Analysis of relationship between bovine lymphocyte antigen DRB3.2 alleles, somatic cell count and milk traits in Iranian Holstein population

A comprehensive review on genomic insights and advanced technologies for mastitis prevention in dairy animals

Mastitis is a multi-etiological disease that significantly impacts milk production and reproductive efficiency. It is highly prevalent in dairy populations subjected to intensive selection for higher milk yield and where inbreeding is common. The issue is amplified by climate change and poor hygiene management, making disease control challenging. Key obstacles include antibiotic resistance, maximum residue levels, horizontal gene transfer, and limited success in breeding for resistance. Predictive genomics offers a promising solution for mastitis prevention by identifying genetic traits linked with susceptibility to mastitis. This review compiles the research and findings on genomics and its allied approaches, such as pan-genomics, epigenetics, proteomics, and transcriptomics, for diagnosing, understanding, and treating mastitis. In dairy production, artificial intelligence (AI), particularly deep learning (DL) techniques like convolutional neural networks (CNNs), has demonstrated significant potential to enhance milk production and improve farm profitability. It highlights the integration of advanced technologies like machine learning (ML), CRISPR, and pan-genomics to improve our knowledge of mastitis epidemiology, pathogen evolution, and the development of more effective diagnostic, preventive and therapeutic strategies for dairy herds. Genomic advancements provide critical insights into the complexities of mastitis, offering new avenues for understanding its dynamics. Integrating these findings with key predisposing factors can drive targeted prevention and more effective disease management.

Graduate Student Literature Review: The DRB3 gene of the bovine major histocompatibility complex-Discovery, diversity, and distribution of alleles in commercial breeds of cattle and applications for development of vaccines

The bovine major histocompatibility complex (MHC), also known as the bovine leukocyte antigen (BoLA) complex, is the genomic region that encodes the most important molecules for antigen presentation to initiate immune responses. The first evidence of MHC in bovines pointed to a locus containing 2 antigens, one detected by cytotoxic antiserum (MHC class I) and another studied by mixed lymphocyte culture tests (MHC class II). The most studied gene in the BoLA region is the highly polymorphic BoLA-DRB3, which encodes a β chain with a peptide groove domain involved in antigen presentation for T cells that will develop and co-stimulate cellular and humoral effector responses. The BoLA-DRB3 alleles have been associated with outcomes in infectious diseases such as mastitis, trypanosomiasis, and tick loads, and with production traits. To catalog these alleles, 2 nomenclature methods were proposed, and the current use of both systems makes it difficult to list, comprehend and apply these data effectively. In this review we have organized the knowledge available in all of the reports on the frequencies of BoLA-DRB3 alleles. It covers information from studies made in at least 26 countries on more than 30 breeds; studies are lacking in countries that are important producers of cattle livestock. We highlight practical applications of BoLA studies for identification of markers associated with resistance to infectious and parasitic diseases, increased production traits and T cell epitope mapping, in addition to genetic diversity and conservation studies of commercial and Creole and locally adapted breeds. Finally, we provide support for the need of studies to discover new BoLA alleles and uncover unknown roles of this locus in production traits.

Genomic Insights into Pig Domestication and Adaptation: An Integrated Approach Using Genome-Wide Selection Analysis and Multiple Public Datasets

As a global focus of animal husbandry, pigs provide essential meat resources for humans. Therefore, analyzing the genetic basis of adaptability, domestication, and artificial selection in pigs will contribute to further breeding. This study performed a genome-wide selection sweep analysis to identify candidate genes related to domestication and adaptive selection via data from 2413 public genotypes. Two complementary statistical analyses, FST (fixation index) and XP-EHH (cross-population extended haplotype homozygosity) were applied. The results revealed that numerous candidate genes were associated with high-altitude adaptability (e.g., SIRPA, FRS2, and GRIN2B) and habitat temperature adaptability (e.g., MITF, PI3KC2A, and FRS2). In addition, candidate genes related to the domestic genetic imprint of indigenous pigs (e.g., TNR, NOCT, and SPATA5) and strong artificial selection pressure in commercial breeds (e.g., ITPR2, HSD17B12, and UGP2) were identified in this study. Specifically, some MHC-related genes (e.g., ZRTB12, TRIM26, and C7H6orf15) were also under selection during domestication and artificial selection. Additionally, a phylogenetic comparative analysis revealed that the genetic divergence between populations does not fully follow the geographical distribution and management history in the major histocompatibility complex region/major histocompatibility complex II haplotypes, unlike that of the genome-wide genotypes. Furthermore, the higher heterozygosity and haplotype alleles of MHC reduce the differences between populations. Briefly, this study not only helps promote the relative theoretical understanding of environmental adaptive selection and domestication but also provides a theoretical reference for disease-resistant breeding in pigs.

