Buffalo milk transcriptome: A comparative analysis of early, mid and late lactation

Evolutionary analysis of buffalo sterol regulatory element-binding factor (SREBF) family genes and their affection on milk traits

The sterol regulatory element-binding factor (SREBF) genes are a vital group of proteins binding to the sterol regulatory element 1 (SRE-1) regulating the synthesis of fatty acid. Two potential candidate genes (SREBF1 and SREBF2) have been identified as affecting milk traits. This study aims to identify the SREBF family of genes and find candidate markers or SREBF genes influencing lactation production in buffalo. A genome-wide study was performed and identified seven SREBF genes randomly distributed on 7 chromosomes and 24 protein isoforms in buffalos. The SREBF family of genes were also characterized in cattle, goat, sheep and horse, and using these all-protein sequences, a phylogenetic tree was built. The SREBF family genes were homologous between each other in the five livestock. Eight single nucleotide polymorphisms (SNPs) within or near the SREBF genes in the buffalo genome were identified and at least one milk production trait was associated with three of the SNP. The expression of SREBF genes at different lactation stages in buffalo and cattle from published data were compared and the SREBF genes retained a high expression throughout lactation with the trend being the same for buffalo and cattle. These results provide valuable information for clarifying the evolutionary relationship of the SREBF family genes and determining the role of SREBF genes in the regulation of milk production in buffalo.

Role of Different Members of the AGPAT Gene Family in Milk Fat Synthesis in Bubalus bubalis

During triacylglycerol synthesis, the acylglycerol-3-phosphate acyltransferase (AGPAT) family catalyzes the conversion of lysophosphatidic acid to phosphatidic acid and the acylation of sn-2 fatty acids. However, the catalytic activity of different AGPAT members is different. Therefore, this study aimed to investigate the mechanism through which different AGPATs affect the efficiency of TAG synthesis and fatty acid composition. The conservation of amino acid sequences and protein domains of the AGPAT family was analyzed, and the functions of AGPAT1, AGPAT3, and AGPAT4 genes in buffalo mammary epithelial cells (BMECs) were studied using RNA interference and gene overexpression. Prediction of the protein tertiary structure of the AGPAT family demonstrated that four conservative motifs (motif1, motif2, motif3, and motif6) formed a hydrophobic pocket in AGPAT proteins, except AGPAT6. According to cytological studies, AGPAT1, AGPAT3, and AGPAT4 were found to promote the synthesis and fatty acid compositions of triacylglycerol, especially UFA compositions of triacylglycerol, by regulating ACSL1, FASN, GPAM, DGAT2, and PPARG gene expression. This study provides new insights into the role of different AGPAT gene family members involved in TAG synthesis, and a reference for improving the fatty acid composition of milk.

Genetic variation in the OPN gene affects milk composition in Chinese Holstein cows

The aim of this study was to investigate the association between genotypes and haplotypes of OPN, and milk composition in dairy cows. A total of 317 Chinese Holstein cows were genotyped via DNA sequencing in this study. Three single nucleotide polymorphisms (SNPs), g.2916G > A, g.58675C > T and g.58899C > A, and eight haplotypes were identified. Of the eight possible haplotypes, four haplotypes i.e., Hap2 (ACC; 55.30%), Hap6 (GCC, 15.6%), Hap1 (ACA, 13.6%) and Hap4 (ATC, 5.70%), were considered to be major with a cumulative estimated frequency of >90%. Single markers (g.2916G > A and g.58899C > A) and Haplotype Hap6/4 were found to be associated with an increase in butter-fat percentage (p < 0.05). Taken together, our results provided evidence that polymorphisms in OPN are associated with milk composition, and could potentially be used for marker-assisted selection in Chinese Holstein cows.

