Duy N. Do

MicroRNA roles in signalling during lactation: an insight from differential expression, time course and pathway analyses of deep sequence data

The study examined microRNA (miRNA) expression and regulatory patterns during an entire bovine lactation cycle. Total RNA from milk fat samples collected at the lactogenesis (LAC, day1 [D1] and D7), galactopoiesis (GAL, D30, D70, D130, D170 and D230) and involution (INV, D290 and when milk production dropped to 5u2009kg/day) stages from 9 cows was used for miRNA sequencing. A total of 475 known and 238 novel miRNAs were identified. Fifteen abundantly expressed miRNAs across lactation stages play regulatory roles in basic metabolic, cellular and immunological functions. About 344, 366 and 209 miRNAs were significantly differentially expressed (DE) between GAL and LAC, INV and GAL, and INV and LAC stages, respectively. MiR-29b/miR-363 and miR-874/miR-6254 are important mediators for transition signals from LAC to GAL and from GAL to INV, respectively. Moreover, 58 miRNAs were dynamically DE in all lactation stages and 19 miRNAs were significantly time-dependently DE throughout lactation. Relevant signalling pathways for transition between lactation stages are involved in apoptosis (PTEN and SAPK/JNK), intracellular signalling (protein kinase A, TGF-β and ERK5), cell cycle regulation (STAT3), cytokines, hormones and growth factors (prolactin, growth hormone and glucocorticoid receptor). Overall, our data suggest diverse, temporal and physiological signal-dependent regulatory and mediator functions for miRNAs during lactation.

Genome-wide association analysis and pathways enrichment for lactation persistency in Canadian Holstein cattle

Lactation persistency (LP), defined as the rate of declining milk yield after milk peak, is an economically important trait for dairy cattle. Improving LP is considered a good alternative method for increasing overall milk production because it does not cause the negative energy balance and other health issues that cows experience during peak milk production. However, little is known about the biology of LP. A genome-wide association study (GWAS) and pathway enrichment were used to explore the genetic mechanisms underlying LP. The GWAS was performed using a univariate regression mixed linear model on LP data of 3,796 cows and 44,100 single nucleotide polymorphisms (SNP). Eight and 47 SNP were significantly and suggestively associated with LP, respectively. The 2 most important quantitative trait loci regions for LP were (1) a region from 106 to 108 Mb on Bos taurus autosome (BTA) 5, where the most significant SNP (ARS-BFGL-NGS-2399) was located and also formed a linkage disequilibrium block with 3 other SNP; and (2) a region from 29.3 to 31.3 Mb on BTA 20, which contained 3 significant SNP. Based on physical positions, MAN1C1, MAP3K5, HCN1, TSPAN9, MRPS30, TEX14, and CCL28 are potential candidate genes for LP because the significant SNP were located in their intronic regions. Enrichment analyses of a list of 536 genes in 0.5-Mb flanking regions of significant and suggestive SNP indicates that synthesis of milk components, regulation of cell apoptosis processes and insulin, and prolactin signaling pathways are important for LP. Upstream regulators relevant for LP positional candidate genes were prolactin (PRL), peroxisome proliferator-activated receptor gamma (PPARG), and Erb-B2 receptor tyrosine kinase 2 (ERBB2). Several networks related to cellular development, proliferation and death were significantly enriched for LP positional candidate genes. In conclusion, this study detected several SNP, genes, and interesting regions for fine mapping and validation of candidate genes and SNP for potential use in selection for improved LP. This study also provided further insights on the biology of LP which will help to prioritize selected candidate genes for functional validation and application.

Co-Expression Network and Pathway Analyses Reveal Important Modules of miRNAs Regulating Milk Yield and Component Traits

