Tissues, Metabolic Pathways and Genes of Key Importance in Lactating Dairy Cattle

Therapeutic Potential of Pectin and Its Derivatives in Chronic Diseases

Non-communicable diseases (NCDs) are described as a collection of chronic diseases that do not typically develop from an acute infection, have long-term health effects, and frequently require ongoing care and therapy. These diseases include heart disease, stroke, cancer, chronic lung disease, neurological diseases, osteoporosis, mental health disorders, etc. Known synthetic drugs for the treatment or prevention of NCDs become increasingly dangerous over time and pose high risks due to side effects such as hallucination, heart attack, liver failure, etc. As a result, scientists have had to look for other alternatives that are natural products and that are known to be less detrimental and contain useful bioactive compounds. The increasing understanding of the biological and pharmacological significance of carbohydrates has helped to raise awareness of their importance in living systems and medicine, given they play numerous biological roles. For example, pectin has been identified as a class of secondary metabolites found in medicinal plants that may play a significant role in the treatment and management of a variety of NCDs. Pectin is mainly made of homogalacturonan, which is a linear polymer composed primarily of D-galacturonic acid units (at least 65%) linked in a chain by α-(1,4)-glycosidic linkages. There are also modified pectins or derivatives that improve pectin's bioavailability. Pectin is found in the cell walls of higher plants (pteridophytes, angiosperms, and gymnosperms), particularly in the middle lamella of the plant material. Citrus pectin is used in various industries. This article compiles information that has been available for years about the therapeutic importance of pectin in chronic diseases, different modes of pectin extraction, the chemistry of pectin, and the potency of pectin and its derivatives.

Genome wide mining of SNPs and INDELs through ddRAD sequencing in Sahiwal cattle

The study was conducted in Sahiwal cattle for genome wide identification and annotation of single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs) in Sahiwal cattle. The double digest restriction-site associated DNA (ddRAD) sequencing, a reduced representation method was used for the identification of variants at nucleotide level. A total of 1,615,211 variants were identified at RD10 and Q30 consisting of 1,480,930 SNPs and 134,281 INDELs with respect to the Bos taurus reference genome. The SNPs were annotated for their location, impact and functional class. The SNPs identified in Sahiwal cattle were found to be associated with a total of 26,229 genes. A total of 1819 SNPs were annotated for 209 candidate genes associated with different production and reproduction traits. The variants identified in the present study may be useful to strengthen the existing bovine SNP chips for reducing the biasness over the taurine cattle breeds. The diversity analysis provides the insight of the genetic architecture of the Sahiwal population Studied. The large genetic variations identified at the nucleotide level provide ample scope for implementing an effective and efficient breed improvement programme for increasing the productivity of Sahiwal cattle.

Metabolomic evolution of the postpartum dairy cow uterus

High rates of early pregnancy loss are a critical issue in dairy herds, particularly in seasonal, grazing systems. Components of the uterine luminal fluid (ULF), on which the early embryo depends for sustenance and growth, partly determine early pregnancy losses. Here, changes in ULF from early to mid-postpartum in crossbred dairy cows were explored, linking them with divergent embryo development. For this, the uteri of 87 cows at Day 7 of pregnancy at first and third estrus postpartum were flushed to collect ULF. Eighteen metabolites (chiefly organic acids and sugars) significantly varied in abundance across postpartum, indicating a molecular signature of physiological recovery consistent of the upregulation of pyrimidine metabolism and glycerophospholipid metabolism, and downregulation of pentose phosphate and taurine metabolism pathways. Joint pathway analysis of metabolomics data and a previously generated proteomics data set on the same ULF samples suggests key links between postpartum recovery and subsequent successful embryo development. These include upregulation of VEGFA and downregulation of metabolism, NRF2, T-cell receptor, which appear to improve the ULF's capacity of sustaining normal embryo development, and a putative osmo-protectant role of beta-alanine. These relationships should be further investigated to develop tools to detect and reduce early pregnancy loss in dairy cows.

Single nucleotide polymorphisms cumulating to genetic variation for fertility in crossbred (Bos taurus × Bos indicus) bull spermatozoa

Spermatozoa from high-fertile (HF) and low-fertile (LF) breeding bulls were subjected to high-throughput next-generation sequencing to identify important Single nucleotide polymorphisms (SNPs) and novel variants associated with fertility. A total of 77,038 genome-wide SNPs were identified, among which, 10,788 were novel variants. A total of 42,290 and 34,748 variants were recorded with 6115 and 4673 novel variants in in HF and LF bulls, respectively. Higher number of SNPs were identified in HF compared to LF bulls. GO analysis of filtered genes with significant variations in HF bulls indicated their involvement in oxidative phosphorylation and metabolic pathways. GO analysis of filtered genes with significant variation in LF bulls revealed their involvement in Ca2++ ion binding, structural constituent of ribosome, and biological processes like translation and ribosomal small subunit assembly. The study identified SNPs in candidate genes including TPT1, BOLA-DRA, CD74, RPS17, RPS28, RPS29, RPL14, RPL13, and RPS27A, which are linked to sperm functionality, survival, oxidative stress, and bull fertility. The identified SNPs could be used in selection of bulls for high fertility and the variation in these genes could be established as an explanation for the fertility differences in bulls upon validation in large number of bulls.

Single nucleotide polymorphisms within exon four of the prolactin gene and their effect on milk traits in cattle populations of Ethiopia

Bovine prolactin (PRL) gene is essential for the initiation and maintenance of lactation and exerts multiple effects on mammary alveoli to promote the synthesis and secretion of major components of milk. The objectives of this study were to identify mutations in PRL gene and to evaluate the mutations as potential markers of milk performance traits in cattle populations of Ethiopia. For this purpose, genomic DNA from whole blood was extracted through salting out procedure from 87 animals of five cattle populations of Ethiopia. Accordingly, three single nucleotide polymorphisms (SNPs) were identified of which one SNP g.8323T > A showed missense mutation while the other two SNPs revealed silent mutations. FST values showed statistically significant genetic differentiation among the studied populations. Intermediate polymorphic information content was noted for most SNPs, which indicates the presence of sufficient genetic variation at this locus. Two SNPs showed heterozygote deficiency as a result of positive FIS values. Only g.8398A > G SNP have statistically significant (p < 0.05) effect on average daily milk yield, fat and solid not fat percentage in all studied cattle populations. Therefore, g.8398A > G SNP identified in this study influences cattle milk production and may be used as possible candidate SNP for marker-assisted selection programs in cattle populations of Ethiopia.

Review: genetic background of milk fatty acid synthesis in bovines

Milk fat composition is an important trait for the dairy industry as it directly influences the nutritional and technological properties of milk and other dairy products. The synthesis of milk fat is a complex process regulated by a network of genes. Thus, understanding the genetic variation and molecular mechanisms regulating milk fat synthesis will help to improve the nutritional quality of dairy products. In this review, we provide an overview of milk fat synthesis in bovines along with the candidate genes involved in the pathway. We also discuss de novo synthesis of fatty acids (ACSS, ACACA, FASN), uptake of FAs (FATP, FAT, LPL), intracellular activation and channelling of FAs (ACSL, FABP), elongation (EVOLV6), desaturation (SCD, FADS), formation of triglycerides (GPAM, AGPAT, LIPIN, DGAT), and milk lipid secretion (BTN1A1, XDH, PLIN2). The genetic variability of individual fatty acids will help to develop selection strategies for obtaining a healthier milk fat profile in bovines. Thus, this review will offer a potential understanding of the molecular mechanisms that regulate milk fat synthesis in bovines.