Comparative analyses of copy number variations between swamp buffaloes and river buffaloes

As an important source of genomic variation, copy number variation (CNV) contributes to environmental adaptation in worldwide buffaloes. Despite this importance, CNV divergence between swamp buffaloes and river buffaloes has not been studied previously. Here, we report 21 152 CNV regions (CNVRs) in 141 buffaloes of 20 breeds detected through multiple CNV calling strategies. Only 248 CNVRs were shared between river buffalo and swamp buffalo, reflecting great variation of CNVRs between the two subspecies. Population structure analysis based on CNVs successfully separated the two buffalo subspecies. We further assessed CNV divergence by calculating F_ST for genome-wide CNVs. Totally, we identified 110 significantly divergent CNV segments and 44 putatively selected genes between river buffaloes and swamp buffaloes. In particular, LALBA, a key gene controlling milk production in cattle, presented a highly differentiated CNV in the promoter region, which makes it a strong functional candidate gene for differences between swamp buffaloes and river buffaloes in traits related to milk production. Our study provides useful information of CNVs in buffaloes, which may help explain the genetic differences between the two subspecies.

Transcriptomic profiles of the ruminal wall in Italian Mediterranean dairy buffaloes fed green forage

BACKGROUND

Green feed diet in ruminants exerts a beneficial effect on rumen metabolism and enhances the content of milk nutraceutical quality. At present, a comprehensive analysis focused on the identification of genes, and therefore, biological processes modulated by the green feed in buffalo rumen has never been reported. We performed RNA-sequencing in the rumen of buffaloes fed a total mixed ration (TMR) + the inclusion of 30% of ryegrass green feed (treated) or TMR (control), and identified differentially expressed genes (DEGs) using EdgeR and NOISeq tools.

RESULTS

We found 155 DEGs using EdgeR (p-values < 0.05) and 61 DEGs using NOISeq (prob ≥0.8), 30 of which are shared. The rt-qPCR validation suggested a higher reliability of EdgeR results as compared with NOISeq data, in our biological context. Gene Ontology analysis of DEGs identified using EdgeR revealed that green feed modulates biological processes relevant for the rumen physiology and, then, health and well-being of buffaloes, such as lipid metabolism, response to the oxidative stress, immune response, and muscle structure and function. Accordingly, we found: (i) up-regulation of HSD17B13, LOC102410803 (or PSAT1) and HYKK, and down-regulation of CDO1, SELENBP1 and PEMT, encoding factors involved in energy, lipid and amino acid metabolism; (ii) enhanced expression of SIM2 and TRIM14, whose products are implicated in the immune response and defense against infections, and reduced expression of LOC112585166 (or SAAL1), ROR2, SMOC2, and S100A11, encoding pro-inflammatory factors; (iii) up-regulation of NUDT18, DNAJA4 and HSF4, whose products counteract stressful conditions, and down-regulation of LOC102396388 (or UGT1A9) and LOC102413340 (or MRP4/ABCC4), encoding detoxifying factors; (iv) increased expression of KCNK10, CACNG4, and ATP2B4, encoding proteins modulating Ca²⁺ homeostasis, and reduced expression of the cytoskeleton-related MYH11 and DES.

CONCLUSION

Although statistically unpowered, this study suggests that green feed modulates the expression of genes involved in biological processes relevant for rumen functionality and physiology, and thus, for welfare and quality production in Italian Mediterranean dairy buffaloes. These findings, that need to be further confirmed through the validation of additional DEGs, allow to speculate a role of green feed in the production of nutraceutical molecules, whose levels might be enhanced also in milk.

Feeding of palm oil fatty acids or rapeseed oil throughout lactation: Effects on mammary gene expression and milk production in Norwegian dairy goats

