We studied the worldwide differentiation of Y-chromosomal haplotypes of cattle in order to clarify their origin and migrations. Previous studies of Y-chromosomal single-nucleotide polymorphisms (Y-SNPs) have defined five Y-chromosomal haplogroups and 10 sub-haplogroups of global cattle. In this study, we collected genomic data for 560 male cattle from Europe, America, Africa and Asia, including 71 Central Chinese cattle (CCC) of mixed taurindicine ancestry. We identified 1418 Y-SNPs, which defined 11 Y-chromosomal sub-haplogroups. Their geographic distributions indicate two paternal founder effects in Europe and Africa, respectively, whereas two other founder effects occurred relatively recently within China in the CCC (Y2B haplogroup) and the South Chinese indicine (Y3A3 sub-haplogroup). This suggests that the environmental adaptation of Chinese cattle was accompanied by consequential paternal founder effects due to population bottlenecks, which is relevant for the conservation and management of the Chinese cattle breeds.

BACKGROUND: Guanling cattle is a vital livestock resource in Guizhou Province, China. Characterizing their genetic diversity provides a foundation for developing effective breeding and conservation strategies. This study employed whole-genome sequencing to analyse the population genetic structure and adaptive evolution of Guanling cattle. RESULTS: The results revealed that Guanling cattle are hybrids of East Asian indicine (EAI, 50%) and East Asian taurine (EAT, 35%) ancestry, exhibiting high genetic diversity and low inbreeding levels. Through local ancestry inference and selection signature analyses, several genes associated with disease resistance, heat tolerance, reproduction, and meat quality (such as STAT6, DNAJC8, HSPA4, PPP1R8, and BASP1) were identified. Notably, DNAJC8 and HSPA4, detected within selection-signal regions showing excessive EAI ancestry, were mainly related to immune and adaptive traits, whereas BASP1, identified in selection-signal regions enriched for EAT ancestry, was associated with muscle development and meat quality. CONCLUSIONS: Our findings reveal that Guanling cattle, composed of both indicine and taurine ancestries, represent a newly recognized and highly valuable genetic resource. The results provide important molecular insights for the conservation and breeding of Guanling cattle.

Skeletal muscle is a crucial tissue involved in body movement and energy metabolism, and its growth and development directly influence the economic value of livestock. This study investigates the effects of the TEX10 gene on the proliferation, differentiation, and apoptosis of bovine myoblasts, as well as the underlying molecular mechanisms. Using techniques such as CCK-8, EdU incorporation, qPCR, Western blotting, and immunofluorescence, we observed that TEX10 significantly promotes the expression of cell cycle factors, including CDK2 and PCNA, thereby increasing cell proliferation and the proportion of cells in the S phase. Overexpression and knockdown experiments demonstrated that TEX10 enhances the differentiation and myotube formation of myoblasts, while upregulating key genes such as MYOG and MYOD. Additionally, flow cytometry analysis of the cell cycle revealed that TEX10 inhibits apoptosis in bovine myoblasts. Transcriptomic analysis showed that TEX10 regulates several signaling pathways associated with proliferation, differentiation, and apoptosis, including PI3K-Akt, cAMP, and IL-17. Overall, these findings suggest that TEX10 plays a significant regulatory role in bovine muscle growth, providing a theoretical foundation for molecular breeding strategies aimed at improving yellow cattle.

Pinan cattle, as the progeny of crossbreeding improvement between Nanyang cattle and Piedmontese, have attracted attention for their excellent growth performance. In this study, we constructed a copy number variation map by whole genome resequencing of 132 Pinan cattle. In the genome of Pinan cattle, deletion-type copy number variants occupied a higher proportion and only 3.31% of CNVRs overlapped with exonic regions. It showed that Pinan cattle was clearly distinguishable from other breeds and Pinan cattle was closer to Nanyang cattle by population genetic structure analysis based on CNVRs. The degree of inbreeding in the Pinan cattle population was explored by ROH analysis, which showed that the degree of inbreeding in Pinan cattle was lower than that in European beef cattle, suggesting that the risk of inbreeding was low. Candidate genes related to muscle development (CADM3, CNTFR, DOCK3), reproductive traits (SCAPER), embryonic development (RERE) and immune traits (CD84) were identified by VST selection analysis, ROH islands and iHS selection analysis, which provided a new scientific basis for the genetic basis of the excellent traits in Pinan cattle.

