Genome-wide association studies for heat stress response in Bos taurus × Bos indicus crossbred cattle

Genetic factors influencing milk and fat yields in tropically adapted dairy cattle: insights from quantitative trait loci analysis and gene associations

OBJECTIVE

The objective of this study was to identify genes associated with 305-day milk yield (MY) and fat yield (FY) that also influence the adaptability of the Thai multibreed dairy cattle population to tropical conditions.

METHODS

A total of 75,776 imputed and actual single nucleotide polymorphisms (SNPs) from 2,661 animals were used to identify genomic regions associated with MY and FY using the single-step genomic best linear unbiased predictions. Fixed effects included herd-yearseason, breed regression, heterosis regression and calving age regression effects. Random effects were animal additive genetic and residual. Individual SNPs with a p-value smaller than 0.05 were selected for gene mapping, function analysis, and quantitative trait loci (QTL) annotation analysis.

RESULTS

A substantial number of QTLs associated with MY (9,334) and FY (8,977) were identified by integrating SNP genotypes and QTL annotations. Notably, we discovered 17 annotated QTLs within the health and exterior QTL classes, corresponding to nine unique genes. Among these genes, Rho GTPase activating protein 15 (ARHGAP15) and catenin alpha 2 (CTNNA2) have previously been linked to physiological traits associated with tropical adaptation in various cattle breeds. Interestingly, these two genes also showed signs of positive selection, indicating their potential role in conferring tolerance to trypanosomiasis, a prevalent tropical disease.

CONCLUSION

Our findings provide valuable insights into the genetic basis of MY and FY in the Thai multibreed dairy cattle population, shedding light on the underlying mechanisms of tropical adaptation. The identified genes represent promising targets for future breeding strategies aimed at improving milk and fat production while ensuring resilience to tropical challenges. This study significantly contributes to our understanding of the genetic factors influencing milk production and adaptability in dairy cattle, facilitating the development of sustainable genetic selection strategies and breeding programs in tropical environments.

Skin transcriptome analysis in Brangus cattle under heat stress

Heat stress is a major factor that negatively affects animal welfare and production systems. Livestock should adapt to tropical and subtropical areas and to meet this, composite breeds have been developed. This work aimed to evaluate gene expression profiles in the skin of Brangus cattle under heat stress using a case-control design, and to correlate this with skin histological characteristics. Two groups of bulls were set using rectal temperature as a criterion to define stress conditions: stressed (N = 5) and non-stressed (N = 5) groups. Skin transcriptomics was performed and correlations between breed composition, phenotypic and skin histological traits were evaluated. Results showed 4309 differentially expressed genes (P < 0.01), 2113 downregulated and 2196 upregulated. Enrichment and ontology analyses revealed 132 GO terms and 67 pathways (P < 0.01), including thermogenesis, glycolysis, gluconeogenesis, mitochondrial activity, antioxidant and immune response, and apoptosis. The identity of the terms and pathways indicated the diversity of mechanisms directed to relieve the animals' suffering, acting from simple passive mechanisms (conduction, convection and radiation) to more complex active ones (behavioural changes, evaporation, vasodilation and wheezing). Furthermore, significant differences between phenotypic and skin histological traits and correlations between pairs of traits suggested a direction towards heat dissipation processes. In this sense, number of vessels was positively correlated with number of sweat glands (P < 0.001) and both were positively correlated with zebuine genetic content (P < 0.05 and P < 0.01, respectively), gland size was positively correlated with epidermal thickness and negatively with hair length (P < 0.05), and epidermal thickness was negatively correlated with gland-epidermis distance (P < 0.0005). These results support the notion that response to heat stress is physiologically complex, producing significant changes in the expression of genes involved in several biological pathways, while the animal's ability to face it depends greatly on their skin features.

Genetic diversity of SNPs associated with candidate genes for heat stress in Coreño Creole cattle in Mexico

Mexican Coreño Creole cattle are an important genetic resource adapted to local environmental conditions, so the study of their genetic diversity is essential to know their status and implement conservation programs and their use for crossbreeding. This study evaluated the genetic diversity of heat stress tolerance characteristics of Coreño Creole cattle, and a gene ontology enrichment was performed to know the biological processes in which candidate genes are involved. A total of 48 samples from three localities of Nayarit were genotyped using 777 K Illumina BovineHD BeadChip and 34 single nucleotide polymorphisms associated with candidate genes were selected. Genetic diversity was analyzed using allelic frequencies, expected heterozygosity (He), and Wright's fixation index (FST) using PLINK v1.9 software. Candidate genes were uploaded to the open-source GOnet for pathway analysis and linkage to biological processes. Coreño Creole cattle showed low genetic diversity (He = 0.35), the average FST obtained was 0.044, and only eight markers had allele frequencies higher than 0.80 in the three locations. We found that the genes GOT1 and NCAD are related in the biological processes of stress response, cell differentiation, and homeostatic process. The results revealed that Coreño Creole cattle have low genetic diversity; this could be due to the isolation of these populations.

Heat stress adaptation in cows - Physiological responses and underlying molecular mechanisms

Heat stress is a key abiotic stressor for dairy production in the tropics which is further compounded by the ongoing climate change. Heat stress not only adversely impacts the production and welfare of dairy cows but severely impacts the economics of dairying due to production losses and increased cost of rearing. Over the years, selection has ensured development of high producing breeds, however, the thermotolerance ability of animals has been largely overlooked. In the past decade, the ill effects of climate change have made it pertinent to rethink the selection strategies to opt for climate resilient breeds, to ensure optimum production and reproduction. This has led to renewed interest in evaluation of the impacts of heat stress on cows and the underlying mechanisms that results in their acclimatization and adaptation to varied thermal ambience. The understanding of heat stress and associated responses at various level of animal is crucial to device amelioration strategies to secure optimum production and welfare of cows. With this review, an effort has been made to provide an overview on temperature humidity index as an important indicator of heat stress, general effect of heat stress in dairy cows, and impact of heat stress and subsequent response at physiological, haematological, molecular and genetic level of dairy cows.

Candidate genes associated with heat stress and breeding strategies to relieve its effects in dairy cattle: a deeper insight into the genetic architecture and immune response to heat stress

The need for food products of animal origin is increasing worldwide. Satisfying these needs in a way that has minimal impact on the environment requires cutting-edge technologies and techniques to enhance the genetic quality of cattle. Heat stress (HS), in particular, is affecting dairy cattle with increasing frequency and severity. As future climatic challenges become more evident, identifying dairy cows that are more tolerant to HS will be important for breeding dairy herds that are better adapted to future environmental conditions and for supporting the sustainability of dairy farming. While research into the genetics of HS in the context of the effect of global warming on dairy cattle is gaining momentum, the specific genomic regions involved in heat tolerance are still not well documented. Advances in omics information, QTL mapping, transcriptome profiling and genome-wide association studies (GWAS) have identified genomic regions and variants associated with tolerance to HS. Such studies could provide deeper insights into the genetic basis for response to HS and make an important contribution to future breeding for heat tolerance, which will help to offset the adverse effects of HS in dairy cattle. Overall, there is a great interest in identifying candidate genes and the proportion of genetic variation associated with heat tolerance in dairy cattle, and this area of research is currently very active worldwide. This review provides comprehensive information pertaining to some of the notable recent studies on the genetic architecture of HS in dairy cattle, with particular emphasis on the identified candidate genes associated with heat tolerance in dairy cattle. Since effective breeding programs require optimal knowledge of the impaired immunity and associated health complications caused by HS, the underlying mechanisms by which HS modulates the immune response and renders animals susceptible to various health disorders are explained. In addition, future breeding strategies to relieve HS in dairy cattle and improve their welfare while maintaining milk production are discussed.

Heat stress effects on milk yield traits and metabolites and mitigation strategies for dairy cattle breeds reared in tropical and sub-tropical countries

Heat stress is an important problem for dairy industry in many parts of the world owing to its adverse effects on productivity and profitability. Heat stress in dairy cattle is caused by an increase in core body temperature, which affects the fat production in the mammary gland. It reduces milk yield, dry matter intake, and alters the milk composition, such as fat, protein, lactose, and solids-not-fats percentages among others. Understanding the biological mechanisms of climatic adaptation, identifying and exploring signatures of selection, genomic diversity and identification of candidate genes for heat tolerance within indicine and taurine dairy breeds is an important progression toward breeding better dairy cattle adapted to changing climatic conditions of the tropics. Identifying breeds that are heat tolerant and their use in genetic improvement programs is crucial for improving dairy cattle productivity and profitability in the tropics. Genetic improvement for heat tolerance requires availability of genetic parameters, but these genetic parameters are currently missing in many tropical countries. In this article, we reviewed the HS effects on dairy cattle with regard to (1) physiological parameters; (2) milk yield and composition traits; and (3) milk and blood metabolites for dairy cattle reared in tropical countries. In addition, mitigation strategies such as physical modification of environment, nutritional, and genetic development of heat tolerant dairy cattle to prevent the adverse effects of HS on dairy cattle are discussed. In tropical climates, a more and cost-effective strategy to overcome HS effects is to genetically select more adaptable and heat tolerant breeds, use of crossbred animals for milk production, i.e., crosses between indicine breeds such as Gir, white fulani, N'Dama, Sahiwal or Boran to taurine breeds such as Holstein-Friesian, Jersey or Brown Swiss. The results of this review will contribute to policy formulations with regard to strategies for mitigating the effects of HS on dairy cattle in tropical countries.