Lipid added as rapeseed or palm oil to the diet of dairy goats over 8 mo of one lactation alters fat secretion and milk fatty acid (FA) and protein composition. In this study, we examined the contribution of mammary gene expression to these changes and included 30 multiparous goats of Norwegian dairy goat breed for a 230-d experimental period, with indoor feeding from 1 to 120 d in milk (DIM), mountain grazing from 120 to 200 DIM, and indoor feeding from 200 to 230 DIM. After an initial period (1-60 DIM) when the control diet was given to all goats, the animals were subdivided into 3 groups of 10 goats. Treatments (60-230 DIM) were basal concentrate (control) alone or supplemented with either 8% (by weight) hydrogenated palm oil enriched with palmitic acid (POFA) or 8% (by weight) rapeseed oil (RSO). Milk was sampled individually from all animals throughout lactation, at 60, 120, 190, and 230 DIM for milk yield and composition. On d 60, 120, 190, and 230, mammary tissue was collected by biopsy to measure mRNA abundance of 19 key genes. None of the 19 genes involved in milk protein, apoptosis, lipid metabolism, transcription factors, and protein of the milk fat globule membrane, as measured by mRNA abundance, were affected by the lipid supplements, although POFA increased milk fat content, and POFA and RSO affected milk FA composition. Over the experimental period (120-230 DIM), the mRNA abundance of 13 of the 19 studied genes was affected by lactation stage. For some genes, expression either gradually increased from 120 to 230 DIM (CSN2,CASP8,CD36,GLUT4) or increased from 120 to 200 and then remained stable (XDH), or decreased (CSN3,G6PD,SREBF1,PPARG1) or increased only at 230 DIM (SCD1,SCD5,ELF3). For a second group of genes (CSN1, LALBA, FABP3, FASN, LPL, MFGE8), expression was stable over the lactation period. Our results suggest that factors other than gene expression, such as substrate availability or posttranscriptional regulation of these genes, could play an important role in the milk fat and FA responses to dietary fat composition in the goat. In conclusion, mammary gene expression in goats was more regulated by stage of lactation than by the dietary treatments applied.

First report on delineation of differentially expressed genes and pathways in milk somatic cells of mastitic and healthy Murrah buffaloes

Despite immense contribution of buffaloes as dairy species, limited studies have addressed the bubaline mastitis as compared to cattle. This was the first differential transcriptomic study investigating the alterations induced by clinical mastitis in buffalo milk relative to healthy controls. Comparative gene expression profiling of three biological replicates of each group identified 1014 up-regulated and 999 down-regulated genes in the diseased buffaloes (Fold change > 2, FDR < 0.05). Activation of immune and inflammatory responses were the most enriched GO terms in the mastitic animals, with higher transcript abundance of many genes coding for anti-microbial proteins such as β-defensins, perforin, granzymes, granulysin, cathelicidins etc. Analysis of the gene regulatory interactions of the up-regulated DEGs identified many hub genes that govern the cellular and macromolecular metabolic processes (E2F4, E2F1, RBL2, FOXM1, IRF1 and MYB). This study contributes to an insightful understanding of molecular mechanisms governing immune response of buffaloes to mastitis.

Nutritional Modulation, Gut, and Omics Crosstalk in Ruminants

Simple Summary

Over the last decade, animal nutrition science has been significantly developed, supported by the great advancements in molecular technologies. For scientists, the present "feedomics and nutrigenomics" era continues to evolve and shape how research is designed, performed, and understood. The new omics interpretations have established a new point of view for the nutrition–gene interaction, integrating more comprehensive findings from animal physiology, molecular genetics, and biochemistry. In the ruminant model, this modern approach addresses rumen microbes as a critical intermediate that can deepen the studies of diet–gut interaction with host genomics. The present review discusses nutrigenomics’ and feedomics’ potential contribution to diminishing the knowledge gap about the DNA cellular activities of different nutrients. It also presents how nutritional management can influence the epigenetic pathway, considering the production type, life stage, and species for more sustainable ruminant nutrition strategies.

Abstract

Ruminant nutrition has significantly revolutionized a new and prodigious molecular approach in livestock sciences over the last decade. Wide-spectrum advances in DNA and RNA technologies and analysis have produced a wealth of data that have shifted the research threshold scheme to a more affluent level. Recently, the published literature has pointed out the nutrient roles in different cellular genomic alterations among different ruminant species, besides the interactions with other factors, such as age, type, and breed. Additionally, it has addressed rumen microbes within the gut health and productivity context, which has made interpreting homogenous evidence more complicated. As a more systematic approach, nutrigenomics can identify how genomics interacts with nutrition and other variables linked to animal performance. Such findings should contribute to crystallizing powerful interpretations correlating feeding management with ruminant production and health through genomics. This review will present a road-mapping discussion of promising trends in ruminant nutrigenomics as a reference for phenotype expression through multi-level omics changes.

