Chinese Cattle Research Articles

Differences in Lipid Metabolism between the Perirenal Adipose Tissue of Chinese Simmental Cattle and Angus Cattle (Bos taurus) Based on Metabolomics Analysis.

The aim of this experiment was to investigate the differences in metabolites in perirenal fat (PF) between Chinese Simmental cattle and Angus cattle. Six healthy 18-month-old male Angus cattle and Chinese Simmental cattle were selected, and the perirenal adipose tissue was collected after slaughtering. HE staining, a triglyceride assay kit, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology were used to compare and analyze the differences in the cell morphology, lipid accumulation, and metabolites of the two types of PF. The results showed that the PF of Angus cattle had a larger cell area and stronger lipid deposition ability than that of Simmental cattle. A total of 567 metabolites were detected by LC-MS/MS technology, of which 119 were significantly upregulated in Angus cattle PF and 129 were significantly upregulated in Simmental cattle PF. Differential metabolites were enriched in pathways such as fatty acid biosynthesis, polyunsaturated fatty acid biosynthesis, regulation of adipocyte lipolysis, and oxidative phosphorylation. Finally, 12 metabolites that may cause phenotypic differences between the two types of perirenal adipose tissue were screened out from these pathways. This study has preliminarily screened out biomarkers that may affect lipid metabolism in PF, providing basic data for the further exploration of the metabolic characteristics of PF.

The Prevalence and Molecular Characterization of Bovine Leukemia Virus among Dairy Cattle in Henan Province, China.

Enzootic bovine leukosis, a neoplastic disease caused by the bovine leukemia virus (BLV), was the primary cancer affecting cattle in China before 1985. Although its prevalence decreased significantly between 1986 and 2000, enzootic bovine leukosis has been re-emerging since 2000. This re-emergence has been largely overlooked, possibly due to the latent nature of BLV infection or the perceived lack of sufficient evidence. This study investigated the molecular epidemiology of BLV infections in dairy cattle in Henan province, Central China. Blood samples from 668 dairy cattle across nine farms were tested using nested polymerase chain reaction assays targeting the partial envelope (env) gene (gp51 fragment). Twenty-three samples tested positive (animal-level prevalence of 3.4%; 95% confidence interval: 2.2, 5.1). The full-length env gene sequences from these positive samples were obtained and phylogenetically analyzed, along with previously reported sequences from the GenBank database. The sequences from positive samples were clustered into four genotypes (1, 4, 6, and 7). The geographical annotation of the maximum clade credibility trees suggested that the two genotype 1 strains in Henan might have originated from Japan, while the genotype 7 strain is likely to have originated from Moldova. Subsequent Bayesian stochastic search variable selection analysis further indicated a strong geographical association between the Henan strains and Japan, as well as Moldova. The estimated substitution rate for the env gene ranged from 4.39 × 10-4 to 2.38 × 10-3 substitutions per site per year. Additionally, codons 291, 326, 385, and 480 were identified as positively selected sites, potentially associated with membrane fusion, epitope peptide vaccine design, and transmembrane signal transduction. These findings contribute to the broader understanding of BLV epidemiology in Chinese dairy cattle and highlight the need for measures to mitigate further BLV transmission within and between cattle herds in China.

Phenotypic and Genetic Analyses of Mastitis, Endometritis, and Ketosis on Milk Production and Reproduction Traits in Chinese Holstein Cattle.

