Identification and Characterization of long non-coding RNAs in Mammary Gland Tissues of Chinese Holstein Cows.

LncRNAs (Long non-coding RNA) is an RNA molecule with a length more than 200bp. LncRNAs can directly act on mRNA, thus affecting the expression of downstream target genes and proteins, and widely participate in many important physiological and pathological regulation processes of the body. In this study, RNA-Seq was performed to detect lncRNAs from mammary gland tissues of 3 Chinese Holstein cows, including 3 cows at 7 days before calving and the same 3 cows at 30 days postpartum (early lactation stage). A total of 1,905 novel lncRNAs were detected, 57.3% of the predicted lncRNAs are ≥ 500bp and 612 lncRNAs are intronic lncRNAs. The exon number of lncRNAs ranged from 2 to 10. A total of 96 lncRNAs were significantly differentially expressed between two stages, which 47 were upregulated and 49 were downregulated. Pathway analysis found that target genes were mainly concentrated on the ECM-receptor interaction, Jak-STAT signaling pathway, PI3K-Akt signaling pathway and TGF-beta signaling pathway. This study revealed the expression profile and characteristics of lncRNAs in the mammary gland tissues of Holstein cows at non-lactation and early lactation period, and providing a basis for studying the functions of lncRNAs in Holstein cows during different lactation periods.

Long non-coding RNA (CMR) involved in autoprotection in S. aureus mastitis in dairy cows by regulating miR-877/FOXM1.

Long non-coding RNAs (LncRNAs) are dysregulated in a variety of human diseases and are highly involved in the development and progression of tumors. Studies on lncRNAs associated with cow mastitis have been lagging behind compared to humans or model animals, therefore, the aim of this study was to explore the mechanism of LncRNAs (CMR) involved in autoprotection against S. aureus mastitis in Bovine Mammary Epithelial Cells (BMECs). First, qRT-PCR was used to examine the relative expression of CMR in a S. aureus mastitis model of BMECs. Then, cell proliferation and apoptosis were detected by EdU and apoptosis assay. Finally, the targeting relationship between miRNAs and mRNA/LncRNAs was determined by dual luciferase reporter gene, qRT-PCR and western blotting techniques. The results showed that CMR was upregulated in the S. aureus mastitis model of BMECs and promoted the expression of inflammatory factors, and SiRNA-mediated CMR inhibited the proliferation of mammary epithelial cells and induced apoptosis. Mechanistically, CMR acts as a competitive endogenous RNA (ceRNA) sponge miR-877, leading to upregulation of FOXM1, a target of miR-877. Importantly, either miR-877 overexpression or FOXM1 inhibition abrogated CMR knockdown-induced apoptosis promoting cell proliferation and reducing inflammatory factor expression levels. In summary, CMR is involved in the regulation of autoprotection against S. aureus mastitis through the miR-877/FOXM1 axis in BMECs and induces immune responses in mammary tissues and cells of dairy cows, providing an important reference for subsequent prevention and control of cow mastitis and the development of targeted drugs.

Body conformation traits in early-lactation associated with clinical mastitis and lameness in lactating Chinese holstein cows.