Transcriptomic in silico analysis of bovine Escherichia coli mastitis highlights its immune-related expressed genes as an effective biomarker

Background

Mastitis is one of the major diseases causing economic loss to the dairy industry by reducing the quantity and quality of milk. Thus, the objective of this scientific study was to find new biomarkers based on genes for the early prediction before its severity.

Methods

In the present study, advanced bioinformatics including hierarchical clustering, enrichment analysis, active site prediction, epigenetic analysis, functional domain identification, and protein docking were used to analyze the important genes that could be utilized as biomarkers and therapeutic targets for mastitis.

Results

Four differentially expressed genes (DEGs) were identified in different regions of the mammary gland (teat cistern, gland cistern, lobuloalveolar, and Furstenberg’s rosette) that resulted in 453, 597, 577, and 636 DEG, respectively. Also, 101 overlapped genes were found by comparing 27 different expressed genes. These genes were associated with eight immune response pathways including NOD-like receptor signaling pathway (IL8, IL18, IL1B, PYDC1) and chemokine signaling pathway (PTK2, IL8, NCF1, CCR1, HCK). Meanwhile, 241 protein-protein interaction networks were developed among overlapped genes. Fifty-seven regulatory events were found between miRNAs, expressed genes, and the transcription factors (TFs) through micro-RNA and transcription factors (miRNA-DEG-TF) regulatory network. The 3D structure docking model of the expressed genes proteins identified their active sites and the binding ligands that could help in choosing the appropriate feed or treatment for affected animals.

Conclusions

The novelty of the distinguished DEG and their pathways in this study is that they can precisely improve the detection biomarkers and treatments techniques of cows’ Escherichia coli mastitis disease due to their high affinity with the target site of the mammary gland before appearing the symptoms.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-021-00235-x.

RNA-seq and nuclear proteomics provide insights into the lactation regulation mechanism of goat transfected IGF-I and GH recombinant vectors

There exists little available information on the mechanisms of lactation regulation until now. In order to explore the underlying mechanism, we injected IGF-I and GH recombinant vectors into the mammary gland, then RNA-seq analysis and nuclear proteomics were used for rapid high-throughput screening of DEGs and DEPs in the two groups linked to lactation regulation. KEGG analysis of 206 DEGs showed that the same 4 of top 10 enrichment pathways (ECM receptor interaction, protein digestion and absorption, focal adhesion and phagosome) involved in 4 co-expressed genes (IDO, BTG1, ITGB6 and keratin 83), the two groups enriched different metabolic pathways yet. Nuclear proteomics analysis showed 75 and 36 DEPs in the IGF-I and GH group respectively; Sixteen common proteins were identified between the IGF-I group and GH group, four of which (ALB, TPT1, CXXC-5 and ACTR2) significantly decreased and three of which (PRP1, PAG-9 and Hsp70) significantly increased. Similarly, DEPs in the two groups were enriched in same one of top 10 enrichment pathways (PI3K-Akt signaling pathway). Protein-protein interaction networks highlighted the contribution of glycosphingolipid biosynthesis, porphyrin and chlorophyll metabolism and the Jak-STAT signaling pathway to lactation regulation of GH and IGFI. GH and IGF-I improve milk yield, which may be linked to important nodal proteins (ALB and ACTB). Our research advances the understanding of the mammary gland transcriptome and nuclear proteomics during GH and IGF-I overexpression. Individual genes, proteins and pathways in this study point towards potential targets for lactation regulation.

Compositional Characteristics of Mediterranean Buffalo Milk and Whey

The main objective of this review is to summarize the compositional characteristics and the health and functional properties of Mediterranean buffalo milk and whey derived from mozzarella cheese production. Several studies have investigated the composition of buffalo milk and in particular its fat, protein, and carbohydrates contents. These characteristics may change depending on the breed, feeding regime, and rearing system of the animals involved in the study, and also with the seasons. In particular, buffalo milk showed a higher nutritional value and higher levels of proteins, vitamins, and minerals when compared to milks produced by other animal species. Additionally, buffalo milk contains beneficial compounds such as gangliosides that can provide antioxidant protection and neuronal protection, and can improve bone, heart, and gastrointestinal health in humans.

