and SPP1 in Texel. Further annotation of genes and bioinformatics analyses revealed that different biological pathways could be involved in the variation in litter size of females: hormone secretion (FSH and LH) in Wadi and Hu, placenta and embryonic lethality in Icelandic, folliculogenesis and LH signaling in Finnsheep, ovulation and preovulatory follicle maturation in Romanov, and estrogen and follicular growth in Texel. Taken together, our results provide new insights into the genetic mechanisms underlying the prolificacy trait in sheep and other mammals, suggesting targets for selection where the aim is to increase prolificacy in breeding projects.

为了了解无棣华兴渤海黑牛原种场渤海黑牛种公牛的遗传多样性水平,确定个体之间的亲缘关系,对无棣华兴渤海黑牛原种场15头渤海黑牛种公牛的细胞色素b基因(Cytb)全序列的测序和分析,发现Cytb基因全长1140bp,共检测到了10种单倍型、34个核苷酸的多态位点,包括15个单变异位点和19个简约信息位点,无插入和缺失.单倍型多样度(Hd)为0.914,核苷酸多样度(Pi)为0.01014,表明渤海黑牛具有丰富的遗传多样性.NJ系统发育树构建的结果表明15头渤海黑牛聚为两大类.

China has a rich resource of native sheep (Ovis aries) breeds associated with historical movements of several nomadic societies. However, the history of sheep and the associated nomadic societies in ancient China remains poorly understood. Here, we studied the genomic diversity of Chinese sheep using genome-wide SNPs, mitochondrial and Y-chromosomal variations in >1,000 modern samples. Population genomic analyses combined with archeological records and historical ethnic demographics data revealed genetic signatures of the origins, secondary expansions and admixtures, of Chinese sheep thereby revealing the peopling patterns of nomads and the expansion of early pastoralism in East Asia. Originating from the Mongolian Plateau similar to 5,000-5,700 years ago, Chinese sheep were inferred to spread in the upper and middle reaches of the Yellow River similar to 3,000-5,000 years ago following the expansions of the Di-Qiang people. Afterwards, sheep were then inferred to reach the Qinghai-Tibetan and Yunnan-Kweichow plateaus similar to 2,000-2,600 years ago by following the north-to-southwest routes of the Di-Qiang migration. We also unveiled two subsequent waves of migrations of fat-tailed sheep into northern China, which were largely commensurate with the migrations of ancestors of Hui Muslims eastward and Mongols southward during the 12th-13th centuries. Furthermore, we revealed signs of argali introgression into domestic sheep, extensive historical mixtures among domestic populations and strong artificial selection for tail type and other traits, reflecting various breeding strategies by nomadic societies in ancient China.

为了了解和掌握渤海黑牛血细胞及血液理化指标,本试验测定了20头不同年龄和性别的舍饲渤海黑牛的各项血液生理生化值.结果显示,血液生理常值指标中,渤海黑牛白细胞数为7.08±1.61×109/L,红细胞数为(7.90±1.06)×10-1/L,血小板数为286.85±121.46)109/L,血红蛋白含量为127.5±17.36 g/L.总蛋白含量为69.83±7.36g/L,其中球蛋白数高于白蛋白数.总胆红素为1.73±0.61umol,总胆固醇为3.69±1.03mmol,葡萄糖含量为4.54±0.91mmol.10项生理指标和12项生化指标在不同性别和年龄组间差异显著(P<0.05).本研究结果为渤海黑牛血液生理生化指标提供参考.