BACKGROUND: Comprehending the correlation between body conformation traits of cows at the early stages of lactation and prevalent lactation diseases might facilitate the execution of selection and feeding strategies that prioritize cow health. This study aimed to evaluate the impact of body conformation traits on the incidence of clinical mastitis and lameness in Chinese Holstein cows. From a pasture herd of 1472 early lactating Chinese Holstein cows, we evaluated 20 body conformation traits. During lactation, this pasture herd was visited weekly to gather clinical mastitis and lameness data. A nine-point scale was used to determine the conformation traits of cows to clarify their linear characters, including frame capacity, rump (RU), feet and leg (FL), mammary system (MS), and dairy character. A longitudinal binary disease (0 = healthy; 1 = diseased) data structure was created by allocating disease records to adjacent official test dates. The impact of body conformation traits on the risk of developing diseases (clinical mastitis and lameness) was analyzed using the logistic regression models. RESULTS: Compared to cows with low total scores (75-79 points), those with high total scores (80-85 points) of body conformation traits had a significantly lower risk of mastitis (P < 0.001). The disease status (0 or 1: binary variable) of clinical mastitis in lactating cows was significantly impacted negatively by age (P < 0.05). The fore udder attachment (FUA), angularity, rear attachment height (RAH), and rear teat placement (RTP) were all significantly associated with clinical mastitis during lactation (P < 0.05). The rear leg-rear view (RLRV) was significantly correlated with correlated considerably (P < 0.05) with lameness during lactation. An ideal score of four points on the lameness risk dimension of the RLRV may indicate a low risk of lameness. Since the risk of mastitis decreased as this trait score increased, the RTP may be an ideal marker for mastitis risk. CONCLUSIONS: According to the study, clinical mastitis and lameness risks in cows can be estimated using their body conformation traits. Cows with more centrally located rear teats have a lower risk of mastitis. These results may help dairy farmers identify cows at high risk of disease early in lactation and aid in breeding for disease resistance in cows.

Characterization of T-cell subsets in response to foot-and-mouth disease bivalent inactivated vaccine in Chinese Holstein cows.

IMPORTANCE: Vaccination plays a crucial role in the prevention and control of FMD; however, outbreaks persist occurring worldwide. Assessing the immune response to FMD vaccines is essential for effective prevention of FMD. In this study, a seven-color flow cytometry protocol was developed to systematically evaluate the T-cell response of Chinese Holstein cows vaccinated with FMD bivalent inactivated vaccine. Our findings showed that while most T-cell subsets (%) decreased post-vaccination, a significant increase was observed in CD4+CD8+ DP T cells, which was consistent with the levels of specific foot-and-mouth disease virus (FMDV) antibodies. These findings suggested that CD4+CD8+ DP T cells could serve as a potential biomarker for the evaluation of cellular and humoral responses to FMDV vaccination. Additionally, we should be aware of the potential decline in cellular immunity among cattle during FMD vaccination, as this may increase the risk of other pathogen-related issues.

The combination of vaccines and adjuvants to prevent the occurrence of high incidence of infectious diseases in bovine.

As the global population grows, the demand for beef and dairy products is also increasing. The cattle industry is facing tremendous pressures and challenges. The expanding cattle industry has led to an increased risk of disease in cattle. These diseases not only cause economic losses but also pose threats to public health and safety. Hence, ensuring the health of cattle is crucial. Vaccination is one of the most economical and effective methods of preventing bovine infectious diseases. However, there are fewer comprehensive reviews of bovine vaccines available. In addition, the variable nature of bovine infectious diseases will result in weakened or even ineffective immune protection from existing vaccines. This shows that it is crucial to improve overall awareness of bovine vaccines. Adjuvants, which are crucial constituents of vaccines, have a significant role in enhancing vaccine response. This review aims to present the latest advances in bovine vaccines mainly including types of bovine vaccines, current status of development of commonly used vaccines, and vaccine adjuvants. In addition, this review highlights the main challenges and outstanding problems of bovine vaccines and adjuvants in the field of research and applications. This review provides a theoretical and practical basis for the eradication of global bovine infectious diseases.

Multiple roles of LncRNA-BMNCR on cell proliferation and apoptosis by targeting miR-145/CBFB axis in BMECs.

Bovine mastitis is one of the most serious and costly disease affecting dairy cattle production. The present study explored the inflammatory response and autoprotective mechanism of a novel specific high expression BMNCR (bovine mastitis related long non-coding RNA) in S. aureus induced mastitis by miR-145/CBFB axis in dairy cows from the perspective of molecular genetics. In bovine mammary epithelial cells, we preformed loss of function experiments to detect changes in cytokine, proliferation and apoptosis by qRT-PCR, western blot, flow cytometry and EdU staining. The results demonstrated that BMNCR significantly increased cell apoptosis, and inhibited cell proliferation. However, the secretion of IL-1α, IL-2, IL-6, IL-8 and IL-12 were enhanced after knock-down BMNCR. Bioinformatics analysis demonstrated that BMNCR could target 8 miRNAs, in-depth analyses indicated that BMNCR acts as a molecular sponge for bta-miR-145 and CBFB was one of 23 target gene of bta-miR-145 . The results of the present study demonstrated that the role of BMNCR in S. aureus induced mastitis can be mediated by sponge bta-miR-145 activating CBFB expression. BMNCR could be a potential target for mastitis diagnosis and therapy, which may enrich the theoretical research of therapeutic intervention, and further increase milk yield and improve milk quality.