BoLA-DRB3 Polymorphism Associated with Bovine Leukemia Virus Infection and Proviral Load in Holstein Cattle in Egypt

Bovine leukemia virus (BLV) is the etiological agent of enzootic bovine leukosis, the most prevalent neoplastic disease of cattle worldwide. The immune response to BLV and disease susceptibility and resistance in cattle are strongly correlated with the bovine leukocyte antigen (BoLA)-DRB3 allelic polymorphism. BLV infection continues to spread in Egypt, in part because the relationships between BLV infection, proviral load in Egypt, and BoLA-DRB3 polymorphism are unknown. Here, we identified 18 previously reported alleles in 121 Holstein cows using a polymerase chain reaction sequence-based typing method. Furthermore, BoLA-DRB3 gene polymorphisms in these animals were investigated for their influence on viral infection. BoLA-DRB3*015:01 and BoLA-DRB3*010:01 were identified as susceptible and resistant alleles, respectively, for BLV infection in the tested Holsteins. In addition, BoLA-DRB3*012:01 was associated with low PVL in previous reports but high PVL in Holstein cattle in Egypt. This study is the first to demonstrate that the BoLA-DRB3 polymorphism confers resistance and susceptibility to PVL and infections of BLV in Holstein cattle in Egypt. Our results can be useful for the disease control and eradication of BLV through genetic selection.

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.

Influence of BoLA-DRB3 Polymorphism and Bovine Leukemia Virus (BLV) Infection on Dairy Cattle Productivity

Enzootic bovine leukosis caused by the bovine leukemia virus (BLV) results in substantial damage to the livestock industry; however, we lack an effective cure or vaccine. BoLA-DRB3 polymorphism in BLV-infected cattle is associated with the proviral load (PVL), infectivity in the blood, development of lymphoma, and in utero infection of calves. Additionally, it is related to the PVL, infectivity, and anti-BLV antibody levels in milk. However, the effects of the BoLA-DRB3 allele and BLV infection on dairy cattle productivity remain poorly understood. Therefore, we investigated the effect of BLV infection and BoLA-DRB3 allele polymorphism on dairy cattle productivity in 147 Holstein dams raised on Japanese dairy farms. Our findings suggested that BLV infection significantly increased milk yield. Furthermore, the BoLA-DRB3 allele alone, and the combined effect of BLV infection and the BoLA-DRB3 allele had no effect. These results indicate that on-farm breeding and selection of resistant cattle, or the preferential elimination of susceptible cattle, does not affect dairy cattle productivity. Additionally, BLV infection is more likely to affect dairy cattle productivity than BoLA-DRB3 polymorphism.

Maternal and direct genetic parameters for tail length, tail lesions, and growth traits in pigs

Tail length and tail lesions are the major triggers for tail biting in pigs. Against this background, 2 datasets were analyzed to estimate genetic parameters for tail characteristics and growth traits. Dataset 1 considered measurements for trait tail length (T-LEN) and for the growth traits birth weight (BW), weaning weight (WW), postweaning weight (PWW), and average daily gain (ADG) from 9,348 piglets. Piglets were born in the period from 2015 to 2018 and kept on the university Gießen research station. Dataset 2 included 4,943 binary observations from 1,648 pigs from the birth years 2016 to 2019 for tail lesions (T-LES) as indicators for nail necrosis, tail abnormalities, or tail biting. T-LES were recorded at 30 ± 7 d after entry for rearing (T-Les-1), at 50 ± 7 d after entry for rearing (end of the rearing period, T-LES-2), and 130 ± 20 d after entry for rearing (end of fattening period, T-LES-3). Genetic statistical model evaluation for dataset 1 based on Akaike's information criterion and likelihood ration tests suggested multiple-trait animal models considering covariances between direct and maternal genetic effects. The direct heritability for T-LEN was 0.42 (±0.03), indicating the potential for genetic selection on short tails. The maternal genetic heritability for T-LEN was 0.05 (±0.04), indicating the influence of uterine characteristics on morphological traits. The negative correlation between direct and maternal effects for T-LEN of -0.35 (±0.13), as well as the antagonistic relationships (i.e., positive direct genetic correlations in the range from 0.03 to 0.40) between T-LEN with the growth traits BW, WW, PWW, and ADG, complicate selection strategies and breeding goal definitions. The correlations between direct effects for T-LEN and maternal effects for breeding goal traits, and vice versa, were positive but associated with a quite large SE. The heritability for T-LES when considering the 3 repeated measurements was 0.23 (±0.04) from the linear (repeatability of 0.30) and 0.21 (±0.06; repeatability of 0.29) from the threshold model. The breeding value correlations between T-LES-3 with breeding values from the repeatability models were quite large (0.74 to 0.90), suggesting trait lesion recording at the end of the rearing period. To understand all genetic mechanisms in detail, ongoing studies are focusing on association analyses between T-LEN and T-LES, and the identification of tail biting from an actor's perspective.