Mastitis (MAS), endometritis (MET), and ketosis (KET) are prevalent diseases in dairy cows that result in substantial economic losses for the dairy farming industry. This study gathered 26,014 records of the health and sickness of dairy cows and 99,102 data of reproduction from 13 Holstein dairy farms in Central China; the milk protein and milk fat content from 56,640 milk samples, as well as the pedigree data of 37,836 dairy cows were obtained. The logistic regression method was used to analyze the variations in the prevalence rates of MAS, MET, and KET among various parities; the mixed linear model was used to examine the effects of the three diseases on milk production, milk quality, and reproductive traits. DMU software (version 5.2) utilized the DMUAI module in conjunction with the single-trait and two-trait animal model, as well as best linear unbiased prediction (BLUP), to estimate the genetic parameters for the three diseases, milk production, milk quality, and reproductive traits in dairy cows. The primary findings of the investigation comprised the following: (1) The prevalence rates of MAS, MET, and KET in dairy farms were 20.04%, 10.68%, and 7.33%, respectively. (2) MAS and MET had a substantial impact (p < 0.01) on milk production, resulting in significant decreases of 112 kg and 372 kg in 305-d Milk Yield (305-d MY), 4 kg and 12 kg in 305-d Protein Yield (305-d PY), and 6 kg and 16 kg in 305-d Fat Yield (305-d FY). As a result of their excessive 305-d MY, some cows were diagnosed with KET due to glucose metabolism disorder. The 305-d MY of cows with KET was significantly higher than that of healthy cows (205 kg, p < 0.01). (3) All three diseases resulted in an increase in the Interval from Calving to First Service (CTFS, 0.60-1.50 d), Interval from First Service to Conception (FSTC, 0.20-16.20 d), Calving Interval (CI, 4.00-7.00 d), and Number of Services (NUMS, 0.07-0.35). (4) The heritabilities of cows with MAS, MET, and KET were found to be low, with values of 0.09, 0.01, and 0.02, respectively. The genetic correlation between these traits ranged from 0.14 to 0.44. This study offers valuable insights on the prevention and control of the three diseases, as well as feeding management and genetic breeding.

Study of Plasma Biochemistry and Plasma Metabolomics Differences in Montbéliard and Holstein Backcross and Holstein Heifers.

Holstein cattle are the main breed of dairy cattle in China. However, given the high degree of purebred selection of Holstein cattle, Chinese dairy cattle are increasingly being characterized by poor disease resistance, poor quality, and declining fertility. In this study, using Montbéliard × Holstein cattle as females and Montbéliard bulls as males for backcross breeding, we sought to provide a reference for improving the quality and performance of Holstein cattle and enhancing the efficiency of dairy farming. On the basis of similar physiological status and age, we selected 24 Montbéliard and Holstein backcross heifers and 11 Holstein heifers fed the same formula for comparative analyses. Plasma samples collected for plasma biochemical index analyses revealed that the content of ALB and BUN in the Montbéliard and Holstein backcross heifers was 20.83% (31.62 g/L to 26.17 g/L) and 42.36% (6.89 mmol/L to 4.84 mmol/L) higher than in the Holsteins (p < 0.01). The ALB/GLB (0.90 to 0.60, p < 0.05) was significantly higher in Montbéliard and Holstein backcross heifers than in Holstein heifers. Similarly, the activity of CAT in the backcross heifers was 61.28% (4.29 U/mL to 2.66 U/mL) higher than that in the Holstein heifers (p < 0.05). Although the activity of GSH-Px in the backcross heifers also showed an increasing trend, the difference did not reach the level of statistical significance (p = 0.052). Compared with Holstein heifers, the concentrations of IgA, IgG, and IL-4 were elevated by 32.52% (24.90 μg/mL to 18.79 μg/mL, p < 0.01), 13.46% (234.32 μg/mL to 206.53 μg/mL, p < 0.01), and 14.59% (306.27 pg/mL to 267.28 pg/mL, p < 0.05), and the contents of IL-6 and TNF-α were decreased by 15.92% (215.71 pg/mL to 256.55 pg/mL, p < 0.01) and 32.17% (7.17 ng/mL to 10.57 ng/mL, p < 0.01) in the plasma of Montbéliard and Holstein backcross heifers. Among the experimental heifers, five animals from each of the two groups were selected for plasma metabolomic analysis based on untargeted liquid chromatography-mass spectrometry. A comparison of the differential metabolites between the two heifer breeds revealed an up-regulation of d-glucuronic acid, s-glutathionyl-l-cysteine, and oleic acid levels in the backcross cattle compared with those in the Holstein heifers. We speculate that changes in the levels of these metabolites may be associated with an enhancement of the anti-inflammatory, antioxidant, and immune systems in these backcross heifers. Collectively, our findings in this study indicate that compared with 12-month-old purebred Holstein heifers, Montbéliard and Holstein backcross heifers of the same age are characterized by higher antioxidant capacity and immunity.