Identification and Classification of Long Non-Coding RNAs in the Mammary Gland of the Holstein Cow.

The mammary glands, responsible for milk secretion, are regulated at a local level by various hormones, growth factors, non-coding RNAs, and other elements. Recent research has discovered the presence of lncRNAs in these glands, with suggestions that they may be essential for the maintenance and function of mammary glands. Besides directly controlling the gene and protein expression, lncRNAs are believed to play a significant part in numerous physiological and pathological processes. This study focused on examining the mammary gland tissues of Chinese Holstein cows, to identify and categorize long non-coding RNAs (lncRNAs). The research intended to distinguish lncRNAs in the mammary tissues of Holstein cows and contrast them between lactation and non-lactation periods. In this study, mammary gland tissues were sampled from three Holstein cows in early lactation (n = 3, 30 days postpartum) and non-lactation (n = 3, 315 days postpartum) on a large dairy farm in Jiangsu province. Mammary tissue samples were collected during early lactation and again during non-lactation. In total, we detected 1905 lncRNAs, with 57.3% being 500 bp and 612 intronic lncRNAs. The exon count for lncRNAs varied from 2 to 10. It was observed that 96 lncRNA expressions markedly differed between the two stages, with 83 genes being upregulated and 53 downregulated. Enrichment analysis results revealed that Gene Ontology (GO) analysis was primarily abundant in cellular processes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that target genes were predominantly abundant in metabolic pathways, fatty acid biosynthesis, the immune system, and glycosphingolipid biosynthesis. This study analyzed the expression profile and characteristics of lncRNAs in the mammary gland tissues of Holstein cows during both lactation and non-lactation stages, forming a foundation for further investigation into the functional roles of lncRNAs in Holstein cows throughout lactation.

Identification cloning and functional analysis of novel natural antisense lncRNA CFL1-AS1 in cattle.

Long noncoding RNAs have been identified as important regulators of gene expression and animal development. The expression of natural antisense transcripts (NATs) transcribed in the opposite direction to protein-coding genes is usually positively correlated with the expression of homologous sense genes and is the key factor for expression. Here, we identified a conserved noncoding antisense transcript, CFL1-AS1, that plays an important role in muscle growth and development. CFL1-AS1 overexpression and knockout vectors were constructed and transfected into 293T and C2C12 cells. CFL1-AS1 positively regulated CFL1 gene expression, and the expression of CFL2 was also downregulated when CFL1-AS1 was knocked down. CFL1-AS1 promoted cell proliferation, inhibited apoptosis and participated in autophagy. This study expands the research on NATs in cattle and lays a foundation for the study of the biological function of bovine CFL1 and its natural antisense chain transcript CFL1-AS1 in bovine skeletal muscle development. The discovery of this NAT can provide a reference for subsequent genetic breeding and data on the characteristics and functional mechanisms of NATs.

Effect of Dam Body Conformations on Birth Traits of Calves in Chinese Holsteins.

The objective of this study was to explore the effect of dam body conformations on birth traits including stillbirth, dystocia, gestation length and birth weight of Chinese Holstein calves and to provide a reference for improving cow reproductive performance. We collected phenotype data on 20 conformation traits of Chinese Holstein cows and analyzed the impact of dam conformation trait linear scores on stillbirth, dystocia, gestation length and calf birth weight. The feet angle, set of rear legs, fore udder attachment and rear attachment height traits of the dairy cows significantly affected the risk of stillbirth. The risk of dystocia decreases with the increase in stature and pin width. The bone quality of dairy cows had a significant positive correlation with gestation length. There was a significant positive correlation between fore udder attachment and calf weight at birth. The birth weight of calves from cows with high body conformation traits was significantly higher than that of calves with a low composite score. These results suggest that improving the body conformation traits, especially the selection of mammary system and body shape total score, will be beneficial in improving the reproductive performance of dairy cows.