Bovine endometritis is a common and serious disease that has caused huge economic losses and a decline in production performance in the dairy cattle industry. This study aimed to investigate the regulatory role of bta-miR-25 in Lipopolysaccharide (LPS)-induced BEND and its impact on endometritis. In this study, an in vitro endometritis model was constructed using LPS. The expression levels of proinflammatory cytokines IL-6, IL-8, IL-1β, and TNF-α were significantly increased in the model, while the expression of bta-miR-25 was upregulated, and its target gene DUSP10 was downregulated. We further validated DUSP10 as a target gene of bta-miR-25 through a dual-luciferase reporter gene assay. Knockdown of bta-miR-25 can increase the decreased expression of DUSP10 levels and inhibited the increase in inflammatory factors induced by LPS. Subsequently, overexpression DUSP10 also inhibited the LPS-induced increase in inflammatory factors. In summary, bta-miR-25 can inhibit LPS-induced endometritis by over the expression of DUSP10. bta-miR-25 and DUSP10 may serve as biomarkers and potential therapeutic targets for endometritis in dairy cows.

During the past 3000 years, cattle on the Qinghai-Xizang Plateau have developed adaptive phenotypes under the selective pressure of hypoxia, ultraviolet (UV) radiation, and extreme cold. The genetic mechanism underlying this rapid adaptation is not yet well understood. Here, we present whole-genome resequencing data for 258 cattle from 32 cattle breeds/populations, including 89 Tibetan cattle representing eight populations distributed at altitudes ranging from 3400 m to 4300 m. Our genomic analysis revealed that Tibetan cattle exhibited a continuous phylogeographic cline from the East Asian taurine to the South Asian indicine ancestries. We found that recently selected genes in Tibetan cattle were related to body size (HMGA2 and NCAPG) and energy expenditure (DUOXA2). We identified signals of sympatric introgression from yak into Tibetan cattle at different altitudes, covering 0.64%–3.26% of their genomes, which included introgressed genes responsible for hypoxia response (EGLN1), cold adaptation (LRP11), DNA damage repair (LATS1), and UV radiation resistance (GNPAT). We observed that introgressed yak alleles were associated with noncoding variants, including those in present EGLN1. In Tibetan cattle, three yak introgressed SNPs in the EGLN1 promoter region reduced the expression of EGLN1, suggesting that these genomic variants enhance hypoxia tolerance. Taken together, our results indicated complex adaptation processes in Tibetan cattle, where recently selected genes and introgressed yak alleles jointly facilitated rapid adaptation to high-altitude environments.

BACKGROUND:The crossbreeding of specialized beef cattle breeds with Chinese indigenous cattle is a common method of genetic improvement. Xia'nan cattle, a crossbreed of Charolais and Nanyang cattle, is China's first specialized beef cattle breed with independent intellectual property rights. After more than two decades of selective breeding, Xia'nan cattle exhibit a robust physique, good environmental adaptability, good tolerance to coarse feed, and high meat production rates. This study analyzed the population genetic structure, genetic diversity, and genomic variations of Xia'nan cattle using whole-genome sequencing data from 30 Xia'nan cattle and 178 published cattle genomic data.RESULT:The ancestry estimating composition analysis showed that the ancestry proportions for Xia'nan cattle were mainly Charolais with a small amount of Nanyang cattle. Through the genetic diversity studies (nucleotide diversity and linkage disequilibrium decay), we found that the genomic diversity of Xia'nan cattle is higher than that of specialized beef cattle breeds in Europe but lower than that of Chinese native cattle. Then, we used four methods to detect genome candidate regions influencing the excellent traits of Xia'nan cattle. Among the detected results, 42 genes (θπ and CLR) and 131 genes (FST and XP-EHH) were detected by two different detection strategies. In addition, we found a region in BTA8 with strong selection signals. Finally, we conducted functional annotation on the detected genes and found that these genes may influence body development (NR6A1), meat quality traits (MCCC1), growth traits (WSCD1, TMEM68, MFN1, NCKAP5), and immunity (IL11RA, CNTFR, CCL27, SLAMF1, SLAMF7, NAA35, and GOLM1).CONCLUSION:We elucidated the genomic features and population structure of Xia'nan cattle and detected some selection signals in genomic regions potentially associated with crucial economic traits in Xia'nan cattle. This research provided a basis for further breeding improvements in Xia'nan cattle and served as a reference for genetic enhancements in other crossbreed cattle.

Cattle are sensitive to temperature fluctuations but adapt well to inclement weather conditions. When environmental temperatures exceed specific thresholds, heat stress becomes a critical concern for cattle. The TRPM2 gene, which resides on cattle chromosome 1 encodes a TRP channel protein, holding a unique capacity to sense temperature changes and facilitate rapid response to avoid heat stress. Here, we utilized the Bovine Genome Variation Database (BGVD) (http://animal.omics.pro/code/index.php/BosVar), and identified a missense mutation site, c.805A > G: p. Met269Val (rs527146862), within the TRPM2 gene. To elucidate the functional assessment of this mutation in temperature adaptation attributes of Chinese cattle, we genotyped 407 samples from 20 distinct breeds representing diverse climatic zones across China. The association analysis incorporates three temperature parameters and revealed compelling insights in terms of allele frequency. Interestingly, the prevalence of the wild-type allele A was notably higher among northern cattle breeds and this trend diminished gradually as observed in southern cattle populations. Conversely, the mutant-type allele G demonstrated a contrasting trend. Moreover, southern cattle exhibited markedly higher frequencies of GG and GA genotypes (P < 0.01). The presence of heterozygous and homozygous mutations appears to confer an enhanced capacity for adaptation to elevated temperatures. These results provide unequivocal correlation evidence between TRPM2 genotypes (AA, GA, GG) and environmental temperature parameters and comprehend the genetic mechanisms governing temperature adaptation in cattle. This provides valuable insights for strategic breed selection across diverse climatic regions, thereby aiding livestock production amid evolving climate challenges.

(1) Background: Mengshan cattle from the Yimeng mountainous region in China stand out as a unique genetic resource, known for their adaptive traits and environmental resilience. However, these cattle are currently endangered and comprehensive genomic characterization remains largely unexplored. This study aims to address this gap by investigating the genomic features and selection signals in Mengshan cattle. (2) Methods: Utilizing whole-genome resequencing data from 122 cattle, including 37 newly sequenced Mengshan cattle, we investigated population structure, genetic diversity, and selection signals. (3) Results: Our analyses revealed that current Mengshan cattle primarily exhibit European taurine cattle ancestry, with distinct genetic characteristics indicative of adaptive traits. We identified candidate genes associated with immune response, growth traits, meat quality, and neurodevelopment, shedding light on the genomic features underlying the unique attributes of Mengshan cattle. Enrichment analysis highlighted pathways related to insulin secretion, calcium signaling, and dopamine synapse, further elucidating the genetic basis of their phenotypic traits. (4) Conclusions: Our results provide valuable insights for further research and conservation efforts aimed at preserving this endangered genetic resource. This study enhances the understanding of population genetics and underscores the importance of genomic research in informing genetic resources and conservation initiatives for indigenous cattle breeds.