DNA Polymorphisms and mRNA Levels of Immune Biomarkers as Candidates for Inflammatory Postpartum Disorders Susceptibility in Italian Buffaloes

The immunological genes that may interact with inflammatory postpartum diseases in Italian buffaloes were examined in this study. A total number of 120 female Italian buffaloes (60 normal and 60 with inflammatory reproductive diseases) were employed. Each buffalo's jugular vein was pierced to get five milliliters of blood. To obtain whole blood and extract DNA and RNA, the blood was placed within tubes containing sodium fluoride or EDTA anticoagulants. The immunological (IKBKG, LGALS, IL1B, CCL2, RANTES, MASP2, HMGB1, and S-LZ) genes' nucleotide sequence differences between healthy buffaloes and buffaloes affected by inflammatory reproductive diseases were found by employing PCR-DNA sequencing. According to Fisher's exact test (p ˂ 0.01), there were noticeably different probabilities of all major nucleotide changes spreading among buffalo groups with and without reproductive problems. Buffaloes were significantly more likely to express the examined genes when they had inflammatory reproductive diseases. The outcomes might support the significance of these markers' nucleotide variations and gene expression patterns as indicators of the prevalence of inflammatory reproductive disorders and provide a workable buffalo management policy.

Genome-wide identification and annotation of SNPs for economically important traits in Frieswal™, newly evolved crossbred cattle of India

The Frieswal™ is a crossbred cattle evolved by ICAR-Central Institute for Research on Cattle utilizing more than 15,000 cattle maintained at more than 37 military farms spread all over the agro-climatic regions of the country. The ddRAD sequencing method was used to identify and annotate the SNPs and INDELs. The results of variant calling revealed 1,487,851 SNPs and 128,175 INDELs at a read depth of 10. A total of 3,775,079 effects were identified, and majority (66.41%) of the effects were in the intron region of the genome followed by intergenic (21.87%). Majority (99.18%) of the variants had the modifier effect. The results revealed a higher magnitude of transitions as compared to the transversion. The classification of SNPs by functional class revealed a majority of missense (43%) and silent (56%) effects. Out of 26,278 genes identified, 1841 SNPs were annotated in 207 candidate genes responsible for various milk production and reproduction traits. The observed heterozygosity was 0.2804 against the expected heterozygosity value of 0.2978. The overall average inbreeding coefficient (FIS) was 0.0604. The pathway analysis revealed that the prolactin signaling pathway (GO:0038161) was significant biological process complete for both milk production and reproduction traits. The SNP variations can be effectively used as markers for early and accurate identification of the QTLs and for formulating an efficient and effective breed improvement program in Frieswal™ cattle.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03701-0.

Comparative expression analysis of water buffalo (Bubalus bubalis) to identify genes associated with economically important traits

The milk, meat, skins, and draft power of domestic water buffalo (Bubalus bubalis) provide substantial contributions to the global agricultural economy. The world's water buffalo population is primarily found in Asia, and the buffalo supports more people per capita than any other livestock species. For evaluating the workflow, output rate, and completeness of transcriptome assemblies within and between reference-free (RF) de novo transcriptome and reference-based (RB) datasets, abundant bioinformatics studies have been carried out to date. However, comprehensive documentation of the degree of consistency and variability of the data produced by comparing gene expression levels using these two separate techniques is lacking. In the present study, we assessed the variations in the number of differentially expressed genes (DEGs) attained with RF and RB approaches. In light of this, we conducted a study to identify, annotate, and analyze the genes associated with four economically important traits of buffalo, viz., milk volume, age at first calving, post-partum cyclicity, and feed conversion efficiency. A total of 14,201 and 279 DEGs were identified in RF and RB assemblies. Gene ontology (GO) terms associated with the identified genes were allocated to traits under study. Identified genes improve the knowledge of the underlying mechanism of trait expression in water buffalo which may support improved breeding plans for higher productivity. The empirical findings of this study using RNA-seq data-based assembly may improve the understanding of genetic diversity in relation to buffalo productivity and provide important contributions to answer biological issues regarding the transcriptome of non-model organisms.

Genome-wide identification and annotation of SNPs and their mapping in candidate genes related to milk production and fertility traits in Badri cattle

This study was conducted in Badri cattle using a double digest restriction-site associated DNA sequencing approach. The study aimed to identify and annotate high confidence single nucleotide polymorphisms (SNPs) and their mapping in candidate genes related to production and fertility in dairy cattle. A total of 7,168,552 genome-wide SNPs were initially identified in Badri cattle by alignment with the Bos indicus reference genome. After filtration of SNPs, 65,483 high confidence SNPs were retained and further used for downstream analysis. Annotation of high confidence SNPs revealed 99.197% SNPs had modifier impact, 0.326% SNPs were low impact, 0.036% were high impact, and 0.441% were moderate impact SNPs. Most SNPs in Badri cattle were found in intergenic, transcript and intronic regions. The candidate genes for milk production PRKCE, ABCG2, GHR, EPS8, CAST and NRXN1 were found to harbour maximum high confidence variants. Among candidate genes for fertility in cattle, ATP2B1, SOX5, WDR27, ARHGAP12, CACNA1D, ANKRD6, GRIA3, ZNF521 and CAST822 have maximum high confidence variants mapped in them. The SNPs found mapped in the candidate genes will be important genetic tools in the search for phenotype-modifying nucleotide changes and will aid in formulating relevant genetic improvement programmes for dairy cattle.

Genome-wide association study for milk production and conformation traits in Canadian Alpine and Saanen dairy goats

Increasing the productivity of Canadian dairy goats is critical to the competitiveness of the sector; however, little is known about the underlying genetic architecture of economically important traits in these populations. Consequently, the objectives of this study were as follows: (1) to perform a single-step GWAS for milk production traits (milk, protein, and fat yields, and protein and fat percentages in first and later lactations) and conformation traits (body capacity, dairy character, feet and legs, fore udder, general appearance, rear udder, suspensory ligament, and teats) in the Canadian Alpine and Saanen breeds; and (2) to identify positional and functional candidate genes related to these traits. The data available for analysis included 305-d milk production records for 6,409 Alpine and 3,434 Saanen does in first lactation and 5,827 Alpine and 2,632 Saanen does in later lactations; as well as linear type conformation records for 5,158 Alpine and 2,342 Saanen does. Genotypes were available for 833 Alpine and 874 Saanen animals. Both single-breed and multiple-breed GWAS were performed using single-trait animal models. Positional and functional candidate genes were then identified in downstream analyses. The GWAS identified 189 unique SNP that were significant at the chromosomal level, corresponding to 271 unique positional candidate genes within 50 kb up- and downstream, across breeds and traits. This study provides evidence for the economic importance of several candidate genes (e.g., CSN1S1, CSN2, CSN1S2, CSN3, DGAT1, and ZNF16) in the Canadian Alpine and Saanen populations that have been previously reported in other dairy goat populations. Moreover, several novel positional and functional candidate genes (e.g., RPL8, DCK, and MOB1B) were also identified. Overall, the results of this study have provided greater insight into the genetic architecture of milk production and conformation traits in the Canadian Alpine and Saanen populations. Greater understanding of these traits will help to improve dairy goat breeding programs.