CircRNA-02191 regulating unsaturated fatty acid synthesis by adsorbing miR-145 to enhance CD36 expression in bovine mammary gland.

CD36 functions as a receptor for long-chain fatty acids, promoting the absorption and transport of long-chain unsaturated fatty acids. However, the regulatory influence of upstream circRNAs or miRNAs on its expression in cow mammary gland remains unclear. Herein, we performed high-throughput sequencing to screen for differentially expressed miRNAs and mRNAs in bovine mammary tissue during the late-lactation and the dry period to screen and conducted bioinformatics analysis to identify 420 miRNA/mRNA pairs, including miR-145/CD36. Experimental results indicate that miR-145 can directly target CD36 and inhibit its expression. Additionally, the circRNA-02191 sequence is predicted to contain a miR-145 binding site. As shown by dual luciferase reporter system detection, circRNA-02191 bound to miR-145 and its overexpression significantly reduced the expression of miR-145. Furthermore, the overexpression of miR-145 inhibited triglyceride accumulation, while circRNA-02191 enhanced the expression of the miR-145 target gene CD36. The above results indicate that circRNA-02191 can regulate triglyceride and fatty acid components by binding miR-145 and subsequently alleviating the inhibitory effect of miR-145 on the expression of CD36. Taken together, these findings present a novel approach to improve milk quality by analyzing the regulatory effect and mechanism regulating the circ02191/miR-145/CD36 pathway on fatty acid synthesis in the mammary gland of dairy cows.

Progress in Research on Key Factors Regulating Lactation Initiation in the Mammary Glands of Dairy Cows.

Lactation initiation refers to a functional change in the mammary organ from a non-lactating state to a lactating state, and a series of cytological changes in the mammary epithelium from a non-secreting state to a secreting state. Like the development of the mammary gland, it is regulated by many factors (including hormones, cytokines, signaling molecules, and proteases). In most non-pregnant animals, a certain degree of lactation also occurs after exposure to specific stimuli, promoting the development of their mammary glands. These specific stimuli can be divided into two categories: before and after parturition. The former inhibits lactation and decreases activity, and the latter promotes lactation and increases activity. Here we present a review of recent progress in research on the key factors of lactation initiation to provide a powerful rationale for the study of the lactation initiation process and mammary gland development.

miR-497 Regulates LATS1 through the PPARG Pathway to Participate in Fatty Acid Synthesis in Bovine Mammary Epithelial Cells.

Nutrient metabolism is required to maintain energy balance in animal organisms, and fatty acids play an irreplaceable role in fat metabolism. In this study, microRNA sequencing was performed on mammary gland tissues collected from cows during early, peak, and late lactation to determine miRNA expression profiles. Differentially expressed miRNA (miR-497) was selected for functional studies of fatty acid substitution. Simulants of miR-497 impaired fat metabolism [triacylglycerol (TAG) and cholesterol], whereas knockdown of miR-497 promoted fat metabolism in bovine mammary epithelial cells (BMECs) in vitro. In addition, in vitro experiments on BMECs showed that miR-497 could down-regulate C16:1, C17:1, C18:1, and C20:1 as well as long-chain polyunsaturated fats. Thus, these data expand the discovery of a critical role for miR-497 in mediating adipocyte differentiation. Through bioinformatics analysis and further validation, we identified large tumor suppressor kinase 1 (LATS1) as a target of miR-497. siRNA-LATS1 increased concentrations of fatty acids, TAG, and cholesterol in cells, indicating an active role of LATS1 in milk fat metabolism. In summary, miR-497/LATS1 can regulate the biological processes associated with TAG, cholesterol, and unsaturated fatty acid synthesis in cells, providing an experimental basis for further elucidating the mechanistic regulation of lipid metabolism in BMECs.