Sequence diversity of major histo-compatibility complex class II DQA1 in Indian Tharparkar cattle: novel alleles and in-silico analysis

Exon 2 of MHC class II gene codes for the first domain of the molecule that forms the peptide-binding groove and its polymorphism partly explains functional MHC diversity. A 850 bp DQA1 gene fragment spanning from intron I to exon III was typed by sequencing of 40 Tharparkar cattle of various agro-climatic zones of northern India along with 10 Tharparkar crossbreds. On analysis of nucleotide sequences, a total of 30 polymorphic sites (1 insertion and 29 SNPs) were identified in 14 MHC alleles leading to amino acid changes in 5 places in 249 bp (exon 2). Five new BoLa DQA1 alleles were identified and reported. The within group mean distance was highest in Tharparkar herd of Bikaner (0.045) and lowest (0.020) in that of Surathgarh (breeding tract) whereas, between groups mean distance was highest in Bikaner Tharparkar-Suratgarh Tharparkar pair. There was excess of nonsynonymous over synonymous nucleotide substitutions in the present study. The effects of these substitutions were predicted using I-Mutant and Panther online resources. The mean ratio of dN/dS was found to be >1.0 at 12 codons with two mutation hotspots at 13th codon (P = 0.002) and 64th codon (P = 0.01). The phylo-geographic analysis revealed that alleles 5, 7 and 13 formed a different cluster with alleles 7 and 13 grouped by the most frequent allele (BoLa-DQA*1401).

Identification of a T-Cell Epitope That Is Globally Conserved among Outer Membrane Proteins (OMPs) OMP7, OMP8, and OMP9 of Anaplasma marginale Strains and with OMP7 from the A. marginale subsp. centrale Vaccine Strain

Within the protective outer membrane (OM) fraction of Anaplasma marginale, several vaccine candidates have emerged, including a family of OM proteins (OMPs) 7 to 9, which share sequence identity with each other and with the single protein OMP7 in the vaccine strain A. marginale subsp. centrale. A. marginale OMPs 7 to 9 are logical vaccine candidates because they are surface exposed, present in the OM immunogen and protective cross-linked OM proteins, recognized by immune serum IgG2 and T cells in cattle immunized with OM, and recognized by immune serum IgG2 from cattle immunized with the A. centrale vaccine strain. We report the identification of a globally conserved 9-amino-acid T-cell epitope FLLVDDAI/VV shared between A. centrale vaccine strain OMP7 and the related A. marginale OMPs 7 to 9, where position 8 of the peptide can be isoleucine or valine. The epitope is conserved in American A. marginale strains, in the Australia Gypsy Plains strain, and in multiple field isolates from Ghana. This epitope, together with additional T-cell epitopes that are present within these proteins, should be considered for inclusion in a multivalent vaccine for A. marginale that can provide protection against disease caused by globally distributed bacterial strains.

Association of BoLA-DRB3.2 Alleles with BLV Infection Profiles (Persistent Lymphocytosis/Lymphosarcoma) and Lymphocyte Subsets in Iranian Holstein Cattle

Major histocompatibility complex (MHC) is the best-characterized genetic region associated with resistance and susceptibility to a wide range of diseases. In cattle, the most important example of the relationship between the MHC and infectious diseases has been established by the resistance to Bovine leukemia virus (BLV) infection. The association of the bovine MHC class II BoLA-DRB3.2 alleles with BLV infection profiles was examined. BoLA-DRB3.2 allelic diversity was determined in 190 Iranian Holstein cattle using direct sequencing method. Association of the DRB3.2 alleles with BLV infection profiles was found as the odds ratio. Effects of the alleles on lymphocyte subsets were also evaluated by multivariate regression analysis and GLM procedures. The studied cattle were categorized into three groups: BLV seronegative, BLV seropositive with persistent lymphocytosis (PL), and BLV seropositive with lymphosarcoma (LS). The PL profile was significantly associated with the BoLA-DRB3.2*0101, *1101 and *4201 alleles, although the *3202 allele mediating resistance to PL was observed. Significant association was found between the BoLA-DRB3.2*1802, *3202, and *0901 alleles and susceptibility to LS, while the *0101 and *1101 alleles were associated with resistance to LS. BoLA-DRB3.2 alleles also showed a significant correlation with CD4, CD8, CD21 cells and CD4/CD8 ratio. Allelic differences influence the immune response to BLV infection and developing the disease profile. These differences also have important consequences for tumor resistance.