Physiological roles and regulation of hepatic angiopoietin-like protein 3 in Japanese Black cattle (Bos taurus) during the fattening period

Angiopoietin-like protein 3 (ANGPTL3) is expressed predominantly in the liver and plays a major role in regulating the circulating triglyceride and lipoprotein fraction concentrations by inhibiting lipoprotein lipase (LPL) activity. Given these physiological roles, ANGPTL3 may play an important role in metabolic changes related to fat accumulation during the fattening period in Japanese Black. This study aimed to reveal the physiological roles of hepatic ANGPTL3 in Japanese Black steers (Bos taurus) during the fattening period and investigate the regulatory effects of hepatic ANGPTL3. To investigate the gene expression and protein localization of ANGPTL3, 18 tissue samples were collected from tree male Holstein bull calves aged 7 wk. Biopsied liver tissues and blood samples were collected from 21 Japanese Black steers during the early (T1; 13 mo of age), middle (T2; 20 mo), and late fattening phases (T3; 28 mo). Relative mRNA expression, blood metabolite concentrations, hormone concentrations, growth, and carcass traits were analyzed. To identify the regulatory factors of hepatic ANGPTL3, primary bovine hepatocytes collected by two Holstein calves aged 7 wk were incubated with insulin, palmitate, oleate, propionate, acetate, or beta-hydroxybutyric acid (BHBA). The ANGPTL3 gene was most highly expressed in the liver, with minor expression in the renal cortex, lungs, reticulum, and jejunum in Holstein bull calves. In Japanese Black steers, relative ANGPTL3 mRNA expressions were less as fattening progressed, and blood triglyceride, total cholesterol, and nonesterified fatty acid (NEFA) concentrations increased. Relative ANGPTL8 and Liver X receptor alpha (LXRα) mRNA expressions decreased in late and middle fattening phases, respectively. Furthermore, relative ANGTPL3 mRNA expression was positively correlated with ANGPTL8 (r = 0.650; P < 0.01) and ANGPTL4 (r = 0.540; P < 0.05) in T3 and T1, respectively, and LXRα showed no correlation with ANGPTL3. Relative ANGTPL3 mRNA expression was negatively correlated with total cholesterol (r = -0.434; P < 0.05) and triglyceride (r = -0.645; P < 0.01) concentrations in T3 and T1, respectively; There was no significant correlation between ANGTPL3 and carcass traits. Relative ANGTPL3 mRNA expression in cultured bovine hepatocytes was downregulated in oleate treatment. Together, these findings suggest that ANGPTL3 downregulation in late fattening phases is associated with the changes in lipid metabolism.

Effects of PUFA-Rich Dietary Strategies on Ruminants' Mammary Gland Gene Network: A Nutrigenomics Review

Although the inclusion of polyunsaturated fatty acids (PUFAs) in ruminants' diets appears to be a well-documented strategy to enrich milk with PUFAs, several gene networks that regulate milk synthesis and mammary gland homeostasis could be impaired. The objective of this literature review is to assess the effects of nutritional strategies focused on enriching milk with PUFAs on gene networks regulating mammary gland function and lipogenesis, as well as the impact of feed additives and bioactive compounds with prominent antioxidant potential on immune-oxidative transcriptional profiling, as a part of mammary gland homeostasis and health. The findings support the conclusion that PUFAs' inclusion in ruminants' diets more strongly downregulate the stearoyl-CoA desaturase (SCD) gene compared to other key genes involved in de novo fatty acid synthesis in the mammary gland. Additionally, it was revealed that seed oils rich in linoleic and linolenic acids have no such strong impact on networks that regulate lipogenic homeostasis compared to marine oils rich in eicosapentaenoic and docosahexaenoic acids. Furthermore, ample evidence supports that cows and sheep are more prone to the suppression of lipogenesis pathways compared to goats under the impact of dietary marine PUFAs. On the other hand, the inclusion of feed additives and bioactive compounds with prominent antioxidant potential in ruminants' diets can strengthen mammary gland immune-oxidative status. Considering that PUFA's high propensity to oxidation can induce a cascade of pro-oxidant incidences, the simultaneous supplementation of antioxidant compounds and especially polyphenols may alleviate any side effects caused by PUFA overload in the mammary gland. In conclusion, future studies should deeply investigate the effects of PUFAs on mammary gland gene networks in an effort to holistically understand their impact on both milk fat depression syndrome and homeostatic disturbance.

Multi-Omics Analysis of Transcriptomic and Metabolomics Profiles Reveal the Molecular Regulatory Network of Marbling in Early Castrated Holstein Steers

The intramuscular fat (IMF), or so-called marbling, is known as potential determinant of the high quality beef in China, Korea, and Japan. Of the methods that affect IMF content in cattle, castration is markedly regarded as an effective and economical way to improve the deposition of IMF but with little attention to its multi-omics in early-castrated cattle. The aim of this study was to investigate the liver transcriptome and metabolome of early-castrated Holstein cattle and conduct a comprehensive analysis of two omics associated with the IMF deposition using transcriptomics and untargeted metabolomics under different treatments: non−castrated and slaughtered at 16 months of age (GL16), castrated at birth and slaughtered at 16 months of age (YL16), and castrated at birth and slaughtered at 26 months of age (YL26). The untargeted metabolome was analyzed using ultrahigh-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. The transcriptome of the hepatic genes was analyzed to identify marbling-related genes. Using untargeted metabolomics, the main altered metabolic pathways in the liver of cattle, including those for lipid and amino acid metabolism, were detected in the YL16 group relative to the GL16 and YL26 groups. Significant increases in the presence of betaine, alanine, and glycerol 3-phosphate were observed in the YL16 group (p < 0.05), which might have contributed to the improved beef-marbling production. Compared to the GL16 and YL26 groups, significant increases in the presence of glutathione, acetylcarnitine, and riboflavin but decreases in diethanolamine and 2-hydroxyglutarate were identified in YL16 group (p < 0.05), which might have been beneficial to the beef’s enhanced functional quality. The gene expressions of GLI1 and NUF2 were downregulated and that of CYP3A4 was upregulated in the YL16 group; these results were strongly correlated with the alanine, betaine, and leucine, respectively, in the liver of the cattle. In conclusion, implementation of early castration modified the hepatic metabolites and the related biological pathways by regulating the relevant gene expressions, which could represent a better rearing method for production of high marbled and healthier beef products.

