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The recent advances in high‐throughput next‐generation sequencing technologies have heralded the arrival of the Big Data era. As a result, the use of pharmacogenetics in drug discovery and individualized drug therapy has transformed the field of precision medicine. This paradigm shift in drug development programs has effectively reshaped the old drug development practices, which were primarily concerned with the physiological status of patients for drug development. Pharmacogenomics bridges the gap between pharmacodynamics and pharmacokinetics, advancing current diagnostic and treatment strategies and enabling personalized and targeted drug therapy. The primary goals of pharmacogenetic studies are to improve drug efficacy and minimize toxicities, to identify novel drug targets, to estimate drug dosage for personalized medicine, and to incorporate it as a routine diagnostic for disease susceptibility. Although pharmacogenetics has numerous applications in individualized drug therapy and drug development, it is in its infancy in veterinary medicine. The objective of this review is to present an overview of historical landmarks, current developments in various animal species, challenges and future perspectives of genomics in drug development and dosage optimization for individualized medicine in veterinary subjects. [ABSTRACT FROM AUTHOR]

The identification of candidate genes related to pigmentation and under selective sweep provides insights into the genetic basis of pigmentation and the evolutionary forces that have shaped this variation. The selective sweep events in the genes responsible for normal coat color in Indian cattle groups are still unknown. To find coat color genes displaying signs of selective sweeps in the indigenous cattle, we compiled a list of candidate genes previously investigated for their association with coat color and pigmentation. After that, we performed a genome-wide scan of positive selection signatures using the BovineSNP50K Bead Chip in 187 individuals of seven indigenous breeds. We applied a wide range of methods to find evidence of selection, such as Tajima's D, CLR, iHS, varLD, ROH, and FST. We found a total of sixteen genes under selective sweep, that were involved in coat color and pigmentation physiology. These genes are CRIM1 in Gir, MC1R in Sahiwal, MYO5A, PMEL and POMC in Tharparkar, TYRP1, ERBB2, and ASIP in Red Sindhi, MITF, LOC789175, PAX3 and TYR in Ongole, and IRF2, SDR165 and, KIT in Nelore, ADAMTS19 in Hariana. These genes are related to melanin synthesis, the biology of melanocytes and melanosomes, and the migration and survival of melanocytes during development. [ABSTRACT FROM AUTHOR]

Riverine Buffaloes, especially the Murrah breed because of their adaptability to harsh climatic conditions, is farmed in many countries to convert low-quality feed into valuable dairy products and meat. Here, we investigated the copy number variations (CNVs) in 296 Murrah buffalo using the Axiom® Buffalo Genotyping Array 90K (Affymetrix, Santa Clara, CA, USA). The CNVs were detected on the autosomes, using the Copy Number Analysis Module (CNAM) using the univariate analysis. 7937 CNVs were detected in 279 Buffaloes, the average length of the CNVs was 119,048.87 bp that ranged between 7800 and 4,561,030 bp. These CNVs were accounting for 10.33% of the buffalo genome, which was comparable to cattle, sheep, and goat CNV analyses. Further, CNVs were merged and 1541 CNVRs were detected using the Bedtools-mergeBed command. 485 genes were annotated within 196 CNVRs that were identified in at least 10 animals of Murrah population. Out of these, 40 CNVRs contained 59 different genes that were associated with 69 different traits. Overall, the study identified a significant number of CNVs and CNVRs in the Murrah breed of buffalo, with a wide range of lengths and frequencies across the autosomes. The identified CNVRs contained genes associated with important traits related to production and reproduction, making them potentially important targets for future breeding and genetic improvement efforts. [ABSTRACT FROM AUTHOR]

Major Histocompatibility Complex (MHC) genes are among the immune genes that have been extensively studied in vertebrates and are necessary for adaptive immunity. In the immunological response to infectious diseases, they play several significant roles. This research paper provides the selection signatures in the MHC region of the bovine genome as well as how certain genes related to innate immunity are undergoing a positive selective sweep. Here, we investigated signatures of historical selection on MHC genes in 15 different cattle populations and a total of 427 individuals. To identify the selection signatures, we have used three separate summary statistics. The findings show potential selection signatures in cattle from whom we isolated genes involved in the MHC. The most significant regions related to the bovine MHC are BOLA, non-classical MHC class I antigen (BOLA-NC1), Microneme protein 1 (MIC1) , Cluster of Differentiation 244 (CD244), Gap Junction Alpha-5 Protein (GJA5). It will be possible to gain new insight into immune system evolution by understanding the distinctive characteristics of MHC in cattle. [ABSTRACT FROM AUTHOR]