Identification of Candidate Genes and Functional Pathways Associated with Body Size Traits in Chinese Holstein Cattle Based on GWAS Analysis.

Body size is one of the most economically important traits of dairy cattle, as it is significantly associated with cow longevity, production, health, fertility, and environmental adaptation. The identification and application of genetic variants using a novel genetic approach, such as genome-wide association studies (GWASs), may give more insights into the genetic architecture of complex traits. The identification of genes, single nucleotide polymorphisms (SNPs), and pathways associated with the body size traits may offer a contribution to genomic selection and long-term planning for selection in dairy cows. In this study, we performed GWAS analysis to identify the genetic markers and genes associated with four body size traits (body height, body depth, chest width, and angularity) in 1000 Chinese Holstein cows. We performed SNPs genotyping in 1000 individuals, based on the GeneSeek Genomic Profiler Bovine 100 K. In total, we identified 11 significant SNPs in association with body size traits at the threshold of Bonferroni correction (5.90 × 10-7) using the fixed and random model circulating probability unification (FarmCPU) model. Several genes within 200 kb distances (upstream or downstream) of the significant SNPs were identified as candidate genes, including MYH15, KHDRBS3, AIP, DCC, SQOR, and UBAP1L. Moreover, genes within 200 kb of the identified SNPs were significantly enriched (p ≤ 0.05) in 25 Gene Ontology terms and five Kyoto Encyclopedia of Genes and Genomes pathways. We anticipate that these results provide a foundation for understanding the genetic architecture of body size traits. They will also contribute to breeding programs and genomic selection work on Chinese Holstein cattle.

Assessment of adaptive immune responses of dairy cows with Burkholderia contaminans-induced mastitis.

Burkholderia contaminans, an emerging pathogen related to cystic fibrosis, is known to cause potentially fatal infections in humans and ruminants, especially in immunocompromised individuals. However, the immune responses in cows following its infection have not been fully elucidated. In this study, T- and B-lymphocytes-mediated immune responses were evaluated in 15 B. contaminans-induced mastitis cows and 15 healthy cows with multi-parameter flow cytometry. The results showed that infection with B. contaminans was associated with a significant decrease in the number and percentage of B lymphocytes but with a significant increase in the proportion of IgG+CD27+ B lymphocytes. This indicated that humoral immune response may not be adequate to fight intracellular infection, which could contribute to the persistent bacterial infection. In addition, B. contaminans infection induced significant increase of γδ T cells and double positive (DP) CD4+CD8+ T cells but not CD4+ or CD8+ (single positive) T cells in blood. Phenotypic analysis showed that the percentages of activated WC1+ γδ T cells in peripheral blood were increased in the B. contaminans infected cows. Interestingly, intracellular cytokine staining showed that cattle naturally infected with B. contaminans exhibited multifunctional TNF-α+IFN-γ+IL-2+ B. contaminans-specific DP T cells. Our results, for the first time, revealed a potential role of IgG+CD27+ B cells, CD4+CD8+ T cells and WC1+ γδ T cells in the defense of B. contaminans-induced mastitis in cows.

Longitudinal genome-wide association studies of milk production traits in Holstein cattle using whole-genome sequence data imputed from medium-density chip data.