Co-expression network analyses provide insights into the molecular interactions underlying complex traits and diseases. In this study, co-expression network analysis was performed to detect expression patterns (modules or clusters) of microRNAs (miRNAs) during lactation, and to identify miRNA regulatory mechanisms for milk yield and component traits (fat, protein, somatic cell count (SCC), lactose, and milk urea nitrogen (MUN)) via miRNA target gene enrichment analysis. miRNA expression (713 miRNAs), and milk yield and components (Fat%, Protein%, lactose, SCC, MUN) data of nine cows at each of six different time points (day 30 (D30), D70, D130, D170, D230 and D290) of an entire lactation curve were used. Four modules or clusters (GREEN, BLUE, RED and TURQUOISE) of miRNAs were identified as important for milk yield and component traits. The GREEN and BLUE modules were significantly correlated (|r| > 0.5) with milk yield and lactose, respectively. The RED and TURQUOISE modules were significantly correlated (|r| > 0.5) with both SCC and lactose. In the GREEN module, three abundantly expressed miRNAs (miR-148a, miR-186 and miR-200a) were most significantly correlated to milk yield, and are probably the most important miRNAs for this trait. DDR1 and DDHX1 are hub genes for miRNA regulatory networks controlling milk yield, while HHEX is an important transcription regulator for these networks. miR-18a, miR-221/222 cluster, and transcription factors HOXA7, and NOTCH 3 and 4, are important for the regulation of lactose. miR-142, miR-146a, and miR-EIA17-14144 (a novel miRNA), and transcription factors in the SMAD family and MYB, are important for the regulation of SCC. Important signaling pathways enriched for target genes of miRNAs of significant modules, included protein kinase A and PTEN signaling for milk yield, eNOS and Noth signaling for lactose, and TGF β, HIPPO, Wnt/β-catenin and cell cycle signaling for SCC. Relevant enriched gene ontology (GO)-terms related to milk and mammary gland traits included cell differentiation, G-protein coupled receptor activity, and intracellular signaling transduction. Overall, this study uncovered regulatory networks in which miRNAs interacted with each other to regulate lactation traits.

Integration of miRNA weighted gene co-expression network and miRNA-mRNA co-expression analyses reveals potential regulatory functions of miRNAs in calf rumen development

This study aimed to explore the roles of microRNAs (miRNAs) in calf rumen development during early life. Rumen tissues were collected from 16 calves (8 at pre-weaning and 8 at post-weaning) for miRNA-sequencing, differential expression (DE), miRNA weighted gene co-expression network (WGCNA) and miRNA-mRNA co-expression analyses. 295 miRNAs were identified. Bta-miR-143, miR-26a, miR-145 and miR-27b were the most abundantly expressed. 122 miRNAs were significantly DE between the pre- and post-weaning periods and the most up- and down-regulated miRNAs were bta-miR-29b and bta-miR-493, respectively. Enrichment analyses of the target genes of DE miRNAs revealed important roles for miRNA in rumen developmental processes, immune system development, protein digestion and processes related to the extracellular matrix. WGCNA indicated that bta-miR-145 and bta-miR-199a-3p are important hub miRNAs in the regulation of these processes. Therefore, bta-miR-143, miR-29b, miR-145, miR-493, miR-26a and miR-199 family members might be key regulators of calf rumen development during early life.

Differential expression and co-expression gene networks reveal candidate biomarkers of boar taint in non-castrated pigs

Boar taint (BT) is an offensive odour or taste observed in pork from a proportion of non-castrated male pigs. Surgical castration is effective in avoiding BT, but animal welfare issues have created an incentive for alternatives such as genomic selection. In order to find candidate biomarkers, gene expression profiles were analysed from tissues of non-castrated pigs grouped by their genetic merit of BT. Differential expression analysis revealed substantial changes with log-transformed fold changes of liver and testis from −3.39 to 2.96 and −7.51 to 3.53, respectively. Co-expression network analysis revealed one module with a correlation of −0.27 in liver and three modules with correlations of 0.31, −0.44 and −0.49 in testis. Differential expression and co-expression analysis revealed candidate biomarkers with varying biological functions: phase I (COQ3, COX6C, CYP2J2, CYP2B6, ACOX2) and phase II metabolism (GSTO1, GSR, FMO3) of skatole and androstenone in liver to steroidgenesis (HSD17B7, HSD17B8, CYP27A1), regulation of steroidgenesis (STARD10, CYB5R3) and GnRH signalling (MAPK3, MAP2K2, MAP3K2) in testis. Overrepresented pathways included “Ribosome”, “Protein export” and “Oxidative phosphorylation” in liver and “Steroid hormone biosynthesis” and “Gap junction” in testis. Future work should evaluate the biomarkers in large populations to ensure their usefulness in genomic selection programs.