Physiological responses and adaptations to high methane production in Japanese Black cattle

In this study, using enteric methane emissions, we investigated the metabolic characteristics of Japanese Black cattle. Their methane emissions were measured at early (age 13 months), middle (20 months), and late fattening phases (28 months). Cattle with the highest and lowest methane emissions were selected based on the residual methane emission values, and their liver transcriptome, blood metabolites, hormones, and rumen fermentation characteristics were analyzed. Blood β-hydroxybutyric acid and insulin levels were high, whereas blood amino acid levels were low in cattle with high methane emissions. Further, propionate and butyrate levels differed depending on the enteric methane emissions. Hepatic genes, such as SERPINI2, SLC7A5, ATP6, and RRAD, which were related to amino acid transport and glucose metabolism, were upregulated or downregulated during the late fattening phase. The above mentioned metabolites and liver transcriptomes could be used to evaluate enteric methanogenesis in Japanese Black cattle.

Genome-wide elucidation of CNV regions and their association with production and reproduction traits in composite Vrindavani cattle

The present study was aimed to analyze the genome-wide copy number variations (CNVs) in Vrindavani composite cattle and concatenate them into CNV regions (CNVRs), and finally test the association of CNVRs with different production and reproduction traits. Genotypic data, generated on BovineSNP50 Beadchip (v3) array for 96 Vrindavani animals, was used to elucidate the CNVs at the genome level. Intensity data covering over 53,218 SNP genotypes on bovine genome was used. Algorithm based on Hidden Markov Model was employed in PennCNV program to detect, normalize and filter CNVs across the genome. 252 putative CNVs, detected via PennCNV program, in different individuals were concatenated into 71 CNV regions (CNVRs) using CNVRuler program. Association of CNVRs with important (re)production traits in Vrindavani animals was assessed using linear regression. Five CNVRs were found to be significantly associated with ten important (re)production traits. The genes harbored in these regions provided useful insights into the association of CNVRs with genes and ultimately the variation at phenotype level. Important genes that overlapped with CNVRs included WASHC4, HS6ST3, MBNL2, TOLLIP, PIDD1 and TSPAN4. Furthermore, the CNVRs were found to overlap with important QTLs available in AnimalQTL database which affect milk yield and composition along with reproduction and immune function traits. The copy number states of three enes were validated using digital droplet PCR technique. The results from the present study significantly enhance the understanding about CNVs in Vrindavani cattle and should help establish its CNV map. The study will also enable further investigation on association of these variants with important traits of economic interest including disease incidence.

Genom-wide analysis identifies single nucleotide polymorphism variations and altered pathways associated with poor semen quality in breeding bulls

The reason for poor semen quality among the breeding bulls is not well understood. In the present study, we performed high-throughput RNAseq analysis of spermatozoa to identify the SNPs present in good and poor-quality semen-producing Holstein Friesian breeding bulls. A total of 21,360 and 44,650 SNPs were identified in good and poor-quality semen with a minimum read depth of 20, among which 4780 and 8710 novel variants were observed in good and poor-quality semen, respectively. Greater SNPs and indels variations were observed in poor compared to good-quality semen. In poor-quality semen, SNP variations were observed in ZNF280B, SLC26A2, DMXL1, OR52A1, MACROD2 and REV1 genes, which are associated with regulation of spermatogenesis, post-testicular maturation, Cl^- channel activity, V-ATPase-mediated intracellular vesicle acidification, a mono-ADP-ribosyl hydrolase and ATR-Chk1 checkpoint activation. GO analysis of filtered genes with significant variations between good and poor-quality semen showed enrichment in important pathways related to semen quality such as MAPK signalling pathway, Akt signalling pathway, focal adhesion, cAMP signalling pathway, and Rap1 signalling pathway. Network analysis of filtered genes in poor-quality semen showed variations in pathways of purine metabolism, pyrimidine metabolism, prolactin signalling pathway and RNA cap-binding complex. It is inferred that SNP in genes involved in maintaining sperm functions could be the reason for poor-quality semen production in bulls, and the identified SNPs hold potential to be used as biomarkers for semen quality in bulls.

Identification of Candidate Genes Regulating Carcass Depth and Hind Leg Circumference in Simmental Beef Cattle Using Illumina Bovine Beadchip and Next-Generation Sequencing Analyses

Genome-wide association studies are a robust means of identifying candidate genes that regulate economically important traits in farm animals. The aim of this study is to identify single-nucleotide polymorphisms (SNPs) and candidate genes potentially related to carcass depth and hind leg circumference in Simmental beef cattle. We performed Illumina Bovine HD Beadchip (~670 k SNPs) and next-generation sequencing (~12 million imputed SNPs) analyses of data from 1252 beef cattle, to which we applied a linear mixed model. Using a statistical threshold (p = 0.05/number of SNPs identified) and adopting a false discovery rate (FDR), we identified many putative SNPs on different bovine chromosomes. We identified 12 candidate genes potentially annotated with the markers identified, including CDKAL1 and E2F3, related to myogenesis and skeletal muscle development. The identification of such genes in Simmental beef cattle will help breeders to understand and improve related traits, such as meat yield.

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.

Changes in the liver transcriptome and physiological parameters of Japanese Black steers during the fattening period

We investigated the physiological changes during the fattening period and production characteristics in Japanese Black steers bred and raised using the typical feeding system in Japan. Here, 21 Japanese Black steers aged 12 months were used, with experimental period divided into early (12–14 months of age), middle (15–22 months), and late fattening phases (23–30 months). The liver transcriptome, blood metabolites, hormones, and rumen fermentation characteristics were analyzed. Blood triglyceride and non-esterified fatty acid concentrations increased, whereas blood ketone levels decreased, with fattening phases. Blood insulin increased with fattening phases and was positively correlated with carcass weight and marbling in late fattening phases. Rumen fermentation characteristics showed high propionate levels and low butyrate levels in late fattening phases, likely due to increased energy intake. Genes related to glucose metabolism, such as SESN3, INSR, LEPR, and FOXO3, were down-regulated in late fattening phases. Genes related to lipid metabolism, such as FABP4, were up-regulated, whereas FADS1 and FADS2 were down-regulated. These findings suggest that the physiological changes resulted from changes in the energy content and composition of diets. Liver metabolism changed with changes in fat metabolism. Insulin was strongly associated with physiological changes and productivity in Japanese Black cattle.

A novel missense mutation (rs464874590) within BoLA-DOB gene associated with the heat-resistance in Chinese cattle

Bovine leukocyte antigen, class II, DO beta (BoLA-DOB) is related to antigen presentation, which can triggered by multicul factors. And the condition of immune function determines how much cattle load to heat stress. To evaluate the relationship between heat-resistance and single nucleotide polymorphisms (SNPs) in BoLA-DOB gene, our study has taken further analysis in Chinese indigenous cattle for the first time. A missense single nucleotide polymorphism (rs464874590) was detected in BoLA-DOB gene. We directly sequenced rs464874590 (NM_001013600.1 g.7122762 A > G) in BoLA-DOB gene of 522 individuals of 26 cattle breeds. The frequency of allele G gradually decreases from south to north with distinct climatic distribution characteristics. Further association analysis was carried out between different genotypes and environmental parameters, including annual mean temperature (T), relative humidity (RH), and temperature-humidity index (THI). The result showed that three genotypes were significantly correlated with T, H, and THI (P < 0.01), indicating that GG genotype was distributed in areas with hot and moist conditions. Therefore, our results suggested that the rs464874590 could be applied as a genetic marker to detect the heat-resistance of Chinese indigenous cattle.

