Level of nutrient intake affects mammary gland gene expression profiles in preweaned Holstein heifers

Investigation of high correlation with carcass traits of SNPs of the PLCB1, C/EBPα, and TDRKH genes and the combinations of SNPs using the MDR method in the Hanwoo

BACKGROUND

Recently, many researchers focus on the best way to produce high-quality meat, as the trend in food consumption today is to focus on quality. In general, consumers' preferences in beef differ depending on taste and meatiness. Therefore, researchers are interested in how the marbling score affects the flavors of meat or the various factors that make up the meatiness to captivate the consumers' tastes.

OBJECTIVE

This study identifies single nucleotide polymorphisms (SNPs) or gene combinations that affect the carcass traits of Korean cattle (Hanwoo) by using the multifactor dimensionality reduction (MDR) method.

METHODS

We collected the candidate SNPs to identify SNPs related to marbling scores from whole-exome sequencing and bovine SNP genotyping data. Using 96 Hanwoo samples, we performed PCR amplification to investigate the polymorphism status. In addition, we investigated genetic relationships between carcass traits and SNPs using 612 Hanwoo samples. Furthermore, each candidate SNP genotype and the combinations of SNP genotypes were verified to improve the accuracy of genetic relationships using MDR method.

RESULTS

Twenty-four candidate SNPs associated with carcass trait and marbling scores were identified from SNP genotyping and whole-exome sequencing. Among them, three SNP markers (c.459 T > C of the PLCB1 gene, c.271 A > C of the C/EBPα gene, and g.17257 A > G of the TDRKH gene) were showed statistically significant differences between intramuscular fat and genotypes. Especially, two candidate SNPs, including c.459 T > C located in the PLCB1 gene and c.271 A > C located in the C/EBPα gene, could be highly associated with the intramuscular fat of Hanwoo quality grade. In addition, the combination of SNP genotypes is showed higher significant differences with carcass weight, backfat thickness, and longissimus dorsi muscle area.

CONCLUSION

Three SNP genotypes and the combination of SNP genotypes in the PLCB1, C/EBPα, and TDRKH genes may be useful genetic markers for improving beef quality.

Effects of Feeding Level and Breed Composition on Intake, Digestibility, and Methane Emissions of Dairy Heifers

The dairy Nutrients Requirements of Cattle (NRC) was developed using data from purebred Holsteins and it might not accurately predict the performance of crossbred cattle. Our objectives were to evaluate the effects of two feeding levels (FLs) and three breed compositions (BCs) on nutrient intake, digestibility, performance, and methane (CH₄) emissions of prepubertal dairy heifers. We used thirty-six heifers from three BCs: purebred Holstein (H), purebred Gyr (G), and F1 Holstein × Gyr (HG). Each BC had 12 animals and the experiment was designed as twelve incomplete three by three Latin squares, in a factorial arrangement three by two, with three BCs and two FLs (400 and 800 g/day). Total tract nutrient digestibility was determined using total fecal collection and DMI was individually measured. The data were analyzed using the PROC MIXED in SAS. Dry matter intake of all nutrients increased from the medium to high feeding level and the nutrients digestibility coefficients did differ among BCs. Achieved body weight gain in the medium FL treatment was greater than those predicted using the NRC, suggesting that crossbred and Gyr heifers have similar performance to Holsteins. Breed composition does not influence body weight gain of confined dairy heifers, but Holstein heifers fed a medium FL had higher feed efficiency and reduced CH₄ emissions intensity.

Understanding seasonal weight loss tolerance in dairy goats: a transcriptomics approach

Background

Seasonal weight loss (SWL) is a very important limitation to the production of ruminants in the Mediterranean and Tropical regions. In these areas, long dry seasons lead to poor pastures with low nutritional value. During the dry season, ruminants, particularly those raised in extensive production systems, lose around 30% of their body weight. Seasonal weight loss has important consequences on animal productive performance and health. In this study, RNA sequencing was used to characterize feed restriction effects in dairy goat of 2 breeds with different SWL tolerance: Majorera (tolerant) and Palmera (susceptible). Nine Majorera and ten Palmera goats were randomly distributed in a control and a restricted group: Majorera Control (adequately fed; MC; n = 4), Palmera Control (adequately fed; PC; n = 6), Majorera Restricted (feed restricted; ME; n = 5) and Palmera Restricted (feed restricted; PE; n = 4). On day 22 of the trial, mammary gland biopsies were collected for transcriptomics analysis.

Results

From these samples, 24,260 unique transcripts were identified. From those, 82 transcripts were differentially expressed between MC and ME, 99 between PC and PE, twelve between both control groups and twenty-nine between both restricted groups.

Conclusions

Feed restriction affected several biochemical pathways in both breeds such as: carbohydrate and lipid transport; intracellular trafficking, RNA processing and signal transduction. This research also highlights the importance or involvement of the genes in tolerance (ENPP1, S-LZ, MT2A and GPNB) and susceptibility (GPD1, CTPS1, ELOVL6 and NR4A1) to SWL with respectively higher expression in the Majorera restriced group and the Palmera restricted group in comparison to the control groups. In addition, results from the study may be extrapolated to other dairy ruminant species.

A Nutrigenomics Approach Using RNA Sequencing Technology to Study Nutrient-Gene Interactions in Agricultural Animals

Thorough understanding of animal gene expression driven by dietary nutrients can be regarded as a bottom line of advanced animal nutrition research. Nutrigenomics (including transcriptomics) studies the effects of dietary nutrients on cellular gene expression and, ultimately, phenotypic changes in living organisms. Transcriptomics can be applied to investigate animal tissue transcriptomes at a defined nutritional state, which can provide a holistic view of intracellular RNA expression. As a novel transcriptomics approach, RNA sequencing (RNA-Seq) technology can monitor all gene expressions simultaneously in response to dietary intervention. The principle and history of RNA-Seq are briefly reviewed, and its 3 principal steps are described in this article. Application of RNA-Seq in different areas of animal nutrition research is summarized. Lastly, the application of RNA-Seq in swine science and nutrition is also reviewed. In short, RNA-Seq holds significant potential to be employed for better understanding the nutrient-gene interactions in agricultural animals.

Effect of weaning age on growth, mammary gland development, and immune function in Holstein Friesian calves fed conserved alfalfa (FiberStart)

This study aimed to evaluate intake, body growth, and the development of the rumen, mammary gland, and immune system in Holstein Friesian calves reared for 100 d on the commercially available feed FiberStart (conserved alfalfa, Medicago sativa; Fiber Fresh Feeds Ltd., Reporoa, New Zealand) and fed calf milk replacer (CMR) for either 56 or 91 d. Eighty calves (40 bulls and 40 heifer calves) were reared indoors in groups (n = 5 of the same sex/pen). All calves were fed 4 L of CMR/d (175 g/L of CMR) in 2 feeds/d for the first 10 d and then 1 feed/d until d 49 or 84. The calves were gradually weaned by d 56 (earlier weaned; n = 8 pens) and d 91 (later weaned; n = 8 pens). All calves were fed FiberStart ad libitum as the only solid feed source from d 1 to 100 of the study. Irrespective of treatment, all calves had similar body weights at d 0 (40.9 ± 3.0 kg) and d 49 (74.2 ± 5.1 kg) of the study. Calf sex had no effect on intake, growth, blood, and immune system parameters. Earlier-weaned calves consumed 18% more solid feed dry matter but had 16% lower body weight gain (28.9 vs. 38.5 kg, respectively) from d 56 to 100 relative to later-weaned calves, resulting in different body weight at 100 d (104 vs. 121 ± 1.3 kg). Although earlier-weaned calves could compensate for the loss of CMR dry matter and crude protein intake from d 56 to 100 by increasing forage intake, they were unable to compensate for the loss of energy from the CMR by increasing solid feed consumption. Plasma β-hydroxybutyrate concentrations were 52% greater in earlier-weaned calves than in later-weaned calves at d 84, indicating greater metabolic activity of the rumen wall. The duration of CMR feeding had no influence on humoral or cell-mediated immune functions of the calves, as evidenced by a lack of effect on antivaccine antibody responses as well as on immune gene expression. Earlier- versus later-weaned heifer calves had 5% lower mammary gland mass, indicating that greater energy supply increased mammary mass. The results of this experiment demonstrate the ability to artificially rear dairy calves on a conserved alfalfa as the only solid feed. Furthermore, earlier weaning off CMR promotes solid feed intake and an associated increase in blood β-hydroxybutyrate, an indicator of rumen development, but increasing the duration of CMR feeding improves growth and mammary gland mass by d 100. The implications of these findings on lifetime growth, health, and milk production in dairy heifers warrant further investigation.