　　羊肉因具有绿色、安全、营养保健的优点越来越受消费者青睐，近年来羊肉消费需求持续增长。由于养羊成本增加，羊的生长周期较长，市场出现供不应求的现状。我国养羊业长期存在良种化水平低、生长期长，而且养殖效益低下，难以形成标准化、产业化效应，严重阻碍了肉羊养殖业的发展壮大。羊产业要走出现有困境，必须加强品种改良，积极发展标准养殖，提高养殖效益，实现标准化、机械化、网络化生产，增加科技含量，提高羊肉品质，增加市场竞争力。

To study the breed resources,protection and utilization of Wadi sheep,body conformation and appearance of Wadi sheep were observed,and the body size and weight,production performance,and reproductive performance were measured.The results showed that Wadi Sheep was an excellent breed in Shandong Province,which had advantages in high fecundity and strong adaptability.This paper introduces the breed characteristics,the situation of resources,and progress on breeding research for Wadi Sheep,and gives an advice on the protection and utliization.

According to the published gene sequences of defensin gene of sheep on GenBank,one pair of primers were designed and defensin sBD-1 gene was amplified by RT-PCR from tongue epithelial tissue of Wadi sheep.PCR product was cloned into the pMD18-T vector and sequenced.The results showed that gene amplication of full-length was 215 bp,encoding 64 amino acids.Phylogenetic tree analysis showed that Wadi sheep and Menggu sheep had close phylogenetic relationship,nucleotide homology was 98.5%;kinship with the Bos taurus as far as the nucleotide homology of 84.6%.Amino acid sequence analysis showed no signal peptide amino acid sequence in the region,with three potential antigenic epitopes.sBD-1 gene SYBR Green Ⅰ fluorescence quantitative PCR method was set up using pMD18-T/sBD-1 plasmid as a template.Nucleic acid electrophoresis,amplification kinetics,dissolution curve and repeatability tests showed that the methods had good stability and specificity,the obtained regression equation(R2=0.998) showed that the logarithm of the amount of PCR product and the amount of starting template existed a good linear relationship,the gene could be effectively detect from the tongue,cecum,and fallopian tubes and other tissue,with detection sensitivity of 83.9 copies/μL.This study laid the foundation for further study on the function of defensin sBD-1 gene on resistance in low-lying land sheep.

To investigate the polymorphism of major histocompatibility complex ⅡDRB1(MHC-DRB1) in Wadi sheep,the second exon of this gene in 82 Wadi Sheep was amplified by nested PCR and the amplified products were characterized by RFLP technique using 2 restriction enzymes,ie,SacⅠandHaeⅢ.The results showed that the extensive polymorphisms of the exon2 of MHC-DRB1 were found at two loci digested with SacⅠandHaeⅢ,respectively,and these sites were controlled by two,five alleles,respectively.As some base mutations were found in MHC-DRB1locus,and according to the results in this paper,fifteen genetypes were found in Wadi sheep.The new allele MHC-DRB1.D was identified only in these Wadi sheep populations.The nucleotide and predicted amino acid sequence alignments of MHC-DRB1 alleles provided the evidence for considerable variation among the five alleles.

The polymorphisms of MHC-DQA 1 gene exonⅡ in four sheep breeds(Wadi sheep,Dorper sheeps,small tailed han sheeps and exel sheep) were analyzed.PCR-RFLP method was used to study the genetic polymorphisms of 315 bp MHC-DQA 1 gene exonⅡ in 224 samples of four sheep breeds,then the genotypic frequences and allelic frenquency were analyzed.Software Popgen32 was employed to calculate the relative genetic parameters.The results of AluI-RELP showed that there are two allele M and N at AluⅠ-RFLP locus in 224 samples of four sheep breeds,and by comparing with the allelic frequency,the predominant allele is N;The results of genetic parameters showed that except for small tailed han sheep,the heterozygosity are higher than homogeneity at AluⅠ-RFLP locus in other three sheep breeds;and the results of genetic parameters showed that there were low polymorphism in exon 2 of MHC-DQA1 gene in Dorper sheep,small tailed han sheep and Texel sheep,while it was moderate polymorphism in Wadi sheep.There were low genetic diversities in exonⅡ of MHC-DQA1 gene at AluⅠ-RFLP locus in 224 samples of four Sheep breeds.