Search

Balancing selection is the process of selection that preserves various alleles within a population. Studying the areas undergoing balancing selection is essential, because it preserves genetic diversity in a population. Finding genes that exhibit signs of balancing selection during the domestication of cattle is the goal of this study. To identify regions where polymorphism has persisted in the cattle population for millions of years, we examined the genome of cattle. In this study, we used bovine SNP 50 k data to conduct a detailed genome-wide assessment of selection signatures for balancing selection. We have included the genotyped data from 427 animals, including five taurines, two crossbreds, and eight Indian cattle breeds. For this study, we employed Tajima's D approach to identify signature regions undergoing balancing selection. Using the NCBI database, PANTHER 17.0, and CattleQTL database, the annotation was carried out after finding the relevant areas under balancing selection. The number of genomic regions undergoing balancing selection in Ayrshire, Brown-Swiss, Frieswal, Gir, Guernsey, Hariana, Holstein Friesian, Jersey, Kankrej, Nelore, Ongole, Red Sindhi, Sahiwal, Tharparkar, and Vrindavani was 11, 13, 13, 19, 18, 11, 17, 14, 14, 12, 10, 12, 13, 13, and 11, respectively. We have observed multiple immune system-related genes going through balancing selection, including KIT, NFATC2, GBP4, LRRC32, SYT7, RAG1, RAG2, LOC513659, and ZBTB17. In our study, we found that the majority of the immune-related genes and a few genes associated with growth, reproduction, production, and adaptation are undergoing balancing selection. [ABSTRACT FROM AUTHOR]

Mammalian X and Y chromosomes independently evolved from various autosomes approximately 300 million years ago (MYA). To fully understand the relationship between genomic composition and phenotypic diversity arising due to the course of evolution, we have scanned regions of selection signatures on the X chromosome in different cattle breeds. In this study, we have prepared the datasets of 184 individuals of different cattle breeds and explored the complete X chromosome by utilizing four within-population and two between-population methods. There were 23, 25, 30, 17, 17, and 12 outlier regions identified in Tajima's D, CLR, iHS, ROH, FST, and XP-EHH. Bioinformatics analysis showed that these regions harbor important candidate genes like AKAP4 for reproduction in Brown Swiss, MBTS2 for production traits in Brown Swiss and Guernsey, CXCR3 and CITED1 for health traits in Jersey and Nelore, and BMX and CD40LG for regulation of X chromosome inactivation in Nelore and Gir. We identified genes shared among multiple methods, such as TRNAC-GCA and IL1RAPL1, which appeared in Tajima's D, ROH, and iHS analyses. The gene TRNAW-CCA was found in ROH, CLR and iHS analyses. The X chromosome exhibits a distinctive interaction between demographic factors and genetic variations, and these findings may provide new insight into the X-linked selection in different cattle breeds. [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 main objective of the current research was to locate, annotate, and highlight specific areas of the bovine genome that are undergoing intense positive selection. Here, we are analyzing selection signatures in crossbred (Bos taurus X Bos indicus), taurine (Bos taurus), and indicine (Bos indicus) cattle breeds. Indicine cattle breeds found throughout India are known for their higher heat tolerance and disease resilience. More breeds and more methods can provide a better understanding of the selection signature. So, we have worked on nine distinct cattle breeds utilizing seven different summary statistics, which is a fairly extensive approach. In this study, we carried out a thorough genome-wide investigation of selection signatures using bovine 50K SNP data. We have included the genotyped data of two taurine, two crossbreds, and five indicine cattle breeds, for a total of 320 animals. During the 1950s, these indicine (cebuine) cattle breeds were exported with the aim of enhancing the resilience of taurine breeds in Western countries. For this study, we employed seven summary statistics, including intra-population, i.e., Tajima's D, CLR, iHS, and ROH and inter-population statistics, i.e., FST, XP-EHH, and Rsb. The NCBI database, PANTHER 17.0, and CattleQTL database were used for annotation after finding the important areas under selection. Some genes, including EPHA6, CTNNA2, NPFFR2, HS6ST3, NPR3, KCNIP4, LIPK, SDCBP, CYP7A1, NSMAF, UBXN2B, UGDH, UBE2K, and DAB1, were shown to be shared by three or more different approaches. Therefore, it gives evidence of the most intense selection in these areas. These genes are mostly linked to milk production and adaptability traits. This study also reveals selection regions that contain genes which are crucial to numerous biological functions, including those associated with milk production, coat color, glucose metabolism, oxidative stress response, immunity and circadian rhythms. [ABSTRACT FROM AUTHOR]

Half a century ago, a seminal article on the hitchhiking effect by Smith and Haigh inaugurated the concept of the selection signature. Selective sweeps are characterised by the rapid spread of an advantageous genetic variant through a population and hence play an important role in shaping evolution and research on genetic diversity. The process by which a beneficial allele arises and becomes fixed in a population, leading to a increase in the frequency of other linked alleles, is known as genetic hitchhiking or genetic draft. Kimura's neutral theory and hitchhiking theory are complementary, with Kimura's neutral evolution as the 'null model' and positive selection as the 'signal'. Both are widely accepted in evolution, especially with genomics enabling precise measurements. Significant advances in genomic technologies, such as next‐generation sequencing, high‐density SNP arrays and powerful bioinformatics tools, have made it possible to systematically investigate selection signatures in a variety of species. Although the history of selection signatures is relatively recent, progress has been made in the last two decades, owing to the increasing availability of large‐scale genomic data and the development of computational methods. In this review, we embark on a journey through the history of research on selective sweeps, ranging from early theoretical work to recent empirical studies that utilise genomic data. [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]

Copy number variations (CNVs) are major forms of genetic variation with an increasing importance in animal genomics. This study used the Illumina BovineSNP 50 K BeadChip to detect the genome-wide CNVs in the Tharparkar cattle. With the aid of PennCNV software, we noticed a total of 447 copy number variation regions (CNVRs) across the autosomal genome, occupying nearly 2.17% of the bovine genome. The average size of detected CNVRs was found to be 122.2 kb, the smallest CNVR being 50.02 kb in size, to the largest being 1,232.87 Kb. Enrichment analyses of the genