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

Unraveling the genetic basis of methane emission in dairy cattle: a comprehensive exploration and breeding approach to lower methane emissions

Ruminant animals, such as dairy cattle, produce CH4, which contributes to global warming emissions and reduces dietary energy for the cows. While the carbon foot print of milk production varies based on production systems, milk yield and farm management practices, enteric fermentation, and manure management are major contributors togreenhouse gas emissions from dairy cattle. Recent emerging evidence has revealed the existence of genetic variation for CH4 emission traits among dairy cattle, suggests their potential inclusion in breeding goals and genetic selection programs. Advancements in high-throughput sequencing technologies and analytical techniques have enabled the identification of potential metabolic biomarkers, candidate genes, and SNPs linked to methane emissions. Indeed, this review critically examines our current understanding of carbon foot print in milk production, major emission sources, rumen microbial community and enteric fermentation, and the genetic architecture of methane emission traits in dairy cattle. It also emphasizes important implications for breeding strategies aimed at halting methane emissions through selective breeding, microbiome driven breeding, breeding for feed efficiency, and breeding by gene editing.

Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics

The muskox (Ovibos moschatus), an integral component and iconic symbol of arctic biocultural diversity, is under threat by rapid environmental disruptions from climate change. We report a chromosomal-level haploid genome assembly of a muskox from Banks Island in the Canadian Arctic Archipelago. The assembly has a contig N50 of 44.7 Mbp, a scaffold N50 of 112.3 Mbp, a complete representation (100%) of the BUSCO v5.2.2 set of 9225 mammalian marker genes and is anchored to the 24 chromosomes of the muskox. Tabulation of heterozygous single nucleotide variants in our specimen revealed a very low level of genetic diversity, which is consistent with recent reports of the muskox having the lowest genome-wide heterozygosity among the ungulates. While muskox populations are currently showing no overt signs of inbreeding depression, environmental disruptions are expected to strain the genomic resilience of the species. One notable impact of rapid climate change in the Arctic is the spread of emerging infectious and parasitic diseases in the muskox, as exemplified by the range expansion of muskox lungworms, and the recent fatal outbreaks of Erysipelothrix rhusiopathiae, a pathogen normally associated with domestic swine and poultry. As a genomics resource for conservation management of the muskox against existing and emerging disease modalities, we annotated the genes of the major histocompatibility complex on chromosome 2 and performed an initial assessment of the genetic diversity of this complex. This resource is further supported by the annotation of the principal genes of the innate immunity system, genes that are rapidly evolving and under positive selection in the muskox, genes associated with environmental adaptations, and the genes associated with socioeconomic benefits for Arctic communities such as wool (qiviut) attributes. These annotations will benefit muskox management and conservation.

Functional transcriptome analysis revealed upregulation of MAPK-SMAD signalling pathways in chronic heat stress in crossbred cattle

Animal geneticists and breeders have the impending challenge of enhancing the resilience of Indian livestock to heat stress through better selection strategies. Climate change's impact on livestock is more intense in tropical countries like India where dairy cattle crossbreeds are more sensitive to heat stress. The main reason for this study was to find the missing relative changes in transcript levels in thermo-neutral and heat stress conditions in crossbred cattle through whole-transcriptome analysis of RNA-Seq data. Differentially expressed genes (DEGs) identified based on the minimum log twofold change value and false discovery rate 0.05 revealed 468 up-regulated genes and 2273 down-regulated significant genes. Functional annotation and pathway analysis of these significant DEGs were compared based on Gene Ontology (Biological process), Kyoto Encyclopedia of Genes and Genome (KEGG), and Reactome pathways using g: Profiler, ShinyGO v0.76, and iDEP.951 web tools. On finding network visualization, the most over-represented and correlated pathways were neuronal and sensory organ development, calcium signalling pathway, Mitogen-activated protein kinase (MAPK) and Smad signalling pathway, Ras-proximate-1, or Ras-related protein 1 (Rap 1) signalling pathway, apoptosis, and oxidative stress. Similarly, down-regulated genes were most expressed in mRNA processing, immune system, B-cell receptor signalling pathway, Nucleotide oligomerization domain (NOD)-like receptors (NLRs) signalling pathway and nonsense-mediated decay (NMD) pathway. The heat stress-responsive genes identified in this study will facilitate our understanding of the molecular basis for climate resilience and heat tolerance in Indian dairy crossbreeds.

Hyperthermia-induced changes in leukocyte survival and phagocytosis: a comparative study in bovine and buffalo leukocytes

Heat stress negatively affects health, welfare, and livestock productivity by impairing immune function, increasing disease incidence. In recent years, there has been increasing interest in understanding the immune system of water buffalo due to the growing economic impact of this species for the high quality and nutritional value of buffalo milk. While there are common responses across bovine and buffalo species, there are also some species-specific variations in the physiological responses to heat stress, mainly attributed to differences in metabolism and heat dissipation efficiency. At cellular level, the exposure to thermal stress induces several anomalies in cell functions. However, there is limited knowledge about the differential response of bovine and buffalo leucocytes to early and late exposure to different degrees of thermal exposure. The aim of this study was to compare the in vitro effect of hyperthermia on apoptosis and phagocytosis in leukocytes from bovine and buffalo species. For this, whole blood samples of six bovines and nine buffaloes were incubated at 39°C (mimicking normothermia condition) or 41°C (mimicking heat stress condition) for 1, 2, and 4 h. Two flow cytometric assays were then performed to evaluate apoptosis and determine functional capacity of phagocytic cells (neutrophils and monocytes). The results showed that the viability of bovine and buffalo leukocytes was differently affected by temperature and time of in vitro exposure. A higher percentage of apoptotic leukocytes was observed in bovines than in buffaloes at 39°C (3.19 vs. 1.51, p < 0.05) and 41°C (4.01 vs. 1.69, p < 0.05) and for all incubation time points (p < 0.05). In contrast, no difference was observed in the fraction of necrotic leukocytes between the two species. In both species, lymphocytes showed the highest sensitivity to hyperthermia, showing an increased apoptosis rates along with increased incubation time. In bovine, apoptotic lymphocytes increased from 5.79 to 12.7% at 39°C (p < 0.05), in buffalo, this population increased from 1.50 to 3.57% at 39°C and from 2.90 to 4.99% at 41°C (p < 0.05). Although no significant differences were found between the two species regarding the percentage of phagocytic neutrophils, lower phagocytosis capacity values (MFI, mean fluorescence intensity) were found in bovines compared with buffaloes at 41°C (27960.72 vs. 53676.45, p > 0.05). However, for monocytes, the differences between species were significant for both phagocytosis activity and capacity with lower percentages of bovine phagocytic monocytes after 2 h at 39°C and after 1 h at 41°C. The bovine monocytes showed lower MFI values for all temperature and time variations than buffaloes (37538.91 vs. 90445.47 at 39°C and 33752.91 vs. 70278.79 at 41°C, p < 0.05). In conclusion, the current study represents the first report on the comparative analysis of the effect of in vitro heat stress on bovine and buffalo leukocyte populations, highlighting that the leukocytes of buffalo exhibit relatively higher thermal adaptation than bovine cells.