Heat Stress: A Serious Disruptor of the Reproductive Physiology of Dairy Cows

Global warming is a significant threat to the sustainability and profitability of the dairy sector, not only in tropical or subtropical regions but also in temperate zones where extreme summer temperatures have become a new and challenging reality. Prolonged exposure of dairy cows to high temperatures compromises animal welfare, increases morbidity, and suppresses fertility, resulting in devastating economic losses for farmers. To counteract the deleterious effects of heat stress, cattl e employ various adaptive thermoregulatory mechanisms including molecular, endocrine, physiological, and behavioral responses. These adaptations involve the immediate secretion of heat shock proteins and cortisol, followed by a complex network of disrupted secretion of metabolic and reproductive hormones such as prolactin, ghrelin, ovarian steroid, and pituitary gonadotrophins. While the strategic heat stress mitigation measures can restore milk production through modifications of the microclimate and nutritional interventions, the summer fertility records remain at low levels compared to those of the thermoneutral periods of the year. This is because sustainment of high fertility is a multifaceted process that requires appropriate energy balance, undisrupted mode of various hormones secretion to sustain the maturation and fertilizing competence of the oocyte, the normal development of the early embryo and unhampered maternal-embryo crosstalk. In this review, we summarize the major molecular and endocrine responses to elevated temperatures in dairy cows, as well as the impacts on maturing oocytes and early embryos, and discuss the consequences that heat stress brings about in dairy cattle fertility.

Invited review: From heat stress to disease-Immune response and candidate genes involved in cattle thermotolerance

Heat stress implies unfavorable effects on primary and functional traits in dairy cattle and, in consequence, on the profitability of the whole production system. The increasing number of days with extreme hot temperatures suggests that it is imperative to detect the heat stress status of animals based on adequate measures. However, confirming the heat stress status of an individual is still challenging, and, in consequence, the identification of novel heat stress biomarkers, including molecular biomarkers, remains a very relevant issue. Currently, it is known that heat stress seems to have unfavorable effects on immune system mechanisms, but this information is of limited use in the context of heat stress phenotyping. In addition, there is a lack of knowledge addressing the molecular mechanisms linking the relevant genes to the observed phenotype. In this review, we explored the potential molecular mechanisms explaining how heat stress affects the immune system and, therefore, increases the occurrence of immune-related diseases in cattle. In this regard, 2 relatively opposite hypotheses are under focus: the immunosuppressive action of cortisol, and the proinflammatory effect of heat stress. In both hypotheses, the modulation of the immune response during heat stress is highlighted. Moreover, it is possible to link candidate genes to these potential mechanisms. In this context, immune markers are very valuable indicators for the detection of heat stress in dairy cattle, broadening the portfolio of potential biomarkers for heat stress.

Genetic Markers Associated with Milk Production and Thermotolerance in Holstein Dairy Cows Managed in a Heat-Stressed Environment

Dairy production in Holstein cows in a semiarid environment is challenging due to heat stress. Under such conditions, genetic selection for heat tolerance appears to be a useful strategy. The objective was to validate molecular markers associated with milk production and thermotolerance traits in Holstein cows managed in a hot and humid environment. Lactating cows (n = 300) exposed to a heat stress environment were genotyped using a medium-density array including 53,218 SNPs. A genome-wide association study (GWAS) detected six SNPs associated with total milk yield (MY305) that surpassed multiple testing (p < 1.14 × 10^-6). These SNPs were further validated in 216 Holstein cows from two independent populations that were genotyped using the TaqMan bi-allelic discrimination method and qPCR. In these cows, only the SNPs rs8193046, rs43410971, and rs382039214, within the genes TLR4, GRM8, and SMAD3, respectively, were associated (p < 0.05) with MY305, rectal temperature (RT), and respiratory rate. Interestingly, these variables improved as the number of favorable genotypes of the SNPs increased from 0 to 3. In addition, a regression analysis detected RT as a significant predictor (R² = 0.362) for MY305 in cows with >1 favorable genotype, suggesting this close relationship was influenced by genetic markers. In conclusion, SNPs in the genes TLR4, GRM8, and SMAD3 appear to be involved in the molecular mechanism that regulates milk production in cows under heat-stressed conditions. These SNPs are proposed as thermotolerance genetic markers for a selection program to improve the milk performance of lactating Holstein cows managed in a semiarid environment.