Local species exhibit distinctive indigenous characteristics while showing unique productive and phenotypic traits. However, the advent of commercialization has posed a substantial threat to the survival of indigenous species. Anxi cattle, an endangered native breed in China, have evolved unique growth and reproductive characteristics in extreme desert and semidesert ecosystems. In this study, we conducted a genomic comparison of 10 Anxi cattle genomes with those of five other global populations/breeds to assess genetic diversity and identify candidate genomic regions in Anxi cattle. Population structure and genetic diversity analyses revealed that Anxi cattle are part of the East Asian cattle clade, exhibiting higher genetic diversity than commercial breeds. Through selective sweep analysis, we identified specific genetic variations linked to the environmental adaptability of Anxi cattle. Notably, we identified several candidate genes, including CERS3 involved in regulating skin permeability and antimicrobial functions, RBFOX2 associated with cardiac development, SLC16A7 participated in the regulation of pancreatic endocrine function, and SPATA3 related to reproduction. Our findings revealed the distinctive genomic features of Anxi cattle in dryland environments, provided invaluable insights for further research and breed preservation, and had important significance for enriching the domestic cattle breeding gene bank.

Lipopolysaccharide (LPS) is one of the main factors inducing endometritis in dairy cows. However, the specific pathogenesis of LPS-induced endometritis in dairy cows is not fully understood. The objective of this study was to establish an in vitro endometritis model using LPS-induced bovine endometrial epithelial (BEND) cells. BEND cells were treated with LPS of different concentrations and times. The cell-counting kit-8 (CCK-8) was used to detect the cell survival rate after LPS treatment, and quantitative real-time PCR (RT-qPCR) was used to detect the expression of control group and LPS-treated group of inflammatory factors interleukin-1 beta (IL-1β), interleukin-6 (IL-6), interleukin-8 (IL-8), and tumor necrosis factor-alpha (TNF-α). The results showed that the survival rate of endometrial epithelial cells stimulated by 5 μg/mL LPS for 6 h was 75.13%, and the expression of inflammatory factors was significantly increased. Therefore, 5 μg/mL LPS for 6 h could be selected as a suitable model for the study of inflammation. In addition, miRNA sequencing and target gene prediction was performed on normal and LPS-treated BEND cells. Among twenty-one differentially expressed miRNAs, six miRNAs were selected and their expression levels were detected by RT-qPCR, which were consistent with the sequencing results. Twenty-one differentially expressed miRNAs collectively predicted 17,050 target genes. This study provides a theoretical basis for further investigation of the pathogenesis of endometritis.

In order to compare the separation methods of bovine fibroblasts,the primary cells were isolated and cultured by tissue attachment method and tissue attachment + double enzyme digestion method(trypsin + collagenase Ⅱ)after the samples of bovine ear skin were collected and brought back to the laboratory at low temperature.The results showed that it took 6～7 days for the cells to migrate from the tissue blocks,spindle-shaped cells were visible at 10～11 days,and swirly growth halos were observed at 16 days.Tissue adhesion + double enzyme digestion method requires only 5 days for cells to migrate out of the tissue block,spindle cells can be seen on the 6th day,and the swirly growth halo can be observed on the 10th day.The comparison of the two methods shows that the tissue adhesion and double enzyme digestion method can quickly separate and obtain bovine fibroblasts,and is the best method to obtain bovine fibroblasts.