Genetic parameters, genome-wide association study, and selection perspective on gestation length in 16 French cattle breeds

Lifetime productivity is a trait of great importance to dairy cattle populations as it combines information from production and longevity variables. Therefore, we investigated the genetic background of lifetime productivity in high-producing dairy cattle by integrating genomics and transcriptomics data sets. A total of 3,365,612 test-day milk yield records from 134,029 Chinese Holstein cows were used to define 6 lifetime productivity traits, including lifetime milk yield covering full lifespan and 5 cumulative milk yield traits covering partial lifespan. Genetic parameters were estimated based on univariate and bivariate linear animal models and the Restricted Maximum Likelihood (REML) method. Genome-wide association studies (GWAS) and weighted gene co-expression network analyses (WGCNA) were performed to identify candidate genes associated with lifetime productivity based on genomic data from 3,424 cows and peripheral blood RNA-seq data from 23 cows, respectively. Lifetime milk yield averaged 24,800.8 ± 14,396.6 kg (mean ± SD) across an average of 2.4 parities in Chinese Holstein population. The heritability estimates for lifetime productivity traits ranged from 0.05 (±0.01 for SE) to 0.10 (±0.02 for SE). The estimate of genetic correlation between lifetime milk yield and productive life is 0.88 (±0.3 for SE) while the genetic correlation with 305d milk yield in the first lactation was 0.49 (±0.08 for SE). Absolute values for most genetic correlation estimates between lifetime productivity and type traits were lower than 0.30. Moderate genetic correlations were found between udder related traits and lifetime productivity, such as with udder depth (0.33), rear udder attachment height (0.33), and udder system (0.34). Some single nucleotide polymorphisms and gene co-expression modules significantly associated with lifetime milk yield were identified based on GWAS and WGCNA analyses, respectively. Functional enrichment analyses of the candidate genes identified revealed important pathways related to immune system, longevity, energy utilization and metabolism, and FoxO signaling. The genes NTMT1, FNBP1, and S1PR1 were considered to be the most important candidate genes influencing lifetime productivity in Holstein cows. Overall, our findings indicate that lifetime productivity is heritable in Chinese Holstein cattle and important candidate genes were identified by integrating genomic and transcriptomic data sets.

Classification accuracy of machine learning algorithms for Chinese local cattle breeds using genomic markers.

Accurate breed classification is required for the conservation and utilization of farm animal genetic resources. Traditional classification methods mainly rely on phenotypic characterization. However, it is difficult to distinguish between the highly similar breeds due to the challenges in qualifying the phenotypic character. Machine learning algorithms show unique advantages in breed classification using genomic information. To evaluate the classification methods for Chinese cattle breeds, this study utilized genomic SNP data from 213 individuals across seven Chinese local breeds and compared the classification accuracies of three feature selection methods (FST value sorting and screening, mRMR, and Relief-F) and three machine learning algorithms (Random Forest, Support Vector Machine, and Naive Bayes). Results showed that: 1) using the FST method to screen more than 1500 SNPs, or using the mRMR algorithm to screen more than 1000 SNPs, the SVM classification algorithm can achieve more than 99.47% classification accuracy; 2) the most effective algorithm was SVM, followed by NB, while the best SNP selection method was FST and mRMR, followed by Relief-F; 3) species misclassification often occurs between breeds with high similarity. This study demonstrates that machine learning classification models combined with genomic data are effective methods for the classification of local cattle breeds, providing a technical basis for the rapid and accurate classification of cattle breeds in China.

Technical Efficiency and Allocative Efficiency of Beef Cattle Fattening in the Content of Digital Economy: An Empirical Study Based on Survey in China

This study applies data envelopment analysis (DEA) to gauge technical efficiency and allocative efficiency in China’s beef cattle-fattening industry using survey data. The Tobit model considers the salient determinants that drive these efficiencies. The results indicate that (1) large-scale farms exhibit robust TE and pure technical efficiencies (PTE), whereas scale efficiencies (SE) diverge significantly between large and medium-sized operations. The cost efficiency (CE) of smaller farms lags behind their larger counterparts, with the latter displaying greater revenue efficiencies (RE) and profit efficiency (PE). (2) The influence of identical factors on the efficiency of beef cattle fattening production can vary, sometimes antithetically, across different scales. Local policy interventions must be differentiated according to farm type and size. (3) The unique context of China’s national conditions and the status quo of livestock farming render the dual implementation of environmental regulations and technological subsidies less viable for Chinese beef cattle farms. These entities should prioritize production over technological innovation and advancement. Policymakers should adopt strategies such as targeted skill/technological training for farm managers at particular scales of operation. This could represent a critical trajectory to augment the efficiency of beef cattle production and increase beef yield in China.