Non-Coding RNA Roles in Ruminant Mammary Gland Development and Lactation

The ruminant mammary gland (MG) is an important organ charged with the production of milk for young and human nourishment. Many factors influence MG productivity, including nutrition, genetics, breed, epigenetics (including non-coding RNA [ncRNA]), disease pathogens and other environmental factors. In recent years, increasing research is beginning to determine the role of non-coding RNA in MG functions. Non-coding RNAs (small interfering RNA [siRNA], microRNA [miRNA], PIWI-interacting RNA [piRNA], small nucleolar RNA [snoRNA] and long non-coding RNA [lncRNA]) are a class of untranslated RNA molecules that function to regulate gene expression, associated biochemical pathways and cellular functions and are involved in many biological processes. This chapter presents a review of the current state of knowledge on the role of ncRNAs (particularly miRNAs and lncRNAs) in the MG and lactation processes, lactation signalling pathways, lipid metabolism, MG health of ruminants as well as miRNA roles in milk recipients. Finally, the potential application of new genome editing technology for ncRNA studies in MG development, the lactation process and milk components is presented.

Direct-fed microbial supplementation influences the bacteria community composition of the gastrointestinal tract of pre- and post-weaned calves.

This study investigated the effect of supplementing the diet of calves with two direct fed microbials (DFMs) (Saccharomyces cerevisiae boulardii CNCM I-1079 (SCB) and Lactobacillus acidophilus BT1386 (LA)), and an antibiotic growth promoter (ATB). Thirty-two dairy calves were fed a control diet (CTL) supplemented with SCB or LA or ATB for 96 days. On day 33 (pre-weaning, nu2009=u200916) and day 96 (post-weaning, nu2009=u200916), digesta from the rumen, ileum, and colon, and mucosa from the ileum and colon were collected. The bacterial diversity and composition of the gastrointestinal tract (GIT) of pre- and post-weaned calves were characterized by sequencing the V3-V4 region of the bacterial 16S rRNA gene. The DFMs had significant impact on bacteria community structure with most changes associated with treatment occurring in the pre-weaning period and mostly in the ileum but less impact on bacteria diversity. Both SCB and LA significantly reduced the potential pathogenic bacteria genera, Streptococcus and Tyzzerella_4 (FDRu2009≤u20098.49E-06) and increased the beneficial bacteria, Fibrobacter (FDR ≤ 5.55E-04) compared to control. Other potential beneficial bacteria, including Rumminococcaceae UCG 005, Roseburia and Olsenella, were only increased (FDR ≤ 1.30E-02) by SCB treatment compared to control. Furthermore, the pathogenic bacterium, Peptoclostridium, was reduced (FDRu2009=u20091.58E-02) by SCB only while LA reduced (FDRu2009=u20091.74E-05) Ruminococcus_2. Functional prediction analysis suggested that both DFMs impacted (pu2009<u20090.05) pathways such as cell cycle, bile secretion, proteasome, cAMP signaling pathway, thyroid hormone synthesis pathway and dopaminergic synapse pathway. Compared to the DFMs, ATB had similar impact on bacterial diversity in all GIT sites but greater impact on the bacterial composition of the ileum. Overall, this study provides an insight on the bacteria genera impacted by DFMs and the potential mechanisms by which DFMs affect the GIT microbiota and may therefore facilitate development of DFMs as alternatives to ATB use in dairy calf management.

Genome wide association study identifies novel potential candidate genes for bovine milk cholesterol content

This study aimed to identify single nucleotide polymorphisms (SNPs) associated with milk cholesterol (CHL) content via a genome wide association study (GWAS). Milk CHL content was determined by gas chromatography and expressed as mg of CHL in 100u2009g of fat (CHL_fat) or in 100u2009mg of milk (CHL_milk). GWAS was performed with 1,183 cows and 40,196 SNPs using a univariate linear mixed model. Two and 20 SNPs were significantly associated with CHL_fat and CHL_milk, respectively. The important regions for CHL_fat and CHL_milk were at 41.9u2009Mb on chromosome (BTA) 17 and 1.6–3.2u2009Mb on BTA 14, respectively. DGAT1, PTPN1, INSIG1, HEXIM1, SDS, and HTR5A genes, also known to be associated with human plasma CHL phenotypes, were identified as potential candidate genes for bovine milk CHL. Additional new potential candidate genes for milk CHL were RXFP1, FAM198B, TMEM144, CXXC4, MAML2 and CDH13. Enrichment analyses suggested that identified candidate genes participated in cell-cell signaling processes and are key members in tight junction, focal adhesion, Notch signaling and glycerolipid metabolism pathways. Furthermore, identified transcription factors such as PPARD, LXR, and NOTCH1 might be important in the regulation of bovine milk CHL content. The expression of several positional candidate genes (such as DGAT1, INSIG1 and FAM198B) and their correlation with milk CHL content were further confirmed with RNA sequence data from mammary gland tissues. This is the first GWAS on bovine milk CHL. The identified markers and candidate genes need further validation in a larger cohort for use in the selection of cows with desired milk CHL content.