CNVs, which are a type of structural variation, make a substantial impact on diverse characteristics in multiple species. Q-PCR and data association analysis were used for STAT5A gene copy in this study. This study aimed to investigate the copy number variation (CNV) of the STAT5A gene in seven Chinese cattle breeds, namely Qinchuan cattle, Xianan cattle, Yunling cattle, Ji'an cattle, Jiaxian Red cattle, Qaidam cattle, and Guyuan yellow cattle. Blood samples were collected for CNV typing, and the correlation between CNV type and growth traits was analyzed using SPSS 23.0 software and ANOVA. The findings revealed variations in the distribution of different copy number types among the different cattle breeds. Furthermore, association analysis demonstrated a positive impact of CNV in the STAT5A gene on cattle growth: in the JX, individuals with duplication types exhibited superior performance in terms of rump length (P < 0.05). Conversely, normal GY cattle demonstrated better body height and abdomen circumference (P < 0.05), while QD cattle exhibited a significant correlation between weight and body length with normal individuals (P < 0.05). Moreover, QC bovine duplication individuals outperformed other types, with copy number variation significantly associated with chest depth, chest width, and body length (P < 0.05). The results validate the correlation between copy number variation (CNV) of the STAT5A gene and growth characteristics in five different cattle breeds, providing a reliable benchmark for the purpose of cattle breeding.

[Objective] Through slaughtering analysis, the slaughter performance and meat quality of hornless Xianan cattle can be understood, which can provide information for the next selection of hornless Xianan cattle. [Method] Slaughter determination and meat quality analysis were performed on 20 24-month-old hornless Xianan fattening bulls. [Result] The slaughter rate, net meat rate, eye muscle area, meat-to-bone ratio, high-grade and high-quality meat chunk ratio, and high-grade meat chunk ratio of 20 hornless Xianan cattle were: 62.62%, 52.8%, 111.17 cm~2, 5.82∶1, 49.69 % and 28.36%; the protein content of shoulder meat, large cucumber strip, and outer ridge were: 23.60% ± 0.19%, 20.85% ± 1.21%, 21.52% ± 1.28%; fat content were 4.26% ± 1.61, 3.12%, respectively 3.122% ± 1.05%, 2.80% ± 2.49%; muscle shear force were: 4.60kg ± 1.92kg, 3.59kg ± 1.58kg, 4.49kg ± 1.44kg, respectively. [Conclusion] The breeding and improvement effect of hornless Xianan cattle is remarkable, the ability to produce high-grade meat pieces is strong, and the meat quality is good.

Perilipin 2 (PLIN2) is a cytosolic protein that regulates intracellular lipid storage and mobilization. However, research reports of the relationship between PLIN2 gene and growth traits in cattle are rare. Here, five novel single nucleotide polymorphisms (SNPs)( g.3036G> C, g.3964C> T, g.6458G> T, g.6555C> T and g.8231G> A) were identified within the bovine PLIN2 gene using DNA sequencing and PCR-SSCP methods in 820 individuals from four Chinese indigenous bovine breeds. Overall, five common haplotypes were identified based on the 5 SNPs, with the most common haplotypes (GCGCG) occurring at a frequency of 69.0%. In addition, The 5 novel SNPs were associated with growth traits at 6, 12, 18 and 24months in Nanyang population, and significant associations were found in body weight and heart girth. These results suggest that PLIN2 possibly is a strong candidate gene marker for body weight in cattle breeding program.

MicroRNAs (miRNAs or miRs) are small noncoding RNAs that play critical roles in muscle cell proliferation and differentiation via post‐transcriptional regulation of gene expression. Here, based on our previous high‐throughput sequencing results, we evaluated miRNA‐499 (miR‐499) functions during myoblast proliferation and differentiation. In addition, we analyzed miR‐499 expression profiles and characterized the associated functional roles. MiR‐499 is known to be a skeletal muscle fiber‐type‐associated miRNA. However, its roles in skeletal myoblast proliferation and differentiation are poorly understood. MiR‐499 overexpression promoted C2C12 cell proliferation and significantly attenuated C2C12 cell myogenic differentiation. Furthermore, miR‐499 inhibition enhanced C2C12 cell proliferation and suppressed C2C12 cell differentiation. Using dual‐luciferase reporter assays and western blot analysis, we confirmed that miR‐499 targeted transforming growth factor β receptor 1 (TGFβR1), a known regulator of skeletal myoblast development. Additionally, our RNA interference analysis, in which TGFβR1 was downregulated, showed that TGFβR1 significantly promoted the differentiation of C2C12 cells and inhibited their proliferation.