Effects of rumen-undegradable protein on intake, performance, and mammary gland development in prepubertal and pubertal dairy heifers

The objective of this study was to evaluate the influence of different amounts of rumen-undegradable protein (RUP) on intake, N balance, performance, mammary gland development, carcass traits, and hormonal status of Holstein heifers at different physiological stages (PS). Sixteen prepubertal (PRE) heifers (initial BW = 106 ± 7.6 kg; age = 4.3 ± 0.46 mo) and 16 pubertal (PUB) heifers (initial BW = 224 ± 7.9 kg; age = 12.6 ± 0.45 mo) were used in an experiment over a period of 84 d. Four diets with increasing RUP contents (38, 44, 51, and 57% of dietary crude protein) and heifers at 2 PS (PRE or PUB) were used in a 4 × 2 factorial arrangement of treatments in a completely randomized design. Throughout the experiment, 2 digestibility trials were performed over 5 consecutive days (starting at d 36 and 78) involving feed and ort sampling and spot collections of feces and urine. At d 0 and 83, body ultrasound images were obtained for real-time carcass trait evaluation. The mammary gland was ultrasonically scanned at d 0 and every 3 wk during the experiment. Blood samples were taken at d 0 and 84 to determine serum concentrations of progesterone, estrogen, insulin-like growth factor I (IGF-I), and insulin. No interaction between PS and the level of RUP was found for any trait. Apparent digestibility of dry matter, organic matter, and neutral detergent fiber corrected for ash and protein was not affected by RUP level but was lower for PRE compared with PUB heifers. Sorting against neutral detergent fiber corrected for ash and protein (tendency only) and for crude protein was greater for PUB than PRE heifers. Pubertal heifers had greater average daily gain (905 vs. 505 g/d) and N retention (25.9 vs. 12.5 g/d) than PRE heifers. In addition, average daily gain and N retention were greatest at 51% RUP of dietary protein. Mammary ultrasonography indicated no effects of RUP amounts on mammary gland composition, whereas PRE heifers had greater pixel values than PUB, indicating higher contents of fat rather than protein in the mammary glands of PRE heifers. Serum progesterone and IGF-I concentration was affected only by PS, and PRE heifers had greater values of progesterone and IGF-I concentrations than PUB heifers. Serum insulin concentration was unaffected by PS but tended to be higher at 51% of RUP. In conclusion, an RUP level of 51% increases body weight, average daily gain, feed efficiency, and N retention in heifers regardless of the PS. In addition, PRE heifers have a lower sorting ability and reduced intake, total-tract digestibility, and N retention. They also have higher amounts of fat in their mammary glands, even at moderate growth rates.

Sunflower oil supplementation affects the expression of miR-20a-5p and miR-142-5p in the lactating bovine mammary gland

Oil supplementation in dairy cattle diets is used to modulate milk fat composition, as well as the expression of mammary lipogenic genes, whose regulation remains unclear. MiRNAs are small non-coding RNA considered as crucial regulators of gene expression, offering clues to explain the mechanism underlying gene nutriregulation. The present study was designed to identify miRNAs whose expression in the cow mammary gland is modulated by sunflower oil supplementation. MiRNomes were obtained using RNAseq technology from the mammary gland of lactating cows receiving a low forage diet, supplemented or not with 4% sunflower oil. Among the 272 miRNAs characterized, eight were selected for RT-qPCR validations, showing the significant down-regulation of miR-142-5p and miR-20a-5p by sunflower supplementation. These two miRNAs are predicted to target genes whose expression was reported as differentially expressed by sunflower supplementation. Among their putative targets, ELOVL6 gene involved in lipid metabolism has been studied. However, a first analysis did not show its significant down-regulation, in response to the over-expression of miR-142-5p, of miR-20a-5p, or both, in a bovine mammary epithelial cell line. However, a clearer understanding of the miRNA expression by lipid supplementation would help to decipher the regulation of lactating cow mammary gland in response to nutrition.