Genome-wide association study of trypanosome prevalence and morphometric traits in purebred and crossbred Baoulé cattle of Burkina Faso

In this study, single-SNP GWAS analyses were conducted to find regions affecting tolerance against trypanosomosis and morphometrics traits in purebred and crossbred Baoulé cattle of Burkina Faso. The trypanosomosis status (positive and negative) and a wide set of morphological traits were recorded for purebred Baoulé and crossbred Zebu x Baoulé cattle, and genotyped with the Illumina Bovine SNP50 BeadChip. After quality control, 36,203 SNPs and 619 animals including 343 purebred Baoulé and 279 crossbreds were used for the GWAS analyses. Several important genes were found that can influence morphological parameters. Although there were no genes identified with a reported strong connection to size traits, many of them were previously identified in various growth-related studies. A re-occurring theme for the genes residing in the regions identified by the most significant SNPs was pleiotropic effect on growth of the body and the cardiovascular system. Regarding trypanosomosis tolerance, two potentially important regions were identified in purebred Baoulé on chromosomes 16 and 24, containing the CFH, CRBN, TRNT1 and, IL5RA genes, and one additional genomic region in Baoulé, x Zebu crossbreds on chromosome 5, containing MGAT4C and NTS. Almost all of these regions and genes were previously related to the trait of interest, while the CRBN gene was to our knowledge presented in the context of trypanosomiasis tolerance for the first time.

Breed Ancestry, Divergence, Admixture, and Selection Patterns of the Simbra Crossbreed

In this study, we evaluated an admixed South African Simbra crossbred population, as well as the Brahman (Indicine) and Simmental (Taurine) ancestor populations to understand their genetic architecture and detect genomic regions showing signatures of selection. Animals were genotyped using the Illumina BovineLD v2 BeadChip (7K). Genomic structure analysis confirmed that the South African Simbra cattle have an admixed genome, composed of 5/8 Taurine and 3/8 Indicine, ensuring that the Simbra genome maintains favorable traits from both breeds. Genomic regions that have been targeted by selection were detected using the linkage disequilibrium-based methods iHS and Rsb. These analyses identified 10 candidate regions that are potentially under strong positive selection, containing genes implicated in cattle health and production (e.g., TRIM63, KCNA10, NCAM1, SMIM5, MIER3, and SLC24A4). These adaptive alleles likely contribute to the biological and cellular functions determining phenotype in the Simbra hybrid cattle breed. Our data suggested that these alleles were introgressed from the breed's original indicine and taurine ancestors. The Simbra breed thus possesses derived parental alleles that combine the superior traits of the founder Brahman and Simmental breeds. These regions and genes might represent good targets for ad-hoc physiological studies, selection of breeding material and eventually even gene editing, for improved traits in modern cattle breeds. This study represents an important step toward developing and improving strategies for selection and population breeding to ultimately contribute meaningfully to the beef production industry.

Comparative accuracies of genetic values predicted for economically important milk traits, genome-wide association, and linkage disequilibrium patterns of Canadian Holstein cows

Genomic selection methodologies and genome-wide association studies use powerful statistical procedures that correlate large amounts of high-density SNP genotypes and phenotypic data. Actual 305-d milk (MY), fat (FY), and protein (PY) yield data on 695 cows and 76,355 genotyping-by-sequencing-generated SNP marker genotypes from Canadian Holstein dairy cows were used to characterize linkage disequilibrium (LD) structure of Canadian Holstein cows. Also, the comparison of pedigree-based BLUP, genomic BLUP (GBLUP), and Bayesian (BayesB) statistical methods in the genomic selection methodologies and the comparison of Bayesian ridge regression and BayesB statistical methods in the genome-wide association studies were carried out for MY, FY, and PY. Results from LD analysis revealed that as marker distance decreases, LD increases through chromosomes. However, unexpected high peaks in LD were observed between marker pairs with larger marker distances on all chromosomes. The GBLUP and BayesB models resulted in similar heritability estimates through 10-fold cross-validation for MY and PY; however, the GBLUP model resulted in higher heritability estimates than BayesB model for FY. The predictive ability of GBLUP model was significantly lower than that of BayesB for MY, FY, and PY. Association analyses indicated that 28 high-effect markers and markers on Bos taurus autosome 14 located within 6 genes (DOP1B, TONSL, CPSF1, ADCK5, PARP10, and GRINA) associated significantly with FY.

Population demographic history and population structure for Pakistani Nili-Ravi breeding bulls based on SNP genotyping to identify genomic regions associated with male effects for milk yield and body weight

The domestic Nili-Ravi water buffalo (Bubalus bubalis) is the best dairy animal contributing 68% to total milk production in Pakistan. In this study, we identified genome-wide single nucleotide polymorphisms (SNPs) to estimate various population genetic parameters such as diversity, pairwise population differentiation, linkage disequilibrium (LD) distribution and for genome-wide association study for milk yield and body weight traits in the Nili-Ravi dairy bulls that they may pass on to their daughters who are retained for milking purposes. The genotyping by sequencing approach revealed 13,039 reference genome-anchored SNPs with minor allele frequency of 0.05 among 167 buffalos. Population structure analysis revealed that the bulls were grouped into two clusters (K = 2), which indicates the presence of two different lineages in the Pakistani Nili-Ravi water buffalo population, and we showed the extent of admixture of these two lineages in our bull collection. LD analysis revealed 4169 significant SNP associations, with an average LD decay of 90 kb for these buffalo genome. Genome-wide association study involved a multi-locus mixed linear model for milk yield and body weight to identify genome-wide male effects. Our study further illustrates the utility of the genotyping by sequencing approach for identifying genomic regions to uncover additional demographic complexity and to improve the complex dairy traits of the Pakistani Nili-Ravi water buffalo population that would provide the lot of economic benefits to dairy industry.

Characterization of bovine MHC DRB3 diversity in global cattle breeds, with a focus on cattle in Myanmar

Background

Myanmar cattle populations predominantly consist of native cattle breeds (Pyer Sein and Shwe), characterized by their geographical location and coat color, and the Holstein-Friesian crossbreed, which is highly adapted to the harsh tropical climates of this region. Here, we analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus that has been linked to the immune response, in Myanmar cattle populations.