Polymorphisms in the prion protein gene (PRNP) have been linked with the occurrence of transmissible spongiform encephalopathies and the expression of some phenotypic traits in healthy animals including cattle. The aim of this study was to verify the 23-bp insertion/deletion (indel) within promoter region and the 12-bp indel within intron 1 of PRNP, as well as to evaluate their associations with growth traits. Two loci of PRNP were genotyped in 1558 healthy Chinese cattle sampled from 6 indigenous breeds. Moreover, phenotypic records for growth were used to find the relationship between PRNP polymorphisms and phenotypic performance. The results confirmed the occurrence of these two indel polymorphisms in the analysed breeds. Association analysis showed that the 23-bp indel was significantly related to the body length and heart girth in 18-months-old Nanyang cattle. The 12-bp indel was significantly related to the growth traits in three cattle breeds, such as the body weight in Xia'nan cattle, the daily gained weight in 12-months-old Nanyang cattle and the cannon circumference and rump length in Ji'an cattle. These findings indicated that these two indels may affect bovine growth traits, which could benefit to healthy cattle selection and breeding through marker-assisted selection. Abbreviations AI: artificial insemination; ANOVA: analysis of variance; Bp: base pair; BSE: bovine spongiform encephalopathy; D: deletion; DD: deletion/deletion; GLM: generalized linear model; reaction; He: heterozygosity; Ho: homozygosity; HWE: Hardy–Weinberg equilibrium; I: insertion; ID: insertion/deletion; II: insertion/insertion; Indel: insertion/deletion; MAS: marker-assisted selection; Ne: effective allele numbers; PCR: polymerase chain reaction; PIC: polymorphism information content; PrP: Prion protein (PrP); PRNP: the prion protein; RP58: repressor protein with a predicted molecular mass of 58 kDa; SNP: single nucleotide polymorphism; Sp1: specific protein 1; SPSS: statistical product and service solutions; TSE: transmissible spongiform encephalopathies

The objective of this study was to examine the association of transient receptor potential vanilloid 1 (TRPV1) and transient receptor potential ankyrin 1 (TRPA1) genes polymorphisms with growth traits in three Chinese cattle breeds (Jiaxian red cattle, Qinchuan cattle and Luxi cattle). Through experiments we identified three single nucleotide polymorphisms (SNPs) in these three cattle breeds TRPV1 and TRPA1 genes using PCR-SSCP, (forced) PCR-RFLP methods. Three of these polymorphisms are all synonymous mutation which includes (NW_003104493.1: 30327 C > T), (NW_003104493.1: 33394 A > G) and (NW_003104493.1: 38471 G > A) are in exons. The other three polymorphisms are located at 3'UTR. Furthermore, we evaluated the haplotype frequency and the statistical analyses indicated that these SNPs of TRPV1 and TRPA1 genes were associated with bovine body height, body length, waist angle width, hucklebone width, cross ministry height, chest qingwidth (p < 0.05) and recommendation height, cannon circumference (p < 0.01) of Qingchuan cattle; body length, waist angle width (p < 0.05) of Jiaxian red cattle; body weight, Body length, cannon circumference, chest circumference (p < 0.05) and body height (p < 0.01) of Luxi cattle. Our result confirms the polymorphisms in the TRPV1 and TRPA1 genes are associated with growth traits that may be used for marker-assisted selection (MAS) in three beef breeds programs.

本规范主要从高档牛肉及其应具备的主要指标、生产高档牛肉必须具备的条件、产地环境、育肥牛只的选择、肥育期的确定、育肥方法、日常管理、屠宰、分割、加工与贮藏等方面对夏南牛高档牛肉生产技术进行了总结,主要用于指导夏南牛高档牛肉生产.