The detection of selection signatures assists in understanding domestication, evolution, and the identification of genomic regions related to adaptation and production traits in buffaloes. The emergence of high-throughput technologies like Next Generation Sequencing and SNP genotyping had expanded our ability to detect these signatures of selection. In this study, we sought to identify signatures of selection in five buffalo populations (Brazilian Murrah, Bulgarian Murrah, Indian Murrah, Nili-Ravi, and Kundi) using Axiom Buffalo 90 K Genotyping Array data. Using seven different methodologies (Tajima's D, CLR, ROH, iHS, FST, FLK and hapFLK), we identified selection signatures in 374 genomic regions, spanning a total of 381 genes and 350 quantitative trait loci (QTLs). Among these, several candidate genes were associated with QTLs for milk production, reproduction, growth and carcass traits. The genes and QTLs reported in this study provide insight into selection signals shaping the genome of buffalo breeds. Our findings can aid in further genomic association studies, genomic prediction, and the implementation of breeding programmes in Indian buffaloes. [ABSTRACT FROM AUTHOR]

Over the years, indigenous cattle have not only played an essential role in securing primary food sources but have also been utilized for labor by humans, making them invaluable genetic resources. The Zhaotong cattle, a native Chinese breed from the Yunnan province, possess excellent meat quality and resistance to heat and humidity. Here we used whole genome sequencing data of 104 animals to delve into the population structure, genomic diversity and potential positive selection signals in Zhaotong cattle. The findings of this study demonstrate that the genetic composition of Zhaotong cattle was primarily derived from Chinese indicine cattle and East Asian cattle. The nucleotide diversity of Zhaotong cattle was only lower than that of Chinese indicine cattle, which was much higher than that of other taurine cattle. Genome‐wide selection scans detected a series of positive candidate regions containing multiple key genes related to bone development and metabolism (CA10, GABRG3, GLDN and NOTUM), meat quality traits (ALG8, LINGO2, MYO5B, PRKG1 and GABRB1), immune response (ADA2, BMF, LEF1 and PAK6) and heat resistance (EIF2AK4 and LEF1). In summary, this study supplies essential genetic insights into the genome diversity within Zhaotong cattle and provides a foundational framework for comprehending the genetic basis of indigenous cattle breeds. [ABSTRACT FROM AUTHOR]

The field of genetics has evolved a lot after the emergence of molecular and advanced genomic technologies. The advent of Next Generation Sequencing, SNP genotyping platforms and simultaneous reduction in the cost of sequencing had opened the door to genomic research in farm animals. There are various applications of genomics in livestock, such as the use of genomic data: (i) to investigate genetic diversity and breed composition/population structure (ii) to identify genetic variants and QTLs related to economically important and ecological traits, genome-wide association studies (GWAS) and genomic signatures of selection; (iii) to enhance breeding programs by genomic selection. Compared to traditional methods, genomic selection is expected to improve selection response by increasing selection accuracy and reducing the generation interval due to early selection. Genomic selection (GS) in developed countries has led to rapid genetic gains, especially in dairy cattle, due to a well-established genetic evaluation system. Indian livestock system is still lagging behind developed nations in adopting these technologies. This review discusses the current status, challenges, and future perspectives of livestock genomics in India. [ABSTRACT FROM AUTHOR]

The process of building a model or copy of a real-world system and assessing its behaviour under various scenarios is referred to as simulation. Simulation in population genetics is the process of simulating a population's genetic makeup and evolutionary history using mathematical models and computer algorithms. It is important in population genetics for a better understanding of the impact of various evolutionary and demographic scenarios on sequence variation and patterns, it allows investigators to better assess and design analytical methods in the study of disease-associated genetic factors. This is an important tool for studying population genetic diversity and how natural selection, genetic drift, mutation, migration, and other evolutionary forces have influenced the genetic makeup of the population. There are three fundamental frameworks for simulation: coalescent, forward, and resampling methods. Numerous simulators that fit under these frameworks can be compared in terms of their evolutionary and demographic scenarios, computing complexity, and particular applications. Population simulation is becoming increasingly important in evolutionary biology, enabling researchers to explore the effects of various genetic models on genetic diversity and DNA sequence patterns. [ABSTRACT FROM AUTHOR]

