Bioinformatics analysis of candidate genes for milk production traits in water buffalo (Bubalus bubalis)

TWAS revealed significant causal loci for milk production and its composition in Murrah buffaloes

Milk yield is the most complex trait in dairy animals, and mapping all causal variants even with smallest effect sizes has been difficult with the genome-wide association study (GWAS) sample sizes available in geographical regions with small livestock holdings such as Indian sub-continent. However, Transcriptome-wide association studies (TWAS) could serve as an alternate for fine mapping of expression quantitative trait loci (eQTLs). This is a maiden attempt to identify milk production and its composition related genes using TWAS in Murrah buffaloes (Bubalus bubalis). TWAS was conducted on a test (N = 136) set of Murrah buffaloes genotyped through ddRAD sequencing. Their gene expression level was predicted using reference (N = 8) animals having both genotype and mammary epithelial cell (MEC) transcriptome information. Gene expression prediction was performed using Elastic-Net and Dirichlet Process Regression (DPR) model with fivefold cross-validation and without any cross-validation. DPR model without cross-validation predicted 80.92% of the total genes in the test group of Murrah buffaloes which was highest compared to other methods. TWAS in test individuals based on predicted gene expression, identified a significant association of one unique gene for Fat%, and two for SNF% at Bonferroni corrected threshold. The false discovery rates (FDR) corrected P-values of the top ten SNPs identified through GWAS were comparatively higher than TWAS. Gene ontology of TWAS-identified genes was performed to understand the function of these genes, it was revealed that milk production and composition genes were mainly involved in Relaxin, AMPK, and JAK-STAT signaling pathway, along with CCRI, and several key metabolic processes. The present study indicates that TWAS offers a lower false discovery rate and higher significant hits than GWAS for milk production and its composition traits. Hence, it is concluded that TWAS can be effectively used to identify genes and cis-SNPs in a population, which can be used for fabricating a low-density genomic chip for predicting milk production in Murrah buffaloes.

Comparative Genomic Analysis of the Thiolase Family and Functional Characterization of the Acetyl-Coenzyme A Acyltransferase-1 Gene for Milk Biosynthesis and Production of Buffalo and Cattle

Cattle and buffalo served as the first and second largest dairy animals, respectively, providing 96% milk products worldwide. Understanding the mechanisms underlying milk synthesis is critical to develop the technique to improve milk production. Thiolases, also known as acetyl-coenzyme A acetyltransferases (ACAT), are an enzyme family that plays vital roles in lipid metabolism, including ACAT1, ACAT2, ACAA1, ACAA2, and HADHB. Our present study showed that these five members were orthologous in six livestock species including buffalo and cattle. Transcriptomic data analyses derived from different lactations stages showed that ACAA1 displayed different expression patterns between buffalo and cattle. Immunohistochemistry staining revealed that ACAA1 were dominantly located in the mammary epithelial cells of these two dairy animals. Knockdown of ACAA1 inhibited mammary epithelial cell proliferation and triglyceride and β-casein secretion by regulating related gene expressions in cattle and buffalo. In contrast, ACAA1 overexpression promoted cell proliferation and triglyceride secretion. Finally, three novel SNPs (g.-681A>T, g.-23117C>T, and g.-24348G>T) were detected and showed significant association with milk production traits of Mediterranean buffaloes. In addition, g.-681A>T mutation located in the promoter region changed transcriptional activity significantly. Our findings suggested that ACAA1 play a key role in regulating buffalo and cattle milk synthesis and provided basic information to further understand the dairy animal lactation physiology.

Peroxisome proliferator-activated receptor gamma regulates genes involved in milk fat synthesis in mammary epithelial cells of water buffalo

Peroxisome proliferator-activated receptor gamma (PPARγ) is a critical transcription factor regulating lipid and glucose metabolism. However, the regulatory effect of PPARγ on milk fat synthesis in buffalo mammary gland is not clear. In order to explore the role of buffalo PPARG gene in milk fat synthesis, lentivirus-mediated interference was used to knock it down and then the recombinant fusion expression vector was transfected into buffalo mammary epithelial cell (BMEC) to overexpress it. PPARG gene knockdown significantly decreased the expression of CD36, FABP3, FABP4, ACSS2, ELOVL6, DGAT2, BTN1A1, AGPAT6, LPIN1, ABCG2, PPARGC1A, INSIG1, FASN, and SREBF2 genes and significantly upregulated the expression of INSIG2 gene but had no significant effect on the expression of ACSL1, GPAM, and SREBF1 genes. PPARG overexpression significantly increased the relative mRNA abundance of CD36, FABP3, FABP4, ACSS2, ELOVL6, DGAT2, BTN1A1, AGPAT6, LPIN1, PPARGC1A, INSIG1, and SREBF2 genes and significantly downregulated the expression of INSIG2 gene but had no significant effect on the expression of ACSL1, GPAM, ABCG2, FASN, and SREBF1 genes. In addition, knockdown/overexpression of PPARG gene significantly decreased/increased triacylglycerol (TAG) content in BMECs. This study revealed that buffalo PPARG gene is a key gene regulating buffalo milk fat synthesis.

