Association of ATP1A1 gene polymorphism with thermotolerance in Tharparkar and Vrindavani cattle

Applications of Next-Generation Sequencing Technologies and Statistical Tools in Identifying Pathways and Biomarkers for Heat Tolerance in Livestock

The climate change-associated abnormal weather patterns negatively influences the productivity and performance of farm animals. Heat stress is the major detrimental factor hampering production, causing substantial economic loss to the livestock industry. Therefore, it is important to identify heat-tolerant breeds that can survive and produce optimally in any given environment. To achieve this goal, a clearer understanding of the genetic differences and the underlying molecular mechanisms associated with climate change impacts and heat tolerance are a prerequisite. Adopting next-generation biotechnological and statistical tools like whole transcriptome analysis, whole metagenome sequencing, bisulphite sequencing, genome-wide association studies (GWAS), and selection signatures provides an opportunity to achieve this goal. Through these techniques, it is possible to identify permanent genetic markers for heat tolerance, and by incorporating those markers in marker-assisted breeding selection, it is possible to achieve the target of breeding for heat tolerance in livestock. This review gives an overview of the recent advancements in assessing heat tolerance in livestock using such 'omics' approaches and statistical models. The salient findings from this research highlighted several candidate biomarkers that have the potential to be incorporated into future heat-tolerance studies. Such approaches could revolutionise livestock production in the changing climate scenario and support the food demands of the growing human population.

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.

The Effects of Heat Shock Protein 70 Addition in the Culture Medium on the Development and Quality of In Vitro Produced Heat Shocked Bovine Embryos

The aims of the present study were to examine the effects of HSP70 addition in the in vitro culture medium of day 3 embryos on their developmental competence and quality. Bovine oocytes (n = 1442) were in vitro matured, inseminated and cultured for the first two days according to standardized methods. The presumptive zygotes were randomly allocated in three experimental groups: Control, C (embryos cultured at 39 °C throughout the culture period), group C41 (temperature was raised to 41 °C from the 48th to 72nd h post insemination (p.i.) and then it returned at 39 °C for the remaining culture period), and group H41 (the temperature modification was the same as in C41 and during heat exposure, HSP70 was added in the culture medium). Cleavage and embryo yield were assessed 48 h p.i. and on days 7, 8, 9, respectively and gene expression in day 7 blastocysts was assessed by RT-PCR. Blastocyst yield was the highest in group C39; and higher in group H41 compared to group C41. From the gene expression analyses, altered expression of 11 genes was detected among groups. The analysis of the orchestrated patterns of gene expression differed between groups. The results of this study confirm the devastating effects of heat stress on embryo development and provide evidence that HSP70 addition at the critical stages can partly counterbalance, without neutralizing, the negative effects of the heat insult on embryos, acting mainly through mechanisms related to energy deployment.

Molecular characterization and identification of SNPs in ATP1A1 isoform of sodium-phosphate adenosine triphosphatase across diverse breeds of riverine buffaloes (Bubalus bubalis) and Indian native cattle (Bos indicus): A plausible candidate gene for heat tolerance

In the present study, efforts were made to sequence characterize the selected exonic region (18–21) of ATP1A1 gene to identify variations/SNPs in different breeds of Indian riverine buffaloes and native cattle. The sequence characterization of selected intronic/exonic region (17–21) of ATP1A1 gene was carried out in a total of 120 samples which included 6 animals each of 8 buffalo breeds and 72 animals of 12 cattle breeds. Genomic DNA was extracted from the whole blood by enzymatic digestion using proteinase K using phenol:chloroform method.. Three sets of primers were designed using Primer3 software to amplify genomic region from intron 17 to intron 21 of ATP1A1 gene in both cattle and buffaloes. The amplified products were purified by enzymatic method and purified PCR products were sequenced using forward primers in an ABI 3100 Automated DNA Sequencer. The chromatogram of each sequence obtained was checked manually. Base calling was performed with Phred and contig assembly was done via Phrap/Cross_match/Swat tool available in the suite Codon code Aligner v. 3.5.1. The results revealed a total of 26 variations in exons 18–21 of ATP1A1 gene in riverine buffalo. Out of 26 variations, 6 (T27006876C, C27006599T, T27006345C, T27006330C, G27006309T and T27006240C) were distributed across 4 exonic regions and the remaining 20 were located in intronic region whereas in native cattle, only 2 SNPs were identified in exonic regions (18–21). SNP T27007767C was found to be a novel one in 18 intronic region of ATP1A1 gene in Indian cattle breeds. All 7 variations found in exonic region of both buffalo and cattle breeds were synonymous with the predicted changes in amino acids. The variations identified in ATP1A1 gene in the present study could be evaluated in future for their roles in heat tolerance trait in riverine buffaloes and native cattle.