SNPs in Mammary Gland Epithelial Cells Unraveling Potential Difference in Milk Production Between Jersey and Kashmiri Cattle Using RNA Sequencing

Deep RNA sequencing experiment was employed to detect putative single nucleotide polymorphisms (SNP) in mammary epithelial cells between two diverse cattle breeds (Jersey and Kashmiri) to understand the variations in the coding regions that reflect differences in milk production traits. The low milk-producing Kashmiri cattle are being replaced by crossbreeding practices with Jersey cattle with the aim of improving milk production. However, crossbred animals are prone to infections and various other diseases resulting in unsustainable milk production. In this study, we tend to identify high-impact SNPs from Jersey and Kashmiri cows (utilizing RNA-Seq data) to delineate key pathways mediating milk production traits in both breeds. A total of 607 (442 SNPs and 169 INDELs) and 684 (464 SNPs and 220 INDELs) high-impact variants were found specific to Jersey and Kashmir cattle, respectively. Based on our results, we conclude that in Jersey cattle, genes with high-impact SNPs were enriched in nucleotide excision repair pathway, ABC transporter, and metabolic pathways like glycerolipid metabolism, pyrimidine metabolism, and amino acid synthesis (glycine, serine, and threonine). Whereas, in Kashmiri cattle, the most enriched pathways include endocytosis pathway, innate immunity pathway, antigen processing pathway, insulin resistance pathway, and signaling pathways like TGF beta and AMPK which could be a possible defense mechanism against mammary gland infections. A varied set of SNPs in both breeds, suggests a clear differentiation at the genomic level; further analysis of high-impact SNPs are required to delineate their effect on these pathways.

Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

BACKGROUND

Porcine milk is a complex fluid, containing a myriad of immunological, biochemical, and cellular components, made to satisfy the nutritional requirements of the neonate. Whole milk contains many different cell types, including mammary epithelial cells, neutrophils, macrophages, and lymphocytes, as well nanoparticles, such as milk exosomes. To-date, only a limited number of livestock transcriptomic studies have reported sequencing of milk. Moreover, those studies focused only on sequencing somatic cells as a proxy for the mammary gland with the goal of investigating differences in the lactation process. Recent studies have indicated that RNA originating from multiple cell types present in milk can withstand harsh environments, such as the digestive system, and transmit regulatory molecules from maternal to neonate. Transcriptomic profiling of porcine whole milk, which is reflective of the combined cell populations, could help elucidate these mechanisms. To this end, total RNA from colostrum and mature milk samples were sequenced from 65 sows at differing parities. A stringent bioinformatic pipeline was used to identify and characterize 70,841 transcripts.

RESULTS

The 70,841 identified transcripts included 42,733 previously annotated transcripts and 28,108 novel transcripts. Differential gene expression analysis was conducted using a generalized linear model coupled with the Lancaster method for P-value aggregation across transcripts. In total, 1667 differentially expressed genes (DEG) were identified for the milk type main effect, and 33 DEG were identified for the milk type x parity interaction. Several gene ontology (GO) terms related to immune response were significant for the milk type main effect, supporting the well-known fact that immunoglobulins and immune cells are transferred to the neonate via colostrum.

CONCLUSIONS

This is the first study to perform global transcriptome analysis from whole milk samples in sows from different parities. Our results provide important information and insight into synthesis of milk proteins and innate immunity and potential targets for future improvement of swine lactation and piglet development.