Longitudinal traits, such as milk production traits in dairy cattle, are featured by having phenotypic values at multiple time points, which change dynamically over time. In this study, we first imputed SNP chip (50-100K) data to whole-genome sequence (WGS) data in a Chinese Holstein population consisting of 6,470 cows. The imputation accuracies were 0.88 to 0.97 on average after quality control. We then performed longitudinal GWAS in this population based on a random regression test-day model using the imputed WGS data. The longitudinal GWAS revealed 16, 39, and 75 quantitative trait locus regions associated with milk yield, fat percentage, and protein percentage, respectively. We estimated the 95% confidence intervals (CI) for these quantitative trait locus regions using the logP drop method and identified 581 genes involved in these CI. Further, we focused on the CI that covered or overlapped with only 1 gene or the CI that contained an extremely significant top SNP. Twenty-eight candidate genes were identified in these CI. Most of them have been reported in the literature to be associated with milk production traits, such as DGAT1, HSF1, MGST1, GHR, ABCG2, ADCK5, and CSN1S1. Among the unreported novel genes, some also showed good potential as candidate genes, such as CCSER1, CUX2, SNTB1, RGS7, OSR2, and STK3, and are worth being further investigated. Our study provided not only new insights into the candidate genes for milk production traits, but also a general framework for longitudinal GWAS based on random regression test-day model using WGS data.

Heme-heme oxygenase-2 reduces the atherosclerosis by preventing inflammation.

Objective: Heme oxygenase (HO) has been shown to have important antioxidant and anti-inflammatory properties, resulting in a vascular antitherogenic effect. This study was undertaken to evaluate the role of HO-2 in atherosclerosis. Method and results: The expression levels of HO-2 were evaluated in M1 and M2 bone marrow macrophage induced by LPS and IL4. The expression of HO-2 was significantly higher in M2 macrophage than in M1 macrophage. Western diet (WD) caused a significant increase in HO-2 expression in ApoE-/- mice. The adeno-associated viral (AAV) vectors expressing HO-2 was constructed, and the mice were received saline (ApoE-/-), AAV (ApoE-/-), AAV-HO-2 (ApoE-/-) on WD at 12 weeks and their plasma lipids, inflammatory cytokines, atherosclerosis were evaluated for 16 weeks. The results showed AAV-HO-2 was robust, with a significant decrease in the en face aortas, lipids levels, inflammatory cytokines and M1 macrophage content in AAV-HO-2 ApoE-/- compared to control AAV-ApoE-/-. Conclusion: HO-2 expression in macrophages plays an important role of the antiatherogenic effect, decreasing the inflammatory component of atherosclerotic lesions. These results suggest that HO-2 may be a novel therapeutic target for cardiovascular diseases.

Eukaryotic initiation factor 6 repression mitigates atherosclerosis progression by inhibiting macrophages expressing Fasn.

Atherosclerosis, a chronic inflammatory disease that often leads to myocardial infarction and stroke, is mainly caused by lipid accumulation. Eukaryotic initiation factor 6 (Eif6) is a rate-limiting factor in protein translation of transcription factors necessary for lipogenesis. To determine whether Eif6 affects atherosclerosis, Eif6+/- mice were crossed into Apoe-/- background. Apoe-/-/Eif6+/- mice on high fat diet showed significant reduction in atherosclerotic lesions and necrotic core content in aortic root sections in comparison with Apoe-/- mice. RNA-Seq was used to investigate the effect of Eif6 in aorta. Deficiency of Eif6 shows broad effect on cell metabolism. Expression of genes for fatty acid synthesis including Fatty acid synthase (Fasn), Elovl3, Elovl6 and Acaca are down-regulated in aortas. Importantly, Fasn is decreased in macrophages. Results suggest that Eif6 deficiency may decrease atherosclerosis through inhibition of Fasn and lipids metabolism in macrophages.

Expression profile and functional prediction of novel LncRNA 5.8S rRNA-OT1 in cattle.

Long non-coding RNAs (LncRNAs) are generally longer than 200 bp in length and play an important regulatory role in the growth and development of skeletal muscle. In the previous work, the non-coding RNAs with abundant expression in bovine tissues were screened out. After quantitative real-time PCR (qPCR), 33 lncRNAs with differential expression in various bovine tissues were identified. Differential expression analysis base on tissue expression profiles of 33 lncRNAs, a long non-coding RNA LncRNA13, which may have effects on bovine muscle development, was found. The expression levels in embryo muscle and adult cattle muscle were significantly different (p < 0.01), so it is speculated that it may have a certain impact on the development of cattle muscle. It was named LncRNA 5.8S rRNA-OT1, and its overexpression vector pcDNA3.1-LncRNA 5.8S rRNA-OT1 was cloned and constructed. The purpose of this study is to further explore its impact on the proliferation and differentiation of bovine muscle cells and accumulate data to lay a foundation for further exploration of the function of LncRNA 5.8S rRNA-OT1 and add basic data for the study of the regulatory mechanism of lncRNA.