Polymorphisms of the SCD1 Gene and Its Association Analysis with Carcass, Meat Quality, Adipogenic Traits, Fatty Acid Composition, and Milk Production Traits in Cattle.

Stearoyl-CoA desaturase-1 (SCD1) is a key enzyme in the biosynthesis of monounsaturated fatty acids and is considered a candidate gene for improving milk and meat quality traits. Sanger sequencing was employed to investigate the genetic polymorphism of the fifth exon and intron of bovine SCD1, revealing four SNPs, g.21272246 A>G, g.21272306 T>C, g.21272422 C>T, and g.21272529 A>G. Further variance analysis and multiple comparisons were conducted to examine the relationship between variation sites and economic traits in Chinese Simmental cattle, as well as milk production traits in Holstein cows. The findings revealed these four loci exhibited significant associations with carcass traits (carcass weight, carcass length, backfat thickness, and waist meat thickness), meat quality (pH value, rib eye area, and marbling score), adipogenic traits (fat score and carcass fat coverage rate), and fatty acid composition (linoleic acid and α-linolenic acid). Furthermore, these loci were additionally found to be significantly associated with average milk yield and milk fat content in cows. In addition, a haplotype analysis of combinations of SNPs showed that H2H3 has a significant association with adipogenic traits and H2H2 was associated with higher levels of linoleic acid and α-linolenic acid than the other combinations. These results suggest that the four SNPs are expected to be prospective genetic markers for the above economic traits. In addition, the function of SNPs in exon 5 of SCD1 on gene expression and protein structure needs to be explored in the future.

Whole-genome sequencing reveals genomic diversity and selection signatures in Xia’nan cattle

BackgroundThe 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.ResultThe 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).ConclusionWe 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.

Genome-wide analysis reveals genomic diversity and signatures of selection in Qinchuan beef cattle

BackgroundIndigenous Chinese cattle have abundant genetic diversity and a long history of artificial selection, giving local breeds advantages in adaptability, forage tolerance and resistance. The detection of selective sweeps and comparative genome analysis of selected breeds and ancestral populations provide a basis for understanding differences among breeds and for the identification and utilization of candidate genes. We investigated genetic diversity, population structure, and signatures of selection using genome-wide sequencing data for a new breed of Qinchuan cattle (QNC, n = 21), ancestral Qinchuan cattle (QCC, n = 20), and Zaosheng cattle (ZSC, n = 19).ResultsA population structure analysis showed that the ancestry components of QNC and ZSC were similar. In addition, the QNC and ZSC groups showed higher proportions of European taurine ancestry than that of QCC, and this may explain the larger body size of QNC, approaching that of European cattle under long-term domestication and selection. A neighbor-joining tree revealed that QCC individuals were closely related, whereas QNC formed a distinct group. To search for signatures of selection in the QNC genome, we evaluated nucleotide diversity (θπ), the fixation index (FST) and Tajima’s D. Overlapping selective sweeps were enriched for one KEGG pathway, the apelin signaling pathway, and included five candidate genes (MEF2A, SMAD2, CAMK4, RPS6, and PIK3CG). We performed a comprehensive review of genomic variants in QNC, QCC, and ZSC using whole-genome sequencing data. QCC was rich in novel genetic diversity, while diversity in QNC and ZSC cattle was reduced due to strong artificial selection, with divergence from the original cattle.ConclusionsWe identified candidate genes associated with production traits. These results support the success of selective breeding and can guide further breeding and resource conservation of Qinchuan cattle.

Whole-genome resequencing deciphers patterns of genetic diversity, phylogeny, and evolutionary dynamics in Kashmir cattle.

Kashmir cattle, which were kept by local pastoralists for centuries, are exceptionally resilient and adaptive to harsh environments. Despite its significance, the genomic characteristics of this cattle breed remain elusive. This study utilized whole genome sequences of Kashmir cattle (n = 20; newly sequenced) alongside published whole genomes of 32 distinct breeds and seven core cattle populations (n = 135). The analysis identified ~25.87 million biallelic single nucleotide polymorphisms in Kashmir cattle, predominantly in intergenic and intron regions. Population structure analyses revealed distinct clustering patterns of Kashmir cattle with proximity to the South Asian, African and Chinese indicine cattle populations. Genetic diversity analysis of Kashmir cattle demonstrated lower inbreeding and greater nucleotide diversity than analyzed global breeds. Homozygosity runs indicated less consanguineous mating in Kashmir cattle compared with European taurine breeds. Furthermore, six selection sweep detection methods were used within Kashmir cattle and other cattle populations to identify genes associated with vital traits, including immunity (BOLA-DQA5, BOLA-DQB, TNFAIP8L, FCRL4, AOAH, HIF1AN, FBXL3, MPEG1, CDC40, etc.), reproduction (GOLGA4, BRWD1, OSBP2, LEO1 ADCY5, etc.), growth (ADPRHL1, NRG2, TCF12, TMOD4, GBP4, IGF2, RSPO3, SCD, etc.), milk composition (MRPS30 and CSF1) and high-altitude adaptation (EDNRA, ITPR2, AGBL4 and SCG3). These findings provide essential genetic insights into the characteristics and establish the foundation for the scientific conservation and utilization of Kashmir cattle breed.

Genomic prediction based on a joint reference population for the Xinjiang Brown cattle.

Introduction: Xinjiang Brown cattle constitute the largest breed of cattle in Xinjiang. Therefore, it is crucial to establish a genomic evaluation system, especially for those with low levels of breed improvement. Methods: This study aimed to establish a cross breed joint reference population by analyzing the genetic structure of 485 Xinjiang Brown cattle and 2,633 Chinese Holstein cattle (Illumina GeneSeek GGP bovine 150K chip). The Bayes method single-step genome-wide best linear unbiased prediction was used to conduct a genomic evaluation of the joint reference population for the milk traits of Xinjiang Brown cattle. The reference population of Chinese Holstein cattle was randomly divided into groups to construct the joint reference population. By comparing the prediction accuracy, estimation bias, and inflation coefficient of the validation population, the optimal number of joint reference populations was determined. Results and Discussion: The results indicated a distinct genetic structure difference between the two breeds of adult cows, and both breeds should be considered when constructing multi-breed joint reference and validation populations. The reliability range of genome prediction of milk traits in the joint reference population was 0.142-0.465. Initially, it was determined that the inclusion of 600 and 900 Chinese Holstein cattle in the joint reference population positively impacted the genomic prediction of Xinjiang Brown cattle to certain extent. It was feasible to incorporate the Chinese Holstein into Xinjiang Brown cattle population to form a joint reference population for multi-breed genomic evaluation. However, for different Xinjiang Brown cattle populations, a fixed number of Chinese Holstein cattle cannot be directly added during multi-breed genomic selection. Pre-evaluation analysis based on the genetic structure, kinship, and other factors of the current population is required to ensure the authenticity and reliability of genomic predictions and improve estimation accuracy.

LncRNA BlncAD1 Modulates Bovine Adipogenesis by Binding to MYH10, PI3K/Akt Signaling Pathway, and miR-27a-5p/CDK6 Axis.

Research on adipogenesis will help to improve the meat quality of livestock. Long noncoding RNAs (lncRNAs) are involved in mammalian adipogenesis as epigenetic modulators. In this study, we analyzed lncRNA expression during bovine adipogenesis and detected 195 differentially expressed lncRNAs, including lncRNA BlncAD1, which was significantly upregulated in mature bovine adipocytes. Gain- and loss-of-function experiments confirmed that BlncAD1 promoted the proliferation, apoptosis, and differentiation of bovine preadipocytes. RNA pull-down revealed that the nonmuscle myosin 10 (MYH10) is a potential binding protein of BlncAD1. Then, we elucidated that loss of BlncAD1 caused increased ubiquitination of MYH10, which confirmed that BlncAD1 regulates adipogenesis by enhancing the stability of the MYH10 protein. Western blotting was used to demonstrate that BlncAD1 activated the PI3K/Akt signaling pathway. Bioinformatic analysis and dual-luciferase reporter assays indicated that BlncAD1 competitively absorbed miR-27a-5p. The overexpression and interference of miR-27a-5p in bovine preadipocytes displayed that miR-27a-5p inhibited proliferation, apoptosis, and differentiation. Further results suggested that miR-27a-5p targeted the CDK6 gene and that BlncAD1 controlled the proliferation of bovine preadipocytes by modulating the miR-27a-5p/CDK6 axis. This study revealed the complex mechanisms of BlncAD1 underlying bovine adipogenesis for the first time, which would provide useful information for genetics and breeding improvement of Chinese beef cattle.