Runs of homozygosity and signatures of selection for number of oocytes and embryos in the Gir Indicine cattle

Runs of homozygosity (ROH) and signatures of selection are the results of selection processes in livestock species that have been shown to affect several traits in cattle. The aim of the current work was to verify the profile of ROH and inbreeding depression in the number of total (TO) and viable oocytes (VO) and the number of embryos (EMBR) in Gir Indicine cattle. In addition, we aim to identify signatures of selection, genes, and enriched regions between Gir subpopulations sorted by breeding value for these traits. The genotype file contained 2093 animals and 420,718 SNP markers. Breeding values used to sort Gir animals were previously obtained. ROH and signature of selection analyses were performed using PLINK software, followed by ROH-based (F_ROH) and pedigree-based inbreeding (F_ped) and a search for genes and their functions. An average of 50 ± 8.59 ROHs were found per animal. ROHs were separated into classes according to size, ranging from 1 to 2 Mb (ROH_1-2Mb: 58.17%), representing ancient inbreeding, ROH_2-4Mb (22.74%), ROH_4-8Mb (11.34%), ROH_8-16Mb (5.51%), and ROH_>16Mb (2.24%). Combining our results, we conclude that the increase in general F_ROH and F_ped significantly decreases TO and VO; however, in different chromosomes traits can increase or decrease with F_ROH. In the analysis for signatures of selection, we identified 15 genes from 47 significant genomic regions, indicating differences in populations with high and low breeding value for the three traits.

Detection of genomic regions that differentiate Bos indicus from Bos taurus ancestral breeds for milk yield in Indian crossbred cows

Introduction: In India, crossbred cows incorporate the high production of B. taurus dairy breeds and the environmental adaptation of local B. indicus cattle. Adaptation to different environments and selection in milk production have shaped the genetic differences between B. indicus and B. taurus cattle. The aim of this paper was to detect, for milk yield of crossbred cows, quantitative trait loci (QTL) that differentiate B. indicus from B. taurus ancestry, as well as QTL that are segregating within the ancestral breeds. Methods: A total of 123,042 test-day milk records for 4,968 crossbred cows, genotyped with real and imputed 770 K SNP, were used. Breed origins were assigned to haplotypes of crossbred cows, and from that, were assigned to SNP alleles. Results: At a false discovery rate (FDR) of 30%, a large number of genomic regions showed significant effects of B. indicus versus B. taurus origin on milk yield, with positive effects coming from both ancestors. No significant regions were detected for Holstein Friesian (HF) versus Jersey effects on milk yield. Additionally, no regions for SNP alleles segregating within indigenous, within HF, and within Jersey were detected. The most significant effects, at FDR 5%, were found in a region on BTA5 (43.98-49.44 Mbp) that differentiates B. indicus from B. taurus, with an estimated difference between homozygotes of approximately 10% of average yield, in favour of B. indicus origin. Discussion: Our results indicate that evolutionary differences between B. indicus and B. taurus cattle for milk yield, as expressed in crossbred cows, occur at many causative loci across the genome. Although subject to the usual first estimation bias, some of the loci appear to have large effects that might make them useful for genomic selection in crossbreds, if confirmed in subsequent studies.

Improving Genomic Selection for Heat Tolerance in Dairy Cattle: Current Opportunities and Future Directions

Heat tolerance is the ability of an animal to maintain production and reproduction levels under hot and humid conditions and is now a trait of economic relevance in dairy systems worldwide because of an escalating warming climate. The Australian dairy population is one of the excellent study models for enhancing our understanding of the biology of heat tolerance because they are predominantly kept outdoors on pastures where they experience direct effects of weather elements (e.g., solar radiation). In this article, we focus on evidence from recent studies in Australia that leveraged large a dataset [∼40,000 animals with phenotypes and 15 million whole-genome sequence variants] to elucidate the genetic basis of thermal stress as a critical part of the strategy to breed cattle adapted to warmer environments. Genotype-by-environment interaction (i.e., G × E) due to temperature and humidity variation is increasing, meaning animals are becoming less adapted (i.e., more sensitive) to changing environments. There are opportunities to reverse this trend and accelerate adaptation to warming climate by 1) selecting robust or heat-resilient animals and 2) including resilience indicators in breeding goals. Candidate causal variants related to the nervous system and metabolic functions are relevant for heat tolerance and, therefore, key for improving this trait. This could include adding these variants in the custom SNP panels used for routine genomic evaluations or as the basis to design specific agonist or antagonist compounds for lowering core body temperature under heat stress conditions. Indeed, it was encouraging to see that adding prioritized functionally relevant variants into the 50k SNP panel (i.e., the industry panel used for genomic evaluation in Australia) increased the prediction accuracy of heat tolerance by up to 10% units. This gain in accuracy is critical because genetic improvement has a linear relationship with prediction accuracy. Overall, while this article used data mainly from Australia, this could benefit other countries that aim to develop breeding values for heat tolerance, considering that the warming climate is becoming a topical issue worldwide.