Transcriptional profiling of buffalo mammary gland with different milk fat contents

Milk fat is the most important energy substance in milk and contributes to its quality and health benefits. Water buffalo milk is well known for its high milk quality with higher fat contents compared with cattle milk. Dehong buffalo is a unique local swamp breed in Yunnan Province with higher milk fat and excellent milk quality which provides a good model for the investigation of the molecular mechanisms of milk fat deposition. In this study, we used RNA-seq to obtain mammary tissue transcriptomics of buffalo with different milk fat phenotypes including high(H), medium (M)and low (L) fat content groups. Comparative analyses of buffalo among three groups yielded differentially expressed genes (DEGs). Analyzing the number of different genes among H_VS_L, H_VS_M, and M_VS_L showed the same expression pattern between H_VS_M. The increasing expression levels of genes including CSN1S1, BTN1A1, LALBA, ALDH1L2, SCD and MUC15, and down-regulated expression levels of genes containing CCL2, CRABP2, ADTRP, CLU and C4A in H_VS_L and M_VS_L were found. GO and KEGG enriched pathways revealed these DEGs involved in milk protein and fat as well as immune response. The findings would enhance the understanding of the interplay between the milk composition and immune response, which suggests that the immune capacity should be considered when we tried to improve the milk quality.

Genes and Pathways Affecting Sheep Productivity Traits: Genetic Parameters, Genome-Wide Association Mapping, and Pathway Enrichment Analysis

Ewe productivity is a composite and maternal trait that is considered the most important economic trait in sheep meat production. The objective of this study was the application of alternative genome-wide association study (GWAS) approaches followed by gene set enrichment analysis (GSEA) on the ewes’ genome to identify genes affecting pregnancy outcomes and lamb growth after parturition in Iranian Baluchi sheep. Three maternal composite traits at birth and weaning were considered. The traits were progeny birth weight, litter mean weight at birth, total litter weight at birth, progeny weaning weight, litter mean weight at weaning, and total litter weight at weaning. GWASs were performed on original phenotypes as well as on estimated breeding values. The significant SNPs associated with composite traits at birth were located within or near genes RDX, FDX1, ARHGAP20, ZC3H12C, THBS1, and EPG5. Identified genes and pathways have functions related to pregnancy, such as autophagy in the placenta, progesterone production by the placenta, placental formation, calcium ion transport, and maternal immune response. For composite traits at weaning, genes (NR2C1, VEZT, HSD17B4, RSU1, CUBN, VIM, PRLR, and FTH1) and pathways affecting feed intake and food conservation, development of mammary glands cytoskeleton structure, and production of milk components like fatty acids, proteins, and vitamin B-12, were identified. The results show that calcium ion transport during pregnancy and feeding lambs by milk after parturition can have the greatest impact on weight gain as compared to other effects of maternal origin.

TMT based deep proteome analysis of buffalo mammary epithelial cells and identification of novel protein signatures during lactogenic differentiation

The lactating mammary gland harbours numerous matured alveoli with their lumen surrounded by differentiated mammary epithelial cells (MECs), which are exclusively involved in milk synthesis and secretion. Buffalo (Bubalus bubalis) is the second major milk-producing animal, and its physiology is different from cattle. The complete protein machinery involved in MECs differentiation is still not defined in ruminants, in particular, buffalo. Therefore, we have studied the differential expression of regulated proteins in the in vitro grown buffalo MECs (BuMECs) at different time points (on 3, 6, 12, and 15 days) of their differentiation in the presence of lactogenic hormones. TMT-based MS analysis identified 4,934 proteins; of them, 681 were differentially expressed proteins (DEPs). The principal component analysis suggested a highly heterogeneous expression of DEPs at the four-time points of hormone treatment, with most of them (307) attained the highest expression on 12 days. Bioinformatics analysis revealed the association of DEPs with 24 KEGG pathways. We observed few new proteins, namely ABCA13, IVL, VPS37, CZIB, RFX7, Rab5, TTLL12, SMEK1, GDI2, and TMEM131 in BuMECs. The function of one of the highly upregulated proteins, namely involucrin in the differentiation of BuMECs was confirmed based on biochemical inhibition assay. The results further conclude that the proteins with higher abundance can be considered as the potential biomarkers for differentiation, and they may have a significant association with the lactation process in buffalo too. The proteome dataset obtained can be used to understand the species-specific variations among other lactating animals.