Influenza D virus infection in China, 2022–2023

ABSTRACT Influenza D virus (IDV) plays an important role in the bovine respiratory disease (BRD) complex. Its potential for the zoonotic transmission is of particular concern. In China, IDV has previously been identified in agricultural animals by molecular surveys with no live virus isolates reported. In this study, live IDVs were successfully isolated from cattle in China, which prompted us to further investigate the national prevalence, antigenic property, and infection biology of the virus. IDV RNA was detected in 11.1% (51/460) of cattle throughout the country in 2022–2023. Moreover, we conducted the first IDV serosurveillance in China, revealing a high seroprevalence (91.4%, 393/430) of IDV in cattle during the 2022–2023 winter season. Notably, all the 16 provinces from which cattle originated possessed seropositive animals, and 3 of them displayed the 100% IDV-seropositivity rate. In contrast, a very low seroprevalence of IDV was observed in pigs (3%, 3/100) and goats (1%, 1/100) during the same period of investigation. Furthermore, besides D/Yama2019 lineage-like IDVs, we discovered the D/660 lineage-like IDV in Chinese cattle, which has not been detected to date in Asia. Finally, the Chinese IDVs replicated robustly in diverse cell lines but less efficiently in the swine cell line. Considering the nationwide distribution, high seroprevalence, and appreciably genetic diversity, further studies are required to fully evaluate the risk of Chinese IDVs for both animal and human health in China, which can be evidently facilitated by IDV isolates reported in this study.

First report of the within-farm prevalence of bovine digital dermatitis in Chinese Holstein dairy cows in Jiangsu, China: A Bayesian modelling approach

Digital dermatitis is one of the most important causes of lameness in dairy cattle, particularly in housed, intensively-managed cattle. The number of modern intensive dairy farms in China has increased markedly in recent years; however, we lack research on digital dermatitis in Chinese dairy cattle. This preliminary study aimed to estimate the prevalence of digital dermatitis on three conveniently selected farms in Jiangsu, China. The washed hind feet of all lactating cows on all three farms were examined during milking with the aid of a mobile phone light source. True prevalence was then estimated from the apparent prevalence using a Bayesian superpopulation approach to account for the imperfect nature of identifying digital dermatitis in cows during milking. Despite none of the farms having thought it necessary to implement routine digital dermatitis monitoring or control, the disease was found on all three sampled farms. All lesions observed were either chronic M4 or M4.1 type-lesions, with no M2 lesions (i.e. acute ulcerated lesions) observed. The estimated true prevalences on the farms were 7.3% (95% credible interval [CrI]: 5.4%–9.6%), 8.3% (95%CrI: 6.3%–10.8%), and 29.8% (95%CrI: 22.9%–37.2%).

Unraveling genomic diversity and positive selection signatures of Qaidam cattle through whole-genome re-sequencing.

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.

Geographic distribution of a missense mutation in the KRT38 gene in Chinese indigenous cattle breeds

Context China has a vast area across many temperature zones and a variety of cattle breeds. These cattle resources are ideal models to research their adaptability to the environment. The KRT38 gene is an acidic protein, and its coding product can be used as a component of hair production. Aims The objective of this study was to investigate the diversity of the KRT38 gene in Chinese local cattle and the association of different genotypes with mean temperature, relative humidity and temperature humidity index. Methods A missense mutation g.41650738 A &gt; G in the KRT38 gene was screened from the database of bovine genomic variation (BGVD) and was genotyped in a total of 246 samples from 15 local cattle breeds in China by polymerase chain reaction amplification and sequencing. Finally, the correlation between the locus and the three climatic factors was analysed. Key results We successfully obtained the frequency of this single-nucelotide polymorphism in three groups of cattle in northern, central and southern China. The frequency of allele A gradually declined from north to south, whereas the frequency of allele G showed the opposite trend with a clear geographic distribution. Conclusions Our results indicate that KRT38 variation in Chinese indigenous cattle might be linked to heat tolerance. Implications Our analysis may assist in determining the importance of the variation as a genetic signal for heat tolerance in cattle reproduction and genetics.