Genome-wide associations for heat stress response suggest potential candidate genes underlying milk fatty acid composition in dairy cattle

Contents of milk fatty acids (FA) display remarkable alterations along climatic gradients. Detecting candidate genes underlying such alterations might be beneficial for the exploration of climate sensitivity in dairy cattle. Consequently, we aimed on the definition of FA heat stress indicators, considering FA breeding values in response to temperature-humidity index (THI) alterations. Indicators were used in GWAS, in ongoing gene annotations and for the estimation of chromosome-wide variance components. The phenotypic data set consisted of 39,600 test-day milk FA records from 5,757 first-lactation Holstein dairy cows kept in 16 large-scale German cooperator herds. The FA traits were C18:0, polyunsaturated fatty acids (PUFA), saturated fatty acids (SFA), and unsaturated fatty acids (UFA). After genotype quality control, 40,523 SNP markers from 3,266 cows and 930 sires were considered. Meteorological data from the weather station in closest herd distance were used for the calculation of maximum hourly daily THI, which were allocated to 10 different THI classes. The same FA from 3 stages of lactation were considered as different, but genetically correlated traits. Consequently, a 3-trait reaction norm model was used to estimate genetic parameters and breeding values for FA along THI classes, considering either pedigree (A) or genomic (G) relationship matrices. De-regressed proofs and genomic estimated breeding values at the intermediate THI class 5 and at the extreme THI class 10 were used as pseudophenotypes in ongoing genomic analyses for thermoneutral (TNC) and heat stress conditions (HSC), respectively. The differences in de-regressed proofs and in genomic estimated breeding values from both THI classes were pseudophenotypes for heat stress response (HSR). Genetic correlations between the same FA under TNC and HSC were smallest in the first lactation stage and ranged from 0.20 for PUFA to 0.87 for SFA when modeling with the A matrix, and from 0.35 for UFA to 0.86 for SFA when modeling with the G matrix. In the first lactation stage, larger additive genetic variances under HSC compared with TNC indicate climate sensitivity for C18:0, PUFA, and UFA. Climate sensitivity was also reflected by pronounced chromosome-wide genetic variances for HSR of PUFA and UFA in the first stage of lactation. For all FA under TNC, HSC, and HSR, quite large genetic variance proportions were explained by BTA14. In GWAS, 30 SNP (within or close to 38 potential candidate genes) overlapped for HSR of the different FA. One unique potential candidate gene (AMFR) was detected for HSR of PUFA, 15 for HSR of SFA (ADGRB1, DENND3, DUSP16, EFR3A, EMP1, ENSBTAG00000003838, EPS8, MGP, PIK3C2G, STYK1, TMEM71, GSG1, SMARCE1, CCDC57, and FASN) and 3 for HSR of UFA (ENSBTAG00000048091, PAEP, and EPPK1). The identified unique genes play key roles in milk FA synthesis and are associated with disease resistance in dairy cattle. The results suggest consideration of FA in combination with climatic responses when inferring genetic mechanisms of heat stress in dairy cows.

The Genetics of Thermoregulation in Pigs: A Review

Heat stress (HS) affects pig performance, health and welfare, resulting in a financial burden to the pig industry. Pigs have a limited number of functional sweat glands and their thermoregulatory mechanisms used to maintain body temperature, are challenged by HS to maintain body temperature. The genetic selection of genotypes tolerant to HS is a promising long-term (adaptation) option that could be combined with other measures at the production system level. This review summarizes the current knowledge on the genetics of thermoregulation in pigs. It also discusses the different phenotypes that can be used in genetic studies, as well as the variability in thermoregulation between pig breeds and the inheritance of traits related to thermoregulation. This review also considers on-going challenges to face for improving heat tolerance in pigs.