Short Time-Series Expression Transcriptome Data Reveal the Gene Expression Patterns of Dairy Cow Mammary Gland as Milk Yield Decreased Process

The existing research on dairy cow mammary gland genes is extensive, but there have been few reports about dynamic changes in dairy cow mammary gland genes as milk yield decrease. For the first time, transcriptome analysis based on short time-series expression miner (STEM) and histological observations were performed using the Holstein dairy cow mammary gland to explore gene expression patterns in this process of decrease (at peak, mid-, and late lactation). Histological observations suggested that the number of mammary acinous cells at peak/mid-lactation was significantly higher than that at mid-/late lactation, and the lipid droplets area secreted by dairy cows was almost unaltered across the three stages of lactation (p > 0.05). Totals of 882 and 1439 genes were differentially expressed at mid- and late lactation, respectively, compared to peak lactation. Function analysis showed that differentially expressed genes (DEGs) were mainly related to apoptosis and energy metabolism (fold change ≥ 2 or fold change ≤ 0.5, p-value ≤ 0.05). Transcriptome analysis based on STEM identified 16 profiles of differential gene expression patterns, including 5 significant profiles (false discovery rate, FDR ≤ 0.05). Function analysis revealed DEGs involved in milk fat synthesis were downregulated in Profile 0 and DEGs in Profile 12 associated with protein synthesis. These findings provide a foundation for future studies on the molecular mechanisms underlying mammary gland development in dairy cows.

Weighted gene co-expression network analysis identifies modules and functionally enriched pathways in the lactation process

The exponential growth in knowledge has resulted in a better understanding of the lactation process in a wide variety of animals. However, the underlying genetic mechanisms are not yet clearly known. In order to identify the mechanisms involved in the lactation process, various mehods, including meta-analysis, weighted gene co-express network analysis (WGCNA), hub genes identification, gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment at before peak (BP), peak (P), and after peak (AP) stages of the lactation processes have been employed. A total of 104, 85, and 26 differentially expressed genes were identified based on PB vs. P, BP vs. AP, and P vs. AP comparisons, respectively. GO and KEGG pathway enrichment analysis revealed that DEGs were significantly enriched in the "ubiquitin-dependent ERAD" and the "chaperone cofactor-dependent protein refolding" in BP vs. P and P vs. P, respectively. WGCNA identified five significant functional modules related to the lactation process. Moreover, GJA1, AP2A2, and NPAS3 were defined as hub genes in the identified modules, highlighting the importance of their regulatory impacts on the lactation process. The findings of this study provide new insights into the complex regulatory networks of the lactation process at three distinct stages, while suggesting several candidate genes that may be useful for future animal breeding programs. Furthermore, this study supports the notion that in combination with a meta-analysis, the WGCNA represents an opportunity to achieve a higher resolution analysis that can better predict the most important functional genes that might provide a more robust bio-signature for phenotypic traits, thus providing more suitable biomarker candidates for future studies.

Abundance of solute carrier family 27 member 6 (SLC27A6) in the bovine mammary gland alters fatty acid metabolism

Milk fatty acid (FA) composition is associated with the nutritional value of milk and is known to vary with the stage of lactation. Although biochemical aspects controlling FA metabolism in the bovine mammary gland are well-established, less is known about the underlying molecular mechanisms. Thus, to address some of these shortcomings, the present study sought to evaluate milk FA composition and mammary transcriptome profiles at different stages of lactation. Compared with 90 d of lactation, at 315 d of lactation, there was an increase in the concentrations of C18:2, polyunsaturated fatty acids (PUFA), and short-chain fatty acids (SCFA), and a decrease in C16:0 and long-chain fatty acids (LCFA) in milk. To further identify candidate genes and pathways responsible for these phenotypic differences, the transcriptome of bovine mammary tissue at 90 d (peak) and 315 d (late) of lactation was profiled using RNA-seq. A total of 827 differentially expressed genes were identified. Bioinformatic analysis revealed that the major differentially modulated lipid metabolic pathways were the PPAR signaling pathway, alpha-linolenic acid metabolism and linoleic acid metabolism. Compared with peak lactation, the mammary tissue at late lactation had lower abundance of genes related to FA transport and activation (CD36, SLC27A6, ACSM1, FABP3 and FABP4). Thus, to further explore the role of FA transport into mammary cells, we knocked down fatty acid transport protein 6 (solute carrier family 27 member 6, SLC27A6) in the bovine mammary epithelial cells (BMECs) using siRNA. The knockdown of SLC27A6 dramatically downregulated the mRNA abundance of genes associated with FA activation (ACSL4), oxidation (CPT1A) and transport (CD36), while the abundance of genes associated with transcription regulation (PPARG), diacylglycerol acyltransferase 1 (DGAT1), FA binding (FABP3), and desaturation (FADS2) was upregulated. In addition, SLC27A6 silenced the intracellular content of triglyceride (TG) and the percentage of C18:1cis9 and C20:4cis5,8,11,14 was greater, whereas that of C16:0 and C18:0 was lower. Overall, in vivo results indicated that LCFA transport into mammary cells during late lactation partly explains the difference in the FA profiles. In vitro analyses underscored how FA transport via SLC27A6 could dictate in part the intracellular utilization of FA for TG synthesis versus oxidation. The data provide strong support for a central role of SLC27A6 in the regulation of FA metabolism in BMECs.