Methods

Blood samples (n = 294) were taken from two native breeds (Pyer Sein, n = 163 and Shwe Ni, n = 69) and a cattle crossbreed (Holstein-Friesian, n = 62) distributed across six regions of Myanmar (Bago, n = 38; Sagaing, n = 77; Mandalay, n = 46; Magway, n = 46; Kayin, n = 43; Yangon, n = 44). In addition, a database that included 2428 BoLA-DRB3 genotypes from European (Angus, Hereford, Holstein, Shorthorn, Overo Negro, Overo Colorado, and Jersey), Zebuine (Nellore, Brahman and Gir), Asian Native from Japan and Philippine and Latin-American Creole breeds was also included. Furthermore, the information from the IPD–MHC database was also used in the present analysis. DNA was genotyped using the sequence-based typing method. DNA electropherograms were analyzed using the Assign 400ATF software.

Results

We detected 71 distinct alleles, including three new variants for the BoLA-DRB3 gene. Venn analysis showed that 11 of these alleles were only detected in Myanmar native breeds and 26 were only shared with Asian native and/or Zebu groups. The number of alleles ranged from 33 in Holstein-Friesians to 58 in Pyer Seins, and the observed versus unbiased expected heterozygosity were higher than 0.84 in all the three the populations analyzed. The F_ST analysis showed a low level of genetic differentiation between the two Myanmar native breeds (F_ST = 0.003), and between these native breeds and the Holstein-Friesians (F_ST <  0.021). The average F_ST value for all the Myanmar Holstein-Friesian crossbred and Myanmar native populations was 0.0136 and 0.0121, respectively. Principal component analysis (PCA) and tree analysis showed that Myanmar native populations grouped in a narrow cluster that diverged clearly from the Holstein-Friesian populations. Furthermore, the BoLA-DRB3 allele frequencies suggested that while some Myanmar native populations from Bago, Mandalay and Yangon regions were more closely related to Zebu breeds (Gir and Brahman), populations from Kayin, Magway and Sagaing regions were more related to the Philippines native breeds. On the contrary, PCA showed that the Holstein-Friesian populations demonstrated a high degree of dispersion, which is likely the result of the different degrees of native admixture in these populations.

Conclusion

This study is the first to report the genetic diversity of the BoLA-DRB3 gene in two native breeds and one exotic cattle crossbreed from Myanmar. The results obtained contribute to our understanding of the genetic diversity and distribution of BoLA-DRB3 gene alleles in Myanmar, and increases our knowledge of the worldwide variability of cattle BoLA-DRB3 genes, an important locus for immune response and protection against pathogens.

Glucose Metabolism and Dynamics of Facilitative Glucose Transporters (GLUTs) under the Influence of Heat Stress in Dairy Cattle

Heat stress is one of the main threats to dairy cow production; in order to resist heat stress, the animal exhibits a variety of physiological and hormonal responses driven by complex molecular mechanisms. Heat-stressed cows have high insulin activity, decreased non-esterified fatty acids, and increased glucose disposal. Glucose, as one of the important biochemical components of the energetic metabolism, is affected at multiple levels by the reciprocal changes in hormonal secretion and adipose metabolism under the influence of heat stress in dairy cattle. Therefore, alterations in glucose metabolism have negative consequences for the animal’s health, production, and reproduction under heat stress. Lactose is a major sugar of milk which is affected by the reshuffle of the whole-body energetic metabolism during heat stress, contributing towards milk production losses. Glucose homeostasis is maintained in the body by one of the glucose transporters’ family called facilitative glucose transporters (GLUTs encoded by SLC2A genes). Besides the glucose level, the GLUTs expression level is also significantly changed under the influence of heat stress. This review aims to describe the effect of heat stress on systemic glucose metabolism, facilitative glucose transporters, and its consequences on health and milk production.

Use of multivariate factor analysis of detailed milk fatty acid profile to perform a genome-wide association study in Italian Simmental and Italian Holstein

Milk fatty acid (FA) profile is a clear example of complex and multiple correlated traits whose genetic basis is difficult to assess. Although genome-wide association (GWA) studies have been successful in the identification of significant genetic variants for complex traits, when correlated phenotypes are analysed separately, the outcomes are difficult to compare and interpret in a metabolic context. Here, we performed a multivariate factor analysis (MFA) on Italian Simmental and Italian Holstein milk fat profiles to extract latent unobserved factors able to explain correlation structure and common metabolic function among different FAs. Individual factor scores obtained by MFA were used to perform a single-SNP based GWA. In both breeds, MFA was able to extract ten latent factors with specific biological meaning, notably: de novo synthesis, desaturation activity and biohydrogenation. The GWA result confirmed the increased power of joint association analysis on multiple correlated traits and allowed us to identify major candidate genes with well-documented function consistent with the metabolic classification of factors obtained, such as DGAT1, FASN and SCD.

Mismatch of Glucose Allocation between Different Life Functions in the Transition Period of Dairy Cows

Immune cell functions such as phagocytosis and synthesis of immunometabolites, as well as immune cell survival, proliferation and differentiation, largely depend on an adequate availability of glucose by immune cells. During inflammation, the glucose demands of the immune system may increase to amounts similar to those required for high milk yields. Similar metabolic pathways are involved in the adaptation to both lactation and inflammation, including changes in the somatotropic axis and glucocorticoid response, as well as adipokine and cytokine release. They affect (i) cell growth, proliferation and activation, which determines the metabolic activity and thus the glucose demand of the respective cells; (ii) the overall availability of glucose through intake, mobilization and gluconeogenesis; and (iii) glucose uptake and utilization by different tissues. Metabolic adaptation to inflammation and milk synthesis is interconnected. An increased demand of one life function has an impact on the supply and utilization of glucose by competing life functions, including glucose receptor expression, blood flow and oxidation characteristics. In cows with high genetic merits for milk production, changes in the somatotropic axis affecting carbohydrate and lipid metabolism as well as immune functions are profound. The ability to cut down milk synthesis during periods when whole-body demand exceeds the supply is limited. Excessive mobilization and allocation of glucose to the mammary gland are likely to contribute considerably to peripartal immune dysfunction.

Identification and characterization of trait-specific SNPs using ddRAD sequencing in water buffalo

Single Nucleotide Polymorphism (SNP) is one of the important molecular markers widely used in animal breeding program for improvement of any desirable genetic traits. Considering this, the present study was carried out to identify, annotate and analyze the SNPs related to four important traits of buffalo viz. milk volume, age at first calving, post-partum cyclicity and feed conversion efficiency. We identified 246,495, 168,202, 74,136 and 194,747 genome-wide SNPs related to mentioned traits, respectively using ddRAD sequencing technique based on 85 samples of Murrah Buffaloes. Distribution of these SNPs were highest (61.69%) and lowest (1.78%) in intron and exon regions, respectively. Under coding regions, the SNPs for the four traits were further classified as synonymous (4697) and non-synonymous (3827). Moreover, Gene Ontology (GO) terms of identified genes assigned to various traits. These characterized SNPs will enhance the knowledge of cellular mechanism for enhancing productivity of water buffalo through molecular breeding.