Prepartum body condition score and plane of nutrition affect the hepatic transcriptome during the transition period in grazing dairy cows

Background

A transcriptomic approach was used to evaluate potential interactions between prepartum body condition score (BCS) and feeding management in the weeks before calving on hepatic metabolism during the periparturient period.

Methods

Thirty-two mid-lactation grazing dairy cows of mixed age and breed were randomly allocated to one of four treatment groups in a 2 × 2 factorial arrangement: two prepartum BCS categories [4.0 (thin, BCS4) and 5.0 (optimal, BCS5); based on a 10-point scale], and two levels of energy intake during the 3 weeks preceding calving (75 and 125 % of estimated requirements). Liver samples were obtained at −7, 7, and 28 d relative to parturition and subsequent RNA was hybridized to the Agilent 44 K Bovine (V2) Microarray chip. The Dynamic Impact Approach was used for pathway analysis, and Ingenuity Pathway Analysis was used for gene network analysis.

Results

The greater number of differentially expressed genes in BCS4 cows in response to prepartum feed allowance (1071 vs 310, over the entire transition period) indicates that these animals were more responsive to prepartum nutrition management than optimally-conditioned cows. However, independent of prepartum BCS, pathway analysis revealed that prepartal feeding level had a marked effect on carbohydrate, amino acid, lipid, and glycan metabolism. Altered carbohydrate and amino acid metabolism suggest a greater and more prolonged negative energy balance postpartum in BCS5 cows overfed prepartum. This is supported by opposite effects of prepartum feeding in BCS4 compared with BCS5 cows in pathways encompassing amino acid, vitamin, and co-factor metabolism. The prepartum feed restriction ameliorates the metabolic adaptation to the onset of lactation in BCS5 cows, while detrimentally affecting BCS4 cows, which seem to better adapt when overfed. Alterations in the glycosaminoglycans synthesis pathway support this idea, indicating better hepatic health status in feed-restricted BCS5 and overfed BCS4 cows. Furthermore, IPA network analysis suggests liver damage in feed-restricted thin cows, likely due to metabolic overload.

Conclusion

Overall, the data support the hypothesis that overfeeding in late-pregnancy should be limited to underconditioned cows, while cows with optimal degree of body condition should be maintained on an energy-restricted diet.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3191-3) contains supplementary material, which is available to authorized users.

Genome-association analysis of Korean Holstein milk traits using genomic estimated breeding value

Objective

Holsteins are known as the world’s highest-milk producing dairy cattle. The purpose of this study was to identify genetic regions strongly associated with milk traits (milk production, fat, and protein) using Korean Holstein data.

Methods

This study was performed using single nucleotide polymorphism (SNP) chip data (Illumina BovineSNP50 Beadchip) of 911 Korean Holstein individuals. We inferred each genomic estimated breeding values based on best linear unbiased prediction (BLUP) and ridge regression using BLUPF90 and R. We then performed a genome-wide association study and identified genetic regions related to milk traits.

Results

We identified 9, 6, and 17 significant genetic regions related to milk production, fat and protein, respectively. These genes are newly reported in the genetic association with milk traits of Holstein.

Conclusion

This study complements a recent Holstein genome-wide association studies that identified other SNPs and genes as the most significant variants. These results will help to expand the knowledge of the polygenic nature of milk production in Holsteins.