Milk somatic cell derived transcriptome analysis identifies regulatory genes and pathways during lactation in Indian Sahiwal cattle (Bos indicus)

BACKGROUND

The present study is an effort to understand the genomic drivers of lactation in Sahiwal (Bos indicus), the best milch cattle breed of the tropics.

METHODS

RNA sequencing of four animals from early, mid and late lactation stages was performed using milk somatic cells as source of RNA.

RESULTS

The genes encoding the milk casein and whey proteins showed highest expression in early and mid lactation, with a declining trend towards the late stage. The enhanced expression of PLIN2, FABP5 and FABP3 genes in mid lactation suggests enrichment of the PPARα pathway which is linked to fatty acid metabolism. A gradual decline in the percentage of genes involved in metabolism of proteins, mRNA and insulin synthesis from early to late lactation reflected transition from lactogenesis to involution. Major biological pathways maintained throughout lactation were adaptive immune system, FGF signaling, EGFR signaling, activated TLR4 signaling, NFkB and MAP kinases activation mediated by TLR4 signaling repertoire. Differential expression analysis revealed 547, 1010 and 1313 differentially expressed genes (p < 0.05) between early-late, early-mid and mid-late stages, respectively. The topmost regulatory genes identified by network analysis from the differentially expressed genes, were involved in Chemokine receptor, GPCR and EGFR1 pathways.

CONCLUSION

The genes and pathways delineated in this study have regulatory implications in cell morphogenesis, lipid droplet formation and protein synthesis in the course of lactation. The study provides an insight into the expression profile of genes influencing milk properties and lactation in Sahiwal cattle.

Comparative gene expression profiling of milk somatic cells of Sahiwal cattle and Murrah buffaloes

India is the world's largest milk producing country because of massive contribution made by cattle and buffaloes. In the present investigation, comprehensive comparative profiling of transcriptomic landscape of milk somatic cells of Sahiwal cattle and Murrah buffaloes was carried out. Genes with highest transcript abundance in both species were enriched for biological processes such as lactation, immune response, cellular oxidant detoxification and response to hormones. Analysis of differential expression identified 377 significantly up-regulated and 847 significantly down-regulated genes with fold change >1.5 in Murrah buffaloes as compared to Sahiwal cattle (p_adj <0.05). Marked enrichment of innate and adaptive immune response related GO terms and higher expression of genes for various host defense peptides such as lysozyme, defensin β and granzymes were evident in buffaloes. Genes related to ECM-receptor interaction, complement and coagulation cascades, cytokine-cytokine receptor interaction and keratinization pathway showed more abundant expression in cattle. Network analysis of the up-regulated genes delineated highly connected genes representing immunity and haematopoietic cell lineage (CBL, CD28, CD247, PECAM1 and ITGA4). For the down-regulated dataset, genes with highest interactions were KRT18, FGFR1, GPR183, ITGB3 and DKK3. Our results lend support to more robust immune mechanisms in buffaloes, possibly explaining lower susceptibility to mammary infections as compared to cattle.