Implications of Gene Inheritance Patterns on the Heterosis of Abdominal Fat Deposition in Chickens

Heterosis, a phenomenon characterized by the superior performance of hybrid individuals relative to their parents, has been widely utilized in livestock and crop breeding, while the underlying genetic basis remains elusive in chickens. Here, we performed a reciprocal crossing experiment with broiler and layer chickens and conducted RNA sequencing on liver tissues for reciprocal crosses and their parental lines to identify inheritance patterns of gene expression. Our results showed that heterosis of the abdominal fat percentage was 69.28%–154.71% in reciprocal crosses. Over-dominant genes of reciprocal crosses were significantly enriched in three biological pathways, namely, butanoate metabolism, the synthesis and degradation of ketone bodies, and valine, leucine, and isoleucine degradation. Among these shared over-dominant genes, we found that a lipid-related gene, HMGCL, was enriched in these pathways. Furthermore, we validated this gene as over-dominant using qRT-PCR. Although no shared significant pathway was detected in the high-parent dominant genes of reciprocal crosses, high-parent dominant gene expression was the major gene inheritance pattern in reciprocal crosses and we could not exclude the effect of high-parent dominant genes. These findings suggest that non-additive genes play important roles in the heterosis of important traits in chickens and have important implications regarding our understanding of heterosis.

Genome-wide association for milk production and lactation curve parameters in Holstein dairy cows

The aim of this study was to identify genomic regions associated with 305‐day milk yield and lactation curve parameters on primiparous (n = 9,910) and multiparous (n = 11,158) Holstein cows. The SNP solutions were estimated using a weighted single‐step genomic BLUP approach and imputed high‐density panel (777k) genotypes. The proportion of genetic variance explained by windows of 50 consecutive SNP (with an average of 165 Kb) was calculated, and regions that accounted for more than 0.50% of the variance were used to search for candidate genes. Estimated heritabilities were 0.37, 0.34, 0.17, 0.12, 0.30 and 0.19, respectively, for 305‐day milk yield, peak yield, peak time, ramp, scale and decay for primiparous cows. Genetic correlations of 305‐day milk yield with peak yield, peak time, ramp, scale and decay in primiparous cows were 0.99, 0.63, 0.20, 0.97 and −0.52, respectively. The results identified three windows on BTA14 associated with 305‐day milk yield and the parameters of lactation curve in primi‐ and multiparous cows. Previously proposed candidate genes for milk yield supported by this work include GRINA, CYHR1, FOXH1, TONSL, PPP1R16A, ARHGAP39, MAF1, OPLAH and MROH1, whereas newly identified candidate genes are MIR2308, ZNF7, ZNF34, SLURP1, MAFA and KIFC2 (BTA14). The protein lipidation biological process term, which plays a key role in controlling protein localization and function, was identified as the most important term enriched by the identified genes.

Genome-wide association analysis for β-hydroxybutyrate concentration in Milk in Holstein dairy cattle

BACKGROUND

Ketosis in dairy cattle has been shown to cause a high morbidity in the farm and substantial financial losses to dairy farmers. Ketosis symptoms, however, are difficult to identify, therefore, the amount of ketone bodies (mainly β-hydroxybutyric acid, BHB) is used as an indicator of subclinical ketosis in cows. It has also been shown that milk BHB concentrations have a strong correlation with ketosis in dairy cattle. Mid-infrared spectroscopy (MIR) has recently became a fast, cheap and high-throughput method for analyzing milk components. The aim of this study was to perform a genome-wide association study (GWAS) on the MIR-predicted milk BHB to identify genomic regions, genes and pathways potentially affecting subclinical ketosis in North American Holstein dairy cattle.

RESULTS

Several significant regions were identified associated with MIR-predicted milk BHB concentrations (indicator of subclinical ketosis) in the first lactation (SCK1) and second and later lactations (SCK2) in Holstein dairy cows. The strongest association was located on BTA6 for SCK1 and BTA14 on SCK2. Several SNPs on BTA6 were identified in regions and variants reported previously to be associated with susceptibility to ketosis and clinical mastitis in Jersey and Holstein dairy cattle, respectively. One highly significant SNP on BTA14 was found within the DGAT1 gene with known functions on fat metabolism and inflammatory response in dairy cattle. A region on BTA6 and three SNPs on BTA20 were found to overlap between SCK1 and SCK2. However, a novel region on BTA20 (55-63 Mb) for SCK2 was also identified, which was not reported in previous association studies. Enrichment analysis of the list of candidate genes within the identified regions for MIR-predicted milk BHB concentrations yielded molecular functions and biological processes that may be involved in the inflammatory response and lipid metabolism in dairy cattle.

CONCLUSIONS

The results of this study confirmed several SNPs and genes identified in previous studies as associated with ketosis susceptibility and immune response, and also found a novel region that can be used for further analysis to identify causal variations and key regulatory genes that affect clinical/ subclinical ketosis.

Genome-wide association for milk production traits and somatic cell score in different lactation stages of Ayrshire, Holstein, and Jersey dairy cattle

We performed genome-wide association analyses for milk, fat, and protein yields and somatic cell score based on lactation stages in the first 3 parities of Canadian Ayrshire, Holstein, and Jersey cattle. The genome-wide association analyses were performed considering 3 different lactation stages for each trait and parity: from 5 to 95, from 96 to 215, and from 216 to 305 d in milk. Effects of single nucleotide polymorphisms (SNP) for each lactation stage, trait, parity, and breed were estimated by back-solving the direct breeding values estimated using the genomic best linear unbiased predictor and single-trait random regression test-day models containing only the fixed population average curve and the random genomic curves. To identify important genomic regions related to the analyzed lactation stages, traits, parities and breeds, moving windows (SNP-by-SNP) of 20 adjacent SNP explaining more than 0.30% of total genetic variance were selected for further analyses of candidate genes. A lower number of genomic windows with a relatively higher proportion of the explained genetic variance was found in the Holstein breed compared with the Ayrshire and Jersey breeds. Genomic regions associated with the analyzed traits were located on 12, 8, and 15 chromosomes for the Ayrshire, Holstein, and Jersey breeds, respectively. Especially for the Holstein breed, many of the identified candidate genes supported previous reports in the literature. However, well-known genes with major effects on milk production traits (e.g., diacylglycerol O-acyltransferase 1) showed contrasting results among lactation stages, traits, and parities of different breeds. Therefore, our results suggest evidence of differential sets of candidate genes underlying the phenotypic expression of the analyzed traits across breeds, parities, and lactation stages. Further functional studies are needed to validate our findings in independent populations.

The use of mid-infrared spectra to map genes affecting milk composition

The aim of this study was to investigate the feasibility of using mid-infrared (MIR) spectroscopy analysis of milk samples to increase the power and precision of genome-wide association studies (GWAS) for milk composition and to better distinguish linked quantitative trait loci (QTL). To achieve this goal, we analyzed phenotypic data of milk composition traits, related MIR spectra, and genotypic data comprising 626,777 SNP on 5,202 Holstein, Jersey, and crossbred cows. We performed a conventional GWAS on protein, lactose, fat, and fatty acid concentrations in milk, a GWAS on individual MIR wavenumbers, and a partial least squares regression (PLS), which is equivalent to a multi-trait GWAS, exploiting MIR data simultaneously to predict SNP genotypes. The PLS detected most of the QTL identified using single-trait GWAS, usually with a higher significance value, as well as previously undetected QTL for milk composition. Each QTL tends to have a different pattern of effects across the MIR spectrum and this explains the increased power. Because SNP tracking different QTL tend to have different patterns of effect, it was possible to distinguish closely linked QTL. Overall, the results of this study suggest that using MIR data through either GWAS or PLS analysis applied to genomic data can provide a powerful tool to distinguish milk composition QTL.