Expression of candidate genes for residual feed intake in tropically adapted Bos taurus and Bos indicus bulls under thermoneutral and heat stress environmental conditions

The objectives of this study were to measure the relative expression of the ATP1A1, NR3C1, POMC, NPY, and LEP genes in Caracu (Bos taurus) and Nelore (Bos indicus) bulls submitted to feed efficiency tests at high environmental temperatures, and to evaluate differences in adaptability to tropical conditions between breeds. Thirty-five Caracu and 30 Nelore bulls were submitted to a feed efficiency test using automated feeding stations. At the end of the test, the animals were subjected to thermoneutral (TN) and heat stress (HS) conditions. Blood samples were collected after the exposure to the TN and HS conditions and the relative expression of genes was measured by qPCR. The bulls exhibited lower expression of ATP1A1 in the HS condition than in the TN condition (1.98 ± 0.27 and 2.86 ± 0.26, P = 0.02), while the relative expression of NR3C1, POMC, and LEP did not differ (P > 0.05) between climatic conditions. The breed and feed intake influenced NPY and LEP expression levels (P < 0.05). Different climate conditions associated with residual feed intake can modify the gene expression patterns of ATP1A1 and NPY. The association observed among all genes studied shows that they are involved in appetite control. Bos taurus and Bos indicus bulls exhibited similar adaptability to tropical climate conditions.

Comparative Expression Profiling and Sequence Characterization of ATP1A1 Gene Associated with Heat Tolerance in Tropically Adapted Cattle

Climate change is an imminent threat to livestock production. One adaptation strategy is selection for heat tolerance. While it is established that the ATP1A1 gene and its product play an important role in the response to many stressors, there has been no attempt to characterize the sequence or to perform expression profiling of the gene in production animals. We undertook a field experiment to compare the expression profiles of ATP1A1 in heat-tolerant Vechur and Kasaragod cattle (Bos taurus indicus) with the profile of a heat-susceptible crossbreed (B. t. taurus × B. t. indicus). The cattle were exposed to heat stress while on pasture in the hot summer season. The environmental stress was quantified using the temperature humidity index (THI), while the heat tolerance of each breed was assessed using a heat tolerance coefficient (HTC). The ATP1A1 mRNA of Vechur cattle was amplified from cDNA and sequenced. The HTC varied significantly between the breeds and with time-of-day (p < 0.01). The breed-time-of-day interaction was also significant (p < 0.01). The relative expression of ATP1A1 differed between heat-tolerant and heat-susceptible breeds (p = 0.02). The expression of ATP1A1 at 08:00, 10:00 and 12:00, and the breed-time-of-day interaction, were not significant. The nucleotide sequence of Vechur ATP1A1 showed 99% homology with the B. t. taurus sequence. The protein sequence showed 98% homology with B. t. taurus cattle and with B. grunniens (yak) and 97.7% homology with Ovis aries (sheep). A molecular clock analysis revealed evidence of divergent adaptive evolution of the ATP1A1 gene favoring climate resilience in Vechur cattle. These findings further our knowledge of the relationship between the ATP1A1 gene and heat tolerance in phenotypically incongruent animals. We propose that ATP1A1 could be used in marker assisted selection (MAS) for heat tolerance.