Alternative strategies for genetic analyses of milk flow in dairy cattle

Measurements for average milk flow (AMF) in kilograms of milk per minute of milking time from 629,161 Holstein cows from calving years 1990 to 2008 were used to estimate genetic covariance components using a variety of statistical models. For bivariate linear-threshold model applications, Gaussian-distributed AMF (linear sire model) was categorized into 2 distinct classes (threshold sire model) by setting arbitrary thresholds for extremely slow or extremely fast milking cows. In different bivariate runs with the 2 traits, Gaussian AMF and binary AMF, within a Bayesian framework, thresholds for the binary trait were 1.2, 1.6, 2.6, and 2.8 kg/min. Posterior heritabilities for AMF from the linear and the threshold models in all runs were in a narrow range and close to 0.26, and the posterior genetic correlation between AMF, defined as either a Gaussian or binary trait, was 0.99. A data subset was used to infer genetic and phenotypic relationships between AMF with test-day traits milk yield, fat percentage, protein percentage, somatic cell score (SCS), fat-to-protein ratio, and energy-corrected milk using recursive linear sire models, standard multiple trait linear sire models, and multiple trait linear sire models accounting for the effect of a trait 1 on a trait 2, and of trait 2 on trait 3, via linear regressions. The time-lagged 3-trait system focused on the first test-day trait after calving (trait 1), on AMF (trait 2), and on the test-day trait (trait 3) after the AMF measurement. Posterior means for heritabilities for AMF from linear and recursive linear models used for the reduced data set ranged between 0.29 and 0.38, and were slightly higher than heritabilities from the threshold models applied to the full data set. Genetic correlations from the recursive linear model and the linear model were similar for identical trait combinations including AMF and test-day traits 1 and 3. The largest difference was found for the genetic correlation between AMF and fat percentage from the first test day (i.e., -0.31 from the recursive linear model vs. -0.26 from the linear model). Genetic correlations from the linear model, including an additional regression coefficient, partly differed, especially when comparing correlations between AMF and SCS and between AMF and fat-to-protein ratio recorded after the AMF measurement data. Structural equation coefficients from the recursive linear model and corresponding regression coefficients from the linear model with additional regression, both depicting associations on the phenotypic scale, were quite similar. From a physiological perspective, all models confirmed the antagonistic relationship between SCS with AMF on genetic and phenotypic scales. A pronounced recursive relationship was also noted between productivity (milk yield and energy-corrected milk) and AMF, suggesting further research using physiological parameters as indicators for cow stress response (e.g., level of hormones) should be conducted.

Bovine mastitis: frontiers in immunogenetics

Mastitis is one of the most prevalent and costly diseases in the dairy industry with losses attributable to reduced milk production, discarded milk, early culling, veterinary services, and labor costs. Typically, mastitis is an inflammation of the mammary gland most often, but not limited to, bacterial infection, and is characterized by the movement of leukocytes and serum proteins from the blood to the site of infection. It contributes to compromised milk quality and the potential spread of antimicrobial resistance if antibiotic treatment is not astutely applied. Despite the implementation of management practises and genetic selection approaches, bovine mastitis control continues to be inadequate. However, some novel genetic strategies have recently been demonstrated to reduce mastitis incidence by taking advantage of a cow's natural ability to make appropriate immune responses against invading pathogens. Specifically, dairy cattle with enhanced and balanced immune responses have a lower occurrence of disease, including mastitis, and they can be identified and selected for using the high immune response (HIR) technology. Enhanced immune responsiveness is also associated with improved response to vaccination, increased milk, and colostrum quality. Since immunity is an important fitness trait, beneficial associations with longevity and reproduction are also often noted. This review highlights the genetic regulation of the bovine immune system and its vital contributions to disease resistance. Genetic selection approaches currently used in the dairy industry to reduce the incidence of disease are reviewed, including the HIR technology, genomics to improve disease resistance or immune response, as well as the Immunity(+)™ sire line. Improving the overall immune responsiveness of cattle is expected to provide superior disease resistance, increasing animal welfare and food quality while maintaining favorable production levels to feed a growing population.