Evaluation of Ovsynch versus modified Ovsynch program on pregnancy rate in water buffaloes: a meta-analysis

Ovsynch is a widely accepted estrus synchronization protocol for improving the reproductive performance of water buffaloes who manifest low reproductive efficiency. Recently, some modified protocols based on Ovsynch such as 2 injections of prostaglandin 14 days apart following the Ovsynch are also introduced to enhance the reproductive potential of this species. In the present study, a meta-analytical assessment was performed with the objective to evaluate the reproductive performance of water buffaloes synchronized with Ovsynch or modified Ovsynch programs. Meta-analysis of the fixed or random effects model was determined by the heterogeneity among the studies. Reproductive outcome of interest was pregnancy per artificial insemination (P/AI) measured on day 25 (25-100). A total of 32 articles including 4003 buffaloes using either Ovsynch or modified Ovsynch protocol were reviewed. In the random effects model for buffaloes, the overall proportion of P/AI was 42.55% [95% confidence interval (CI): 37.48-47.70; n = 3,089] and 46.44% (95% CI: 39.63-53.31; n = 914) on day 25 after AI for Ovsynch and modified Ovsynch, respectively. Results for P/AI were then categorized by ovarian activity, where P/AI was available for 3575 cyclic buffaloes and 320 non-cyclic buffaloes. For cyclic buffaloes, the overall proportion of P/AI was 47.54% (95% CI: 42.72-52.38; n = 2911) and 57.97% (95% CI: 54.12-61.77; n = 664) on day 25 after AI for Ovsynch and modified Ovsynch, respectively. In the fixed effects model for non-cyclic buffaloes, the overall proportion of P/AI was 19.68% (95% CI: 13.48-26.58; n = 167) and 33.01% (95% CI: 25.50-40.94; n = 153) on day 25 after AI for Ovsynch and modified Ovsynch, respectively. In conclusion, a benefit for P/AI is detected in buffaloes with the modified Ovsynch protocol. Besides, whichever estrus synchronization protocols (Ovsynch or modified Ovsynch), cyclic buffaloes have higher P/AI compared with non-cyclic buffaloes.

Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein Cattle

Simple Summary

Milk production traits that are economically important in the dairy industry have been considered the main selection criteria for breeding. The present genome-wide association study was performed to identify chromosomal loci and candidate genes with potential effects on milk production phenotypes in a Korean Holstein population. A total of eight significant quantitative trait locus regions were identified for milk yield (Bos taurus autosome (BTA) 7 and 14), adjusted 305-d fat yield (BTA 3, 5, and 14), adjusted 305-d protein yield (BTA 8), and somatic cell score (BTA 8 and 23) of milk production traits. Furthermore, we discovered three main candidate genes (diacylglycerol O-acyltransferase 1 (DGAT1), phosphodiesterase 4B (PDE4B), and anoctamin 2 (ANO2)) through bioinformatics analysis. These genes may help to understand better the underlying genetic and molecular mechanisms for milk production phenotypes in the Korean Holstein population.

Abstract

We performed a genome-wide association study and fine mapping using two methods (single marker regression: frequentist approach and Bayesian C (BayesC): fitting selected single nucleotide polymorphisms (SNPs) in a Bayesian framework) through three high-density SNP chip platforms to analyze milk production phenotypes in Korean Holstein cattle (n = 2780). We identified four significant SNPs for each phenotype in the single marker regression model: AX-311625843 and AX-115099068 on Bos taurus autosome (BTA) 14 for milk yield (MY) and adjusted 305-d fat yield (FY), respectively, AX-428357234 on BTA 18 for adjusted 305-d protein yield (PY), and AX-185120896 on BTA 5 for somatic cell score (SCS). Using the BayesC model, we discovered significant 1-Mb window regions that harbored over 0.5% of the additive genetic variance effects for four milk production phenotypes. The concordant significant SNPs and 1-Mb window regions were characterized into quantitative trait loci (QTL). Among the QTL regions, we focused on a well-known gene (diacylglycerol O-acyltransferase 1 (DGAT1)) and newly identified genes (phosphodiesterase 4B (PDE4B), and anoctamin 2 (ANO2)) for MY and FY, and observed that DGAT1 is involved in glycerolipid metabolism, fat digestion and absorption, metabolic pathways, and retinol metabolism, and PDE4B is involved in cAMP signaling. Our findings suggest that the candidate genes in QTL are strongly related to physiological mechanisms related to the fat production and consequent total MY in Korean Holstein cattle.