Effect of different exogenous fatty acids on the cytosolic triacylglycerol content in bovine mammary cells

The objective of this study was to determine how cytosolic triacylglycerols (TAG) are stored in mammary cells and whether this depends on the individual chemical configuration of fatty acids (FA). This objective was accomplished by addition of different FA to a FA-free medium used to culture mammary alveolar cells-large T antigen cells (MAC-T). Treatments consisted of adding FA (palmitate, stearate, oleate, linoleate, rumenic acid [CLA], elaidate and vaccinate) solutions to the medium at 100, 200, 300 and 400 mmol/L concentrations for a 24-h incubation period. At the end of each incubation period, cytosolic TAG, DNA and protein contents were measured. Palmitate, vaccenate, linoleate and CLA increased (P < 0.05) cytosolic TAG (μg/mg protein). Palmitate and CLA increased (P < 0.05) cytosolic TAG adjusted for DNA content. Overall, effects on cytosolic TAG accumulation depended on individual FA structure (chain length, degree of saturation, and number and orientation of FA double bonds). In addition, the long-chain FA used in this study did not have a detrimental effect on MAC-T cells as indicated by cytosolic protein and DNA contents reflecting their biological role in lipid accumulation.

Genetic diversity of BoLA-DRB3 in South American Zebu cattle populations

Background

Bovine leukocyte antigens (BoLAs) are used extensively as markers of disease and immunological traits in cattle. However, until now, characterization of BoLA gene polymorphisms in Zebu breeds using high resolution typing methods has been poor. Here, we used a polymerase chain reaction sequence-based typing (PCR-SBT) method to sequence exon 2 of the BoLA class II DRB3 gene from 421 cattle (116 Bolivian Nellore, 110 Bolivian Gir, and 195 Peruvian Nellore-Brahman). Data from 1416 Taurine and Zebu samples were also included in the analysis.

Results

We identified 46 previously reported alleles and no novel variants. Of note, 1/3 of the alleles were detected only in Zebu cattle. Comparison of the degree of genetic variability at the population and sequence levels with genetic distance in the three above mentioned breeds and nine previously reported breeds revealed that Zebu breeds had a gene diversity score higher than 0.86, a nucleotide diversity score higher than 0.06, and a mean number of pairwise differences greater than 16, being similar to those estimated for other cattle breeds. A neutrality test revealed that only Nellore-Brahman cattle showed the even gene frequency distribution expected under a balanced selection scenario. The F_ST index and the exact G test showed significant differences across all cattle populations (F_ST = 0.057; p <  0.001). Neighbor-joining trees and principal component analysis identified two major clusters: one comprising mainly European Taurine breeds and a second comprising Zebu breeds. This is consistent with the historical and geographical origin of these breeds. Some of these differences may be explained by variation of amino acid motifs at antigen-binding sites.

Conclusions

The results presented herein show that the historical divergence between Taurine and Zebu cattle breeds is a result of origin, selection, and adaptation events, which would explain the observed differences in BoLA-DRB3 gene diversity between the two major bovine types. This allelic information will be important for investigating the relationship between the major histocompatibility complex and disease, and contribute to an ongoing effort to catalog bovine MHC allele frequencies according to breed and location.

Electronic supplementary material

The online version of this article (10.1186/s12863-018-0618-7) contains supplementary material, which is available to authorized users.

TRIENNIAL LACTATION SYMPOSIUM/BOLFA: Mammary growth during pregnancy and lactation and its relationship with milk yield

The number of secretory cells in the mammary gland is often cited as a major determinant of milk production. However, literature data for proxy measures of secretory cell number do not fully support such a claim. In particular, measurements of total mammary DNA in livestock explain only <25% of variation in milk yield, probably because of tissue heterogeneity for DNA concentration. Relative to BW, measurements of udder size in dairy cattle, as total DNA or udder weight, are approximately double those seen in most other livestock classes. Therefore, selection for dairy production, not surprisingly, has resulted in cows with greater secretory capacity. There is limited evidence that genetic selection is still increasing udder size in some cattle populations, but more recent data are needed. It is contended that the most important period of mammary growth for determination of milk yield is that occurring in pregnancy and early lactation. Mammary development is largely complete, at term, in sheep, goats, and cattle, but in pigs, the udder continues to grow during the first 3 wk of lactation, depending, in part, on litter size. Increased litter size in sheep and goats will enhance the extent of mammary development at the end of gestation (and milk yield) by 20 to 25%. However, twinning in dairy cattle does not affect milk production and, by inference only, is not likely to affect numbers of secretory cells at term. Milking frequency and suckling intensity in very early lactation will increase milk yield in cows and increase mammogenesis and milk yield in sheep, indicating that even at term, the ruminant gland retains some capacity for further development, if demand requires it. There is limited understanding of the hormonal signals in pregnancy that regulate mammary development relative to the number of young carried. Furthermore, the genetic differences between dairy and beef cattle that lead to substantially greater udder size in the dairy breeds have not been identified. During lactation, the drivers for secretory cell loss in relation to milking frequency and nutritional status are still not known. Measurement of mammary development and using this phenotype in genomewide association studies to identify key genetic variants for mammogenesis will provide knowledge that is fundamental to understanding the quantitative regulation of milk production.

Association analysis for udder index and milking speed with imputed whole-genome sequence variants in Nordic Holstein cattle

Genome-wide association testing facilitates the identification of genetic variants associated with complex traits. Mapping genes that promote genetic resistance to mastitis could reduce the cost of antibiotic use and enhance animal welfare and milk production by improving outcomes of breeding for udder health. Using imputed whole-genome sequence variants, we carried out association studies for 2 traits related to udder health, udder index, and milking speed in Nordic Holstein cattle. A total of 4,921 bulls genotyped with the BovineSNP50 BeadChip array were imputed to high-density genotypes (Illumina BovineHD BeadChip, Illumina, San Diego, CA) and, subsequently, to whole-genome sequence variants. An association analysis was carried out using a linear mixed model. Phenotypes used in the association analyses were deregressed breeding values. Multitrait meta-analysis was carried out for these 2 traits. We identified 10 and 8 chromosomes harboring markers that were significantly associated with udder index and milking speed, respectively. Strongest association signals were observed on chromosome 20 for udder index and chromosome 19 for milking speed. Multitrait meta-analysis identified 13 chromosomes harboring associated markers for the combination of udder index and milking speed. The associated region on chromosome 20 overlapped with earlier reported quantitative trait loci for similar traits in other cattle populations. Moreover, this region was located close to the FYB gene, which is involved in platelet activation and controls IL-2 expression; FYB is a strong candidate gene for udder health and worthy of further investigation.