Breadth of the CD4+ T cell response to Anaplasma marginale VirB9-1, VirB9-2 and VirB10 and MHC class II DR and DQ restriction elements

MHC class II molecules influence antigen-specific CD4+ T lymphocyte responses primed by immunization and infection. CD4+ T cell responses are important for controlling infection by many bacterial pathogens including Anaplasma marginale and are observed in cattle immunized with the protective A. marginale outer membrane (OM) vaccine. Immunogenic proteins that comprise the protective OM vaccine include type IV secretion system (T4SS) proteins VirB9-1, VirB9-2 and VirB10, candidates for inclusion in a multiepitope vaccine. Our goal was to determine the breadth of the VirB9-1, VirB9-2 and VirB10 T cell response and MHC class II restriction elements in six cattle with different MHC class II haplotypes defined by DRB3, DQA and DQB allele combinations for each animal. Overlapping peptides spanning each T4SS protein were tested in T cell proliferation assays with autologous antigen-presenting cells (APC) and artificial APC expressing combinations of bovine DR and DQ molecules. Twenty immunostimulatory peptides were identified; three representing two or more epitopes in VirB9-1, ten representing eight or more epitopes in VirB9-2 and seven representing seven or more epitopes in VirB10. Of the eight DRA/DRB3 molecules, four presented 15 peptides, which was biased as DRA/DRB3*1201 presented ten and DRA/DRB3*1101 presented four peptides. Four DQA/DQB molecules composed of two intrahaplotype and two interhaplotype pairs presented seven peptides, of which five were uniquely presented by DQ molecules. In addition, three functional mixed isotype (DQA/DRB3) restriction elements were identified. The immunogenicity and broad MHC class II presentation of multiple VirB9-1, VirB9-2 and VirB10 peptide epitopes justify their testing as a multiepitope vaccine against A. marginale.

The major histocompatibility complex in bovines: a review

Productivity in dairy cattle and buffaloes depends on the genetic factors governing the production of milk and milk constituents as well as genetic factors controlling disease resistance or susceptibility. The immune system is the adaptive defense system that has evolved in vertebrates to protect them from invading pathogens and also carcinomas. It is remarkable in the sense that it is able to generate an enormous variety of cells and biomolecules which interact with each other in numerous ways to form a complex network that helps to recognize, counteract, and eliminate the apparently limitless number of foreign invading pathogens/molecules. The major histocompatibility complex which is found to occur in all mammalian species plays a central role in the development of the immune system. It is an important candidate gene involved in susceptibility/resistance to various diseases. It is associated with intercellular recognition and with self/nonself discrimination. It plays major role in determining whether transplanted tissue will be accepted as self or rejected as foreign.

Polymorphism of exon 2 of BoLA-DRB3 gene and its relationship with somatic cell score in Beijing Holstein cows

In the present study, the exon 2 and 3' end sequence of intron 1 of BoLA-DRB3 gene of 211 Beijing Holstein cows was amplified and a uniform fragment of 284 bp was obtained. The genetic polymorphism was investigated by PCR-RFLP using two restriction endonucleases HaeIII and BstYI. Seven genotypes were detected by digesting the PCR products with HaeIII. The frequency of AA, AB, AC, AD, BB, BC and BF genotypes was 0.4638, 0.0193, 0.0193, 0.3478, 0.0290, 0.0386 and 0.0822, respectively. Three genotypes were found by digesting the PCR products with BstYI. The frequency of AA, AB and BB genotypes was 0.0569, 0.2844 and 0.6587, respectively. The relationship between the polymorphisms in exon 2 of BoLA-DRB3 gene and somatic cell score (SCS) in Beijing Holstein cows was analyzed by least squares linear model. No significant difference was detected among least squares means of SCS for seven HaeIII-RFLP genotypes (P > 0.05). As for BstYI-RFLP analysis, least squares mean of SCS for AA was significantly lower than that for AB (P < 0.05) or BB (P < 0.05), and no significant difference was detected between AB and BB genotypes (P > 0.05). BstYI AA was the most favorable genotype and BstYI BB was the most unfavorable genotype for mastitis resistance. The information found in the present study is very important for improving mastitis resistance in dairy cattle by marker assisted selection.