Milk production potential and reproductive performance of Egyptian buffalo cows

Limited data are available on the phenotypic factors related to the productive and reproductive performance of Egyptian buffalo cows, based on a large sample size. This study aims to estimate the effect of phenotypic factors on productive and reproductive traits of Egyptian buffaloes. Data were collected from five dairy buffalo stations and include 3787 lactation records. For the analysis of variance, four seasons were considered in each year, and the parity included seven classes. Dry periods were divided into three intervals (< 90, 90-170, and > 170 d). Birth weight was divided into four categories (<25, 25-30, 31-35, and >35 kg). The results indicated that winter-calving buffaloes had the highest total milk yield (TMY) of the whole lactation, with the shortest (p<0.001) lactation length (LL), days open (DO), and calving interval (CI). Both, total milk TMY/kg and LL/days were increased (p<0.001), but the CI was linearly decreased (p<0.001). Overall, buffaloes with age at first mating (AFM<25month), age at first calving (AFC<35 month), and a dry period (DP<90days), produced the highest TMY (p<0.001) and maintained the longest LL (p<0.001). By increasing the body weight at birth (BWB), milk production level significantly increased. Buffaloes of BWB<25kg had the shortest DO (p<0.004; 168.10±3.598 days) and CI (p<0.006; 17.01±.135 months). In conclusion, body weight at birth, season, parity, DO, CI, AFM, AFC, and DP could be used as predictors to improve reproductive and productive traits in buffalo breeding programs. The wide range in milk yield and reproductive traits indicated significant potential in increasing the productive and reproductive performances of Egyptian buffalo cows.

Genome-wide scan reveals genomic regions and candidate genes underlying direct and maternal effects of preweaning calf mortality in Nellore cattle

We conducted analysis to estimate genetic parameters and to identify genomic regions and candidate genes affecting direct and maternal effects of preweaning calf mortality (PWM) in Nellore cattle. Phenotypic records of 67,196 animals, and 8443 genotypes for 410,936 SNPs were used. Analysis were performed through the weighted single-step GBLUP approach and considering a threshold animal model via Bayesian Inference. Direct and maternal heritability estimates were of 0.2143 ± 0.0348 and 0.0137 ± 0.0066, respectively. The top 10 genomic regions accounted for 13.61 and 14.23% of the direct and maternal additive genetic variances and harbored a total of 63 and 91 positional candidate genes, respectively. Two overlapping regions on BTA2 were identified for both direct and maternal effects. Candidate genes are involved in biological mechanisms i.e. embryogenesis, immune response, feto-maternal communication, circadian rhythm, hormone alterations, myometrium adaptation, and milk secretion, which are critical for the successful calf growth and survival during preweaning period.

Identification, molecular characteristics, and tissue differential expression of DGAT2 full-CDS cDNA sequence in Binglangjiang buffalo (Bubalus bubalis)

It has been found that diacylglycerol acyltransferase-2 (DGAT2) plays a crucial role in the synthesis of triglycerides (TGs) in some mammals, but its role in buffalo lactation is unclear. In the present study, the DGAT2 full-CDS cDNA sequence of Binglangjiang buffalo was isolated, and the physicochemical characteristics and structure of its encoding protein were characterized. Furthermore, the differential expressions of this gene in 10 tissues of lactating and non-lactating buffalo were analyzed by real-time quantitative PCR (RT-qPCR). The results showed that the coding region (CDS) of this gene was 1086 bp in length, encoding a peptide composed of 361 amino acid residues. The deduced amino acid sequence shared more than 98.6 % identity with that of cattle, zebu, yak, and bison in the Bovidae family. Buffalo DGAT2 protein is a slightly hydrophobic protein with a transmembrane region, which functions in membrane of endoplasmic reticulum. Besides, this protein belongs to the LPLAT_MGAT-like family and contains a conserved domain of DAGAT that has a function in the synthesis of TGs. The multi-tissue differential expression analysis demonstrated that DGAT2 was expressed in the heart, liver, mammary gland, and muscle in both non-lactating and lactating buffalo. And its expression level in the heart, liver, and mammary gland during lactation was significantly higher than that during non-lactation. The results indicate that buffalo DGAT2 may be involved in milk fat synthesis. This study can establish a foundation for further elucidating mechanisms of the buffalo DGAT2 gene in milk fat synthesis.