Genetic Parameters and Genome-Wide Association Studies for Anti-Müllerian Hormone Levels and Antral Follicle Populations Measured After Estrus Synchronization in Nellore Cattle

Reproductive efficiency plays a major role in the long-term sustainability of livestock industries and can be improved through genetic and genomic selection. This study aimed to estimate genetic parameters (heritability and genetic correlation) and identify genomic regions and candidate genes associated with anti-Müllerian hormone levels (AMH) and antral follicle populations measured after estrous synchronization (AFP) in Nellore cattle. The datasets included phenotypic records for 1099 and 289 Nellore females for AFP and AMH, respectively, high-density single nucleotide polymorphism (SNP) genotypes for 944 animals, and 4129 individuals in the pedigree. The heritability estimates for AMH and AFP were 0.28 ± 0.07 and 0.30 ± 0.09, and the traits were highly and positively genetically correlated (rG = 0.81 ± 0.02). These findings indicated that these traits can be improved through selective breeding, and substantial indirect genetic gains are expected by selecting for only one of the two traits. A total of 31 genomic regions were shown to be associated with AMH or AFP, and two genomic regions located on BTA1 (64.9-65.0 Mb and 109.1-109.2 Mb) overlapped between the traits. Various candidate genes were identified to be potentially linked to important biological processes such as ovulation, tissue remodeling, and the immune system. Our findings support the use of AMH and AFP as indicator traits to genetically improve fertility rates in Nellore cattle and identify better oocyte donors.

Differential expression and characterization of ATP1A1 exon17 gene by high resolution melting analysis and RT-PCR in Indian goats

The investigation was carried out to analyse the genetic polymorphism and gene expression of ATP1A1 gene in four different Indian goat breeds by using high resolution melting (HRM) and real time-PCR. ATPase is electro-genic ion pump which is maintains the balance of sodium and potassium ions in animal cells. The transport of Na⁺& K⁺ is variable at cellular level during extreme hot period. Therefore, susceptible and tolerant animals were selected based on the physiological responses during hot period. Blood samples were collected from individuals, DNA was isolated. The 300 bp fragment of ATP1A1 gene was amplified by PCR and HRM genotyping was performed. The melting curves were analysed, differential temperature-shift plot showed three different genotypes in all the analysed samples. Out of the 135 samples, the distribution percentages were 55.56% (AA/blue), 33.33% (AC/red) and 11.11% (CC/green). The sequence variation revealed a SNP at 143rd position (A>C). The nucleotide diversity was 0.695 ± 0.403, 0.732 ± 0.424, 0.662 ± 0.433 and 0.687 ± 0.398 in Barbari, Jamunapari, Jakharna and Sirohi, respectively. The respiration rate (RR) was significantly different (P < 0.05) between AA and AC (t = 1.875, df = 38) genotype and heart rate (HR) was significantly different (P < 0.05) between AA and CC genotype. The relative expression pattern of ATP1A1 in SNP variants and non-variants animal tissues showed 19.09 and 6.93 fold higher than control (non-variant), respectively. Jamunapari showed higher fold value of ATP1A1 gene in comparison to Barbari, Jakharna and Sirohi. However, the heat stress-susceptible phenotype had significantly higher gene expression than stress-tolerant in all the breeds. The variation may be used as a marker for selection on the basis of physiological parameters and expression of ATP1A1 gene in goats indicating the specificity of expression in each tissue.

Genome-wide association studies identified multiple genetic loci for body size at four growth stages in Chinese Holstein cattle

The growth and maturity of cattle body size affect not only feed efficiency, but also productivity and longevity. Dissecting the genetic architecture of body size is critical for cattle breeding to improve both efficiency and productivity. The volume and weight of body size are indicated by several measurements. Among them, Heart Girth (HG) and Hip Height (HH) are the most important traits. They are widely used as predictors of body weight (BW). Few association studies have been conducted for HG and HH in cattle focusing on single growth stage. In this study, we extended the Genome-wide association studies to a full spectrum of four growth stages (6-, 12-, 18-, and 24-months after birth) in Chinese Holstein heifers. The whole genomic single nucleotide polymorphisms (SNPs) were obtained from the Illumina BovineSNP50 v2 BeadChip genotyped on 3,325 individuals. Estimated breeding values (EBVs) were derived for both HG and HH at the four different ages and analyzed separately for GWAS by using the Fixed and random model Circuitous Probability Unification (FarmCPU) method. In total, 27 SNPs were identified to be significantly associated with HG and HH at different growth stages. We found 66 candidate genes located nearby the associated SNPs, including nine genes that were known as highly related to development and skeletal and muscular growth. In addition, biological function analysis was performed by Ingenuity Pathway Analysis and an interaction network related to development was obtained, which contained 16 genes out of the 66 candidates. The set of putative genes provided valuable resources and can help elucidate the genomic architecture and mechanisms underlying growth traits in dairy cattle.