The present study was conducted on the MHC class I (BoLA-A/BuLA-A) gene in Sahiwal, Jersey, Hariana, and Tharparkar breeds of cattle and Murrah, Mehsana, and Bhadawari breeds of buffalo to study the polymorphism. Exons 7–8 of the MHC class I gene was first characterized for polymorphism study in buffalo and the results reveal that this gene has a higher level of nucleotide changes than the cattle. Genes were investigated for polymorphisms in 285 animals of cattle and buffalo breeds. Molecular characterization of the MHC class I (BoLa-A/Bula-A) gene reveals a higher degree of polymorphism at the nucleotide level in cattle and buffalo. Results revealed this region has a higher level of polymorphisms in buffalo as campared to the cattle. Alul restriction patterns were monomorphic except for three different patterns but it was able to illustrate the differences in buffalo and cattle. SSCP analysis of exons 7–8 showed remarkable differences in cattle and buffalo. Sequence analysis revealed more closeness of Murrah breed with crossbred and indigenous cattle than Holstein Friesian. Exon 8 had more deletion and stop codon as compared to exon 7. The investigation confirmed that MHC class I BoLa-A/Bula-A exons 7–8 is highly polymorphic in buffalo as compared to cattle. [ABSTRACT FROM AUTHOR]

The present investigation was performed to compare the global gene expression profile in peripheral blood mononuclear cells (PBMCs) of Bos indicus and crossbred (Bos taurus × B. indicus) cattle. Previously, several studies revealed the disease tolerance potential of B. indicus cattle but underlying genetic mechanism is still not fully explored. The PBMCs model was used for this investigation as it plays crucial role in the immune system regulation. Transcriptomic analysis revealed total 6767 significantly differentially expressed transcripts (fold change (absolute) >2.0, p <.05). In addition, 4149 transcripts were upregulated, 2618 transcripts were downregulated and fold change (absolute) of differentially expressed transcript varied from −223.32 to 213.63. Functional annotation analysis of differentially expressed genes confirmed their role in various molecular pathways viz. innate immune response, antigen processing and presentation, MHC protein complex, defense response to bacterium, regulation of immune response, positive regulation of JAK-STAT cascade, cytoskeletal protein binding, etc. Protein–protein interaction network analysis provided understanding of inter-relationship of immune genes with differentially expressed genes. In conclusion, this study could provide comprehensive information about the dysregulated genes and biological pathways in PBMCs which might be responsible for disease tolerance in B. indicus cattle. [ABSTRACT FROM AUTHOR]

The BoLA class II DQA and DQB genes in crossbred cattle were studied using PCR-RFLP, cloning, and sequencing techniques. Seventy-two crossbred cattle (Vrindavani) were used in the current study. HaeIII and XbaI restriction enzymes digested DQA exon 2-3, revealing seven (HaeIII-A-G) and three (XbaI A-C) motifs, respectively. The BoLA-DQB gene was analyzed using PCR-RFLP with PstI and TaqI restriction enzymes, yielding five restriction motifs for each restriction enzyme (PstI-A-E and TaqI-A-E). In crossbred cattle, addition, deletion, and substitutions were observed in distinct sequences, resulting in variations in overall gene length. Changes in nucleotides at positions 64–80, 110–200, and 207–264 were largely responsible for polymorphism in DQA exon 2. The phylogenetic analysis predicted a high degree of nucleotide and amino acid changes in DQA exon 2-3 and DQB exon 2. DQA genes had a nucleotide dissimilarity of 0.3–25.4 percent, while DQB genes had a nucleotide dissimilarity of 1.5–14.3 percent. We cloned and sequenced 20 genotypes based on PCR-RFLP of the DQA and DQB genes. The current study observed variation in the DQA and DQB genes and will serve as a foundation for future research on the BoLA DQA and DQB genes. [ABSTRACT FROM AUTHOR]

Leptin is an adipokine hormone secreted primarily from the white adipose tissue and leptin levels are usually elevated in obese individuals. Leptin is known to mediate the relaxation of the uterus in the pregnant mouse by increasing Nitric Oxide (NO) synthesis in late pregnancy. The present study aimed to assess the effect of a pathological concentration of leptin (3 nM) on NO synthesis in the uterus of early pregnant mice and also to evaluate its effect on the transcription of genes responsible for NO synthesis. mRNA expression studies using real-time PCR revealed that leptin (3 nM) increased the relative expression of the inducible Nitric Oxide synthase (iNOS) gene which also resulted in increased NO levels. The results suggest that higher leptin levels during early pregnancy may increase NO levels in the uterus which may result in a net decrease in uterine contractions further leading to complications in pregnancy. [ABSTRACT FROM AUTHOR]