Effects of the COVID-19 Pandemic on Dairy Consumption Trends: An Empirical Investigation of Accounting Data in China.

The COVID-19 pandemic may have had a negative impact on dairy consumption trends. Many dairy products are perishable and have relatively high income elasticity, causing their susceptibility to market fluctuations in general, including those specifically caused by the pandemic. However, the pandemic has also brought some other prospective possibilities. For example, during the pandemic, people paid more attention to nutrition and health issues and increased the number of meals prepared and eaten at home. In consideration of the particular circumstances during the pandemic, the Chinese government issued several policies to promote the population's dairy consumption, and the Chinese dairy cattle sector actively implemented the policy of "guarantee price, quality, and supply". These factors may have caused the Chinese population to increase their consumption of dairy products during the pandemic. Before the pandemic, the consumption of dairy products in the Chinese population showed an overall upward trend. The question addressed in this study is how has COVID-19 affected dairy consumption trends during the pandemic? This study uses accounting data from the Chinese dairy cattle sector to empirically analyze the impact of the COVID-19 pandemic on dairy consumption trends through economic theories and translog revenue function. Our study found that COVID-19 increased consumers' consumption of dairy products in China, but those people experiencing poverty may still have experienced inadequate dairy intake. This study has contributed to the body of work in this area in the literature and provides response strategies for the dairy cattle sector and the authorities.

Copy number variations within fibroblast growth factor 13 gene influence growth traits and alternative splicing in cattle

Previous researches revealed a copy number variation (CNV) region in the bovine fibroblast growth factor 13 (FGF13) gene. However, its effects remain unknown. This study detected the various copy number types in seven Chinese cattle breeds and analysed their population genetic characteristics and effects on growth traits and transcription levels. Copy number Loss was more frequent in Caoyuan Red cattle and Xianan cattle than in the other breeds. Association analysis between CNV and growth traits of Qinchuan indicated that the CNV was significantly related to chest depth, hip width and hucklebone width (P < 0.05). Additionally, the growth traits of individuals with copy number Loss were significantly inferior to those with copy number Gain or Median (P < 0.05). Besides, we found two splicing isoforms, AS1 and AS2, in FGF13 gene, which resulted from alternative 5′ splicing sites of intron 1. These isoforms showed varied expression levels in various tissues. Moreover, CNV was significantly and negatively associated with the mRNA expression of AS1 (r = −0.525, P < 0.05). The CNVs in bovine FGF13 gene negatively regulated growth traits and gene transcription. These observations provide new insights into bovine FGF13 gene, delivering potentially useful information for future Chinese cattle breeding programs.

Comprehensive Analysis of Transcriptome and Metabolome Reveals Regulatory Mechanism of Intramuscular Fat Content in Beef Cattle.

The intramuscular fat (IMF) content of beef determined the meat quality, and the market value of beef varies with different breeds. To provide some new approaches for improving meat quality and cattle breed improvement, 24-month-old Qinchuan cattle (Q, n = 6), Nanyang cattle (N, n = 6), and Japanese black cattle (J, n = 6) were selected. IMF content of the J group (16.92 ± 1.08%) is remarkably higher than that of indigenous Chinese cattle (Q, 13.38 ± 1.08%, and N, 12.35 ± 1.22%). Monounsaturated fatty acids and polyunsaturated fatty acids in the J group are higher than the Q and creatine, lysine, and glutamine are the three most abundant amino acids in beef, which contribute to the flavor formation. Similarly, IMF content-related genes were enriched in four vital KEGG pathways, including fatty acid metabolism, biosynthesis of unsaturated fatty acids, fatty acid elongation, and insulin resistance. Moreover, weighted genes coexpression network analysis (WGCNA) revealed that ITGB1 is the critical gene associated with the IMF content. This study compares transcriptome and metabolome of local and high-IMF cattle breeds, providing data for native cattle breeding and improvement of beef quality.