Co-Expression Network Analysis Identifies miRNA–mRNA Networks Potentially Regulating Milk Traits and Blood Metabolites

MicroRNAs (miRNA) regulate mRNA networks to coordinate cellular functions. In this study, we constructed gene co-expression networks to detect miRNA modules (clusters of miRNAs with similar expression patterns) and miRNA–mRNA pairs associated with blood (triacylglyceride and nonesterified fatty acids) and milk (milk yield, fat, protein, and lactose) components and milk fatty acid traits following dietary supplementation of cows’ diets with 5% linseed oil (LSO) (n = 6 cows) or 5% safflower oil (SFO) (n = 6 cows) for 28 days. Using miRNA transcriptome data from mammary tissues of cows for co-expression network analysis, we identified three consensus modules: blue, brown, and turquoise, composed of 70, 34, and 86 miRNA members, respectively. The hub miRNAs (miRNAs with the most connections with other miRNAs) were miR-30d, miR-484 and miR-16b for blue, brown, and turquoise modules, respectively. Cell cycle arrest, and p53 signaling and transforming growth factor–beta (TGF-β) signaling pathways were the common gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched for target genes of the three modules. Protein percent (p = 0.03) correlated with the turquoise module in LSO treatment while protein yield (p = 0.003) and milk yield (p = 7 × 10−04) correlated with the turquoise model, protein and milk yields and lactose percent (p < 0.05) correlated with the blue module and fat percent (p = 0.04) correlated with the brown module in SFO treatment. Several fatty acids correlated (p < 0.05) with the blue (CLA:9,11) and brown (C4:0, C12:0, C22:0, C18:1n9c and CLA:10,12) modules in LSO treatment and with the turquoise (C14:0, C18:3n3 and CLA:9,11), blue (C14:0 and C23:0) and brown (C6:0, C16:0, C22:0, C22:6n3 and CLA:10,12) modules in SFO treatment. Correlation of miRNA and mRNA data from the same animals identified the following miRNA–mRNA pairs: miR-183/RHBDD2 (p = 0.003), miR-484/EIF1AD (p = 0.011) and miR-130a/SBSPON (p = 0.004) with lowest p-values for the blue, brown, and turquoise modules, respectively. Milk yield, protein yield, and protein percentage correlated (p < 0.05) with 28, 31 and 5 miRNA–mRNA pairs, respectively. Our results suggest that, the blue, brown, and turquoise modules miRNAs, hub miRNAs, miRNA–mRNA networks, cell cycle arrest GO term, p53 signaling and TGF-β signaling pathways have considerable influence on milk and blood phenotypes following dietary supplementation of dairy cows’ diets with 5% LSO or 5% SFO.

Integration of lncRNA and mRNA Transcriptome Analyses Reveals Genes and Pathways Potentially Involved in Calf Intestinal Growth and Development during the Early Weeks of Life

A better understanding of the factors that regulate growth and immune response of the gastrointestinal tract (GIT) of calves will promote informed management practices in calf rearing. This study aimed to explore genomics (messenger RNA (mRNA)) and epigenomics (long non-coding RNA (lncRNA)) mechanisms regulating the development of the rumen and ileum in calves. Thirty-two calves (≈5-days-old) were reared for 96 days following standard procedures. Sixteen calves were humanely euthanized on experiment day 33 (D33) (pre-weaning) and another 16 on D96 (post-weaning) for collection of ileum and rumen tissues. RNA from tissues was subjected to next generation sequencing and 3310 and 4217 mRNAs were differentially expressed (DE) between D33 and D96 in ileum and rumen tissues, respectively. Gene ontology and pathways enrichment of DE genes confirmed their roles in developmental processes, immunity and lipid metabolism. A total of 1568 (63 known and 1505 novel) and 4243 (88 known and 4155 novel) lncRNAs were detected in ileum and rumen tissues, respectively. Cis target gene analysis identified BMPR1A, an important gene for a GIT disease (juvenile polyposis syndrome) in humans, as a candidate cis target gene for lncRNAs in both tissues. LncRNA cis target gene enrichment suggested that lncRNAs might regulate growth and development in both tissues as well as posttranscriptional gene silencing by RNA or microRNA processing in rumen, or disease resistance mechanisms in ileum. This study provides a catalog of bovine lncRNAs and set a baseline for exploring their functions in calf GIT development.