Genome-wide association study of a thermo-tolerance indicator in pregnant ewes exposed to an artificial heat-stressed environment

Environmental heat stress negatively influences sheep production in warm semi-arid regions. An animal's ability to tolerate warm weather is difficult to measure naturally due to environmental variability and genetic variation between animals. In this study we developed a thermo-tolerance indicator (TTI) to define heat stress tolerance in pregnant sheep in a controlled environment. Next, we performed a genome-wide association study (GWAS) to identify genomic regions and target genes associated with thermo-tolerance in sheep. Pregnant Columbia-Rambouillet crossbred ewes (n = 127) were heat-stressed inside a climate-controlled chamber for 57 days by increasing the temperature-humidity index to ≥30. Rectal temperature (RT) and feed intake (FI) data were collected daily and used for the predictive TTI analysis. After the tenth day of heat stress, the regression analyses revealed that FI was stable; however, when the ewe's RT exceeded 39.8 °C their FI was less than thermo-tolerant ewes. This average predicted temperature was used to classify each ewe as heat stress tolerant (≤39.8 °C) and non-heat stress tolerant (>39.8 °C). A GWAS analysis was performed and genomic regions were compared between heat stress tolerant and non-tolerant ewes. The single-marker genomic analysis detected 16 single nucleotide polymorphisms (SNP) associated with heat stress tolerance (P < 0.0001), whereas the multi-marker Bayesian analysis identified 8 overlapped 1-Mb chromosomal regions accounting for 11.39% of the genetic variation associated with tolerance to heat stress. Four intragenic SNP showed a remarkable contribution to thermo-tolerance, and these markers were within the genes FBXO11 (rs407804467), PHC3 (rs414179061), TSHR (rs418575898) and STAT1 (rs417581105). In conclusion, genomic regions harboring four intragenic SNP were associated with heat stress tolerance, and these candidate genes are proposed to influence heat tolerance in pregnant ewes subjected to an artificially induced warm climate. Moreover, these genetic markers could be suitable for use in further genetic selection programs in sheep managed in semi-arid regions.

Identification and in silico characterization of structural and functional impacts of genetic variants in milk protein genes in the Zebu breeds Guzerat and Gyr

Whole genome sequencing of bovine breeds has allowed identification of genetic variants in milk protein genes. However, functional repercussion of such variants at a molecular level has seldom been investigated. Here, the results of a multistep Bioinformatic analysis for functional characterization of recently identified genetic variants in Brazilian Gyr and Guzerat breeds is described, including predicted effects on the following: (i) evolutionary conserved nucleotide positions/regions; (ii) protein function, stability, and interactions; (iii) splicing, branching, and miRNA binding sites; (iv) promoters and transcription factor binding sites; and (v) collocation with QTL. Seventy-one genetic variants were identified in the caseins (CSN1S1, CSN2, CSN1S2, and CSN3), LALBA, LGB, and LTF genes. Eleven potentially regulatory variants and two missense mutations were identified. LALBA Ile60Val was predicted to affect protein stability and flexibility, by reducing the number the disulfide bonds established. LTF Thr546Asn is predicted to generate steric clashes, which could mildly affect iron coordination. In addition, LALBA Ile60Val and LTF Thr546Asn affect exonic splicing enhancers and silencers. Consequently, both mutations have the potential of affecting immune response at individual level, not only in the mammary gland. Although laborious, this multistep procedure for classifying variants allowed the identification of potentially functional variants for milk protein genes.

Identification of candidate genes on the basis of SNP by time-lagged heat stress interactions for milk production traits in German Holstein cattle

The aim of this study was to estimate genotype by time-lagged heat stress (HS) variance components as well as main and interaction SNP-marker effects for maternal HS during the last eight weeks of cow pregnancy, considering milk production traits recorded in the offspring generation. The HS indicator was the temperature humidity index (THI) for each week. A dummy variable with the code = 1 for the respective week for THI ≥ 60 indicated HS, otherwise, for no HS, the code = 0 was assigned. The dataset included test-day and lactation production traits from 14,188 genotyped first parity Holstein cows. After genotype quality control, 41,139 SNP markers remained for the genomic analyses. Genomic animal models without (model VC_nHS) and with in-utero HS effects (model VC_wHS) were applied to estimate variance components. Accordingly, for genome-wide associations, models GWA_nHS and GWA_wHS, respectively, were applied to estimate main and interaction SNP effects. Common genomic and residual variances for the same traits were very similar from models VC_nHS and VC_wHS. Genotype by HS interaction variances varied, depending on the week with in-utero HS. Among all traits, lactation milk yield with HS from week 5 displayed the largest proportion for interaction variances (0.07). For main effects from model GWA_wHS, 380 SNPs were suggestively associated with all production traits. For the SNP interaction effects from model GWA_wHS, we identified 31 suggestive SNPs, which were located in close distance to 62 potential candidate genes. The inferred candidate genes have various biological functions, including mechanisms of immune response, growth processes and disease resistance. Two biological processes excessively represented in the overrepresentation tests addressed lymphocyte and monocyte chemotaxis, ultimately affecting immune response. The modelling approach considering time-lagged genotype by HS interactions for production traits inferred physiological mechanisms being associated with health and immunity, enabling improvements in selection of robust animals.