Growth targets and rearing strategies for replacement heifers in pasture-based systems: a review

Dairy heifer growth and liveweight at first calving are regarded as important management variables affecting profitability and animal welfare. However, the appropriateness of heifer growth rate targets for different farming systems is not clear. Retrospective assessments of the association between heifer liveweight and subsequent productivity indicate significant benefits in milk production and, even, reproduction from increasing liveweight at breeding and first calving. However, prospective interventionist experiments do not concur, with very variable effects of liveweight at breeding on milk production and with only limited evidence of a positive effect of first-calving liveweight on first-lactation milk yield. In addition, any benefit in the first lactation is not evident in subsequent lactations in the limited number of long-term studies reported. Pre-weaning nutrition and average daily weight gain are areas of increasing interest, with lifelong increases in milk production resulting from accelerated growth rates during the first 8 weeks of life, indicating a possible significant return from a short-term investment. This could be one reason for the inconsistent effects of heifer liveweight at breeding and first lactation on milk production. Although the effect of pre-weaning average daily gain on heifer liveweight is short-lived, a recent meta-analysis indicated that pre-weaning average daily gain explains 22% of the variation in first-lactation milk production. Whether these differences in animal physiology have relevance in grazing systems, wherein heifers and cows do not consume sufficient nutrients to reach their potential, requires investigation. Despite considerable extension efforts over successive decades, current evidence indicates that failure to provide the new-born calf with sufficient high-quality colostrum is common. To understand the reasons for suboptimal colostrum feeding requires social research, with appropriate extension strategies developed to elicit practice change. Although there can be little doubt regarding the importance of heifer rearing to the profitability and sustainability of the farming business, the collective literature points to a failure of retrospective analyses in determining the cause of poor heifer performance. In reality, it is likely to be a combination of factors. The objective of this review is to investigate the effect of liveweight gain at various stages of the growth cycle of the heifer on the milk-production capacity of the lactating animal.

Postpartal subclinical endometritis alters transcriptome profiles in liver and adipose tissue of dairy cows

Transcriptome alterations in liver and adipose tissue of cows with subclinical endometritis (SCE) at 29 d postpartum were evaluated. Bioinformatics analysis was performed using the Dynamic Impact Approach by means of KEGG and DAVID databases. Milk production, blood metabolites (non-esterified fatty acids, magnesium), and disease biomarkers (albumin, aspartate aminotransferase) did not differ greatly between healthy and SCE cows. In liver tissue of cows with SCE, alterations in gene expression revealed an activation of complement and coagulation cascade, steroid hormone biosynthesis, apoptosis, inflammation, oxidative stress, MAPK signaling, and the formation of fibrinogen complex. Bioinformatics analysis also revealed an inhibition of vitamin B3 and B6 metabolism with SCE. In adipose, the most activated pathways by SCE were nicotinate and nicotinamide metabolism, long-chain fatty acid transport, oxidative phosphorylation, inflammation, T cell and B cell receptor signaling, and mTOR signaling. Results indicate that SCE in dairy cattle during early lactation induces molecular alterations in liver and adipose tissue indicative of immune activation and cellular stress.

Application of Top-Down and Bottom-up Systems Approaches in Ruminant Physiology and Metabolism

Systems biology is a computational field that has been used for several years across different scientific areas of biological research to uncover the complex interactions occurring in living organisms. Applications of systems concepts at the mammalian genome level are quite challenging, and new complimentary computational/experimental techniques are being introduced. Most recent work applying modern systems biology techniques has been conducted on bacteria, yeast, mouse, and human genomes. However, these concepts and tools are equally applicable to other species including ruminants (e.g., livestock). In systems biology, both bottom-up and top-down approaches are central to assemble information from all levels of biological pathways that must coordinate physiological processes. A bottom-up approach encompasses draft reconstruction, manual curation, network reconstruction through mathematical methods, and validation of these models through literature analysis (i.e., bibliomics). Whereas top-down approach encompasses metabolic network reconstructions using ‘omics’ data (e.g., transcriptomics, proteomics) generated through DNA microarrays, RNA-Seq or other modern high-throughput genomic techniques using appropriate statistical and bioinformatics methodologies. In this review we focus on top-down approach as a means to improve our knowledge of underlying metabolic processes in ruminants in the context of nutrition. We also explore the usefulness of tissue specific reconstructions (e.g., liver and adipose tissue) in cattle as a means to enhance productive efficiency.