Molecular mechanisms in the miR-33a/LPPR4 pathway regulating unsaturated fatty acid synthesis in bovine mammary epithelial cells.

The regulatory mechanisms governing metabolism of fatty acids in cow mammary gland are crucial for establishing relationships between milk quality and fatty acid content. Both, microRNAs (miRNAs) and protein-coding genes are important factors involved in the regulation of milk fat synthesis. In this study, high-throughput sequencing of miRNAs and mRNAs in bovine mammary gland tissue was performed during peak lactation (3 samples) and late lactation (3 samples) periods to characterize expression profiles. Differential expression (DE) analyses of miRNA and mRNA and miRNA-mRNA regulatory pathway screening were performed. Two-hundred eighty regulatory miRNA-mRNA pairs were identified, including the miR-33a-lipid phosphate phosphatase-related protein type 4 (LPPR4) pathway. Bioinformatics prediction, dual-luciferase reporter system detection, qRT-PCR, and Western blotting revealed that miR-33a can directly target LPPR4 and inhibit its expression. Experiments also revealed that miR-33a promotes the synthesis of triglycerides and increases the content of unsaturated fatty acids (UFAs) in bovine mammary epithelial cells (BMECs). These results indicate that miR-33a via LPPR4 plays an important role in the regulation of milk fat synthesis and UFA levels.

Descriptive Statistics and Genome-Wide Copy Number Analysis of Milk Production Traits of Jiangsu Chinese Holstein Cows.

Milk production traits are the most important quantitative economic traits in dairy cow production; improving the yield and quality of milk is an important way to ensure the production efficiency of the dairy industry. This study carried out a series of in-depth statistical genetics studies and molecular analyses on the Chinese Holstein cows in the Jiangsu Province, such as descriptive statistics and copy number variation analysis. A genetic correlation, phenotypic correlation, and descriptive statistical analysis of five milk production traits (milk yield, milk fat percentage, milk fat yield, milk protein percentage, and milk protein yield) of the dairy cows were analyzed using the SPSS and DMU software. Through quality control, 4173 cows and their genomes were used for genomic study. Then, SNPs were detected using DNA chips, and a copy number variation (CNV) analysis was carried out to locate the quantitative trait loci (QTL) of the milk production traits by Perl program software Penn CNV and hidden Markov model (HMM). The phenotypic means of the milk yield, milk fat percentage, milk fat mass, milk protein percentage, and milk protein mass at the first trimester were lower than those at the other trimesters by 8.821%, 1.031%, 0.930%, 0.003%, and 0.826%, respectively. The five milk production traits showed a significant phenotypic positive correlation (p < 0.01) and a high genetic positive correlation among the three parities. Based on the GGPBovine 100 K SNP data, QTL-detecting research on the fist-parity milk performance of dairy cows was carried out via the CNV. We identified 1731 CNVs and 236 CNVRs in the 29 autosomes of 984 Holstein dairy cows, and 19 CNVRs were significantly associated with the milk production traits (p < 0.05). These CNVRs were analyzed via a bioinformatics analysis; a total of 13 gene ontology (GO) terms and 20 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly enriched (p < 0.05), and these terms and pathways are mainly related to lipid metabolism, amino acid metabolism, and cellular catabolic processes. This study provided a theoretical basis for the molecular-marker-assisted selection of dairy cows by developing descriptive statistics on the milk production traits of dairy cows and by locating the QTL and functional genes that affect the milk production traits of first-born dairy cows. The results describe the basic status of the milk production traits of the Chinese Holstein cows in Jiangsu and locate the QTL and functional genes that affect the milk production traits of the first-born cows, providing a theoretical basis for the molecular-marker-assisted selection of dairy cows.