New loci and neuronal pathways for resilience to heat stress in cattle

While understanding the genetic basis of heat tolerance is crucial in the context of global warming's effect on humans, livestock, and wildlife, the specific genetic variants and biological features that confer thermotolerance in animals are still not well characterized. We used dairy cows as a model to study heat tolerance because they are lactating, and therefore often prone to thermal stress. The data comprised almost 0.5 million milk records (milk, fat, and proteins) of 29,107 Australian Holsteins, each having around 15 million imputed sequence variants. Dairy animals often reduce their milk production when temperature and humidity rise; thus, the phenotypes used to measure an individual's heat tolerance were defined as the rate of milk production decline (slope traits) with a rising temperature-humidity index. With these slope traits, we performed a genome-wide association study (GWAS) using different approaches, including conditional analyses, to correct for the relationship between heat tolerance and level of milk production. The results revealed multiple novel loci for heat tolerance, including 61 potential functional variants at sites highly conserved across 100 vertebrate species. Moreover, it was interesting that specific candidate variants and genes are related to the neuronal system (ITPR1, ITPR2, and GRIA4) and neuroactive ligand-receptor interaction functions for heat tolerance (NPFFR2, CALCR, and GHR), providing a novel insight that can help to develop genetic and management approaches to combat heat stress.

Climate-Resilient Dairy Cattle Production: Applications of Genomic Tools and Statistical Models

The current changing climate trend poses a threat to the productive efficacy and welfare of livestock across the globe. This review is an attempt to synthesize information pertaining to the applications of various genomic tools and statistical models that are available to identify climate-resilient dairy cows. The different functional and economical traits which govern milk production play a significant role in determining the cost of milk production. Thus, identification of these traits may revolutionize the breeding programs to develop climate-resilient dairy cattle. Moreover, the genotype–environment interaction also influences the performance of dairy cattle especially during a challenging situation. The recent advancement in molecular biology has led to the development of a few biotechnological tools and statistical models like next-generation sequencing (NGS), microarray technology, whole transcriptome analysis, and genome-wide association studies (GWAS) which can be used to quantify the molecular mechanisms which govern the climate resilience capacity of dairy cows. Among these, the most preferred option for researchers around the globe was GWAS as this approach jointly takes into account all the genotype, phenotype, and pedigree information of farm animals. Furthermore, selection signatures can also help to demarcate functionally important regions in the genome which can be used to detect potential loci and candidate genes that have undergone positive selection in complex milk production traits of dairy cattle. These identified biomarkers can be incorporated in the existing breeding policies using genomic selection to develop climate-resilient dairy cattle.

Genomic analyses and biological validation of candidate genes for rectal temperature as an indicator of heat stress in Holstein cattle

Heat stress is a major cause of welfare issues and economic losses to the worldwide dairy cattle industry. Genetic selection for heat tolerance has a great potential to positively affect the dairy industry, as the gains are permanent and cumulative over generations. Rectal temperature (RT) is hypothesized to be a good indicator trait of heat tolerance. Therefore, this study investigated the genetic architecture of RT by estimating genetic parameters, performing genome-wide association studies, and biologically validating potential candidate genes identified to be related to RT in Holstein cattle. A total of 33,013 RT records from 7,598 cows were used in this study. In addition, 1,114 cows were genotyped using the Illumina 150K Bovine BeadChip (Illumina, San Diego, CA). Rectal temperature measurements taken in the morning (AMRT) and in the afternoon (PMRT) are moderately heritable traits, with estimates of 0.09 ± 0.02 and 0.04 ± 0.01, respectively. These 2 traits are also highly genetically correlated (r = 0.90 ± 0.08). A total of 10 SNPs (located on BTA3, BTA4, BTA8, BTA13, BTA14, and BTA29) were found to be significantly associated with AMRT and PMRT. Subsequently, gene expression analyses were performed to validate the key functional genes identified (SPAG17, FAM107B, TSNARE1, RALYL, and PHRF1). This was done through in vitro exposure of peripheral blood mononuclear cells (PBMC) to different temperatures (37°C, 39°C, and 42°C). The relative mRNA expression of 2 genes, FAM107B and PHRF1, significantly changed between the control and heat stressed PBMC. In summary, RT is heritable, and enough genetic variability exists to enable genetic improvement of heat tolerance in Holstein cattle. Important genomic regions were identified and biologically validated; FAM107B and PHRF1 are the main candidate genes identified to influence heat stress response in dairy cattle.

Inheritance patterns of leukocyte gene expression under heat stress in F1 hybrid cattle and their parents

Crossbreeding capitalizes on heterosis effects and results in increased performance of crossbred animals. Dominance hypothesis and overdominance hypothesis are 2 common models proposed to explain heterosis. Differential gene expression between parents and hybrids is hypothesized to be responsible for heterosis. This study aimed to investigate the heat tolerance and inheritance patterns of leukocyte transcriptomics in F₁ hybrid cattle (Angus males × Droughtmaster females) and their parents Red Angus (AN) and Droughtmaster (DR) under heat stress. According to the respiratory rate and heat tolerance coefficient index, DR was better adapted to heat stress than AN. The physiological responses to heat stress of F₁ hybrids were similar to AN. We identified 802 differentially expressed genes in leukocytes between AN and DR under heat stress using mRNA sequencing. Compared with AN, upregulated genes in DR were enriched in biological processes of response to stress, external and chemical stimulus, and cytokine, cell surface receptor signaling pathway, and cardiovascular system development. In contrast, upregulated genes in AN were enriched in B cell activation and regulation of B cell activation. Gene expression levels can be inherited additively or nonadditively and are classified into additive (35%), dominance (44%), and overdominance and underdominance (18%) modes in F₁ hybrids and their parents. Inheritance patterns of gene expression showed that 97% (249/255) of the dominant genes were classified as paternal AN dominant in hybrids. The paternal imprinted PEG10 gene and its regulatory transcription factor MYC showed an AN dominant expression pattern. The MYC interacted with most AN dominant genes. These transcriptomic analyses revealed that DR and AN had specific cellular and humoral immunity and cardiovascular systems development function under heat stress. Inheritance pattern analyses from gene expression partly explained phenotypic differences between parents and F₁ hybrids. The paternal imprinted PEG10 gene interaction with transcription factor MYC may contribute to explaining paternal dominant gene expression in hybrids.

Prospects for gene introgression or gene editing as a strategy for reduction of the impact of heat stress on production and reproduction in cattle

In cattle, genetic variation exists in regulation of body temperature and stabilization of cellular function during heat stress. There are opportunities to reduce the impact of heat stress on cattle production by identifying the causative mutations responsible for genetic variation in thermotolerance and transferring specific alleles that confer thermotolerance to breeds not adapted to hot climates. An example of a mutation conferring superior ability to regulate body temperature is the group of frame-sift mutations in the prolactin receptor gene (PRLR) that lead to a truncated receptor and development of cattle with a short, sleek hair coat. Slick mutations in PRLR have been found in several extant breeds derived from criollo cattle. The slick mutation in Senepol cattle has been introgressed into dairy cattle in Puerto Rico, Florida and New Zealand. An example of a mutation that confers cellular protection against elevated body temperature is a deletion mutation in the promoter region of a heat shock protein 70 gene called HSPA1L. Inheritance of the mutation results in amplification of the transcriptional response of HSPA1L to heat shock and increased cell survival. The case of PRLR provides a promising example of the efficacy of the genetic approach outlined in this paper. Identification of other mutations conferring thermotolerance at the whole-animal or cellular level will lead to additional opportunities for using genetic solutions to reduce the impact of heat stress.

Biomarkers of health and welfare: A One Health perspective from the laboratory side

A biomarker is any measurement reflecting an interaction between a biological system and a potential hazard, which may be chemical, physical, or biological. The One World, One Health concept established that human and animal health and the environmental state are highly interconnected, sharing common aspects that can be applied globally in these three components. In this paper, we review how the concept of One Health can be applied to biomarkers of health and welfare, with a special focus on five points that can be applied to any biomarker when it is expected to be used to evaluate the human, animal or environmental health. Three of these points are: (1) the different biomarkers that can be used, (2) the different sample types where the biomarkers can be analysed, and (3) the main methods that can be used for their measurement. In addition, we will evaluate two key points needed for adequate use of a biomarker in any situation: (4) a proper analytical validation in the sample that it is going to be used, and (5) a correct selection of the biomarker. It is expected that this knowledge will help to have a broader idea about the use of biomarkers of health and welfare and also will contribute to a better and more accurate use of these biomarkers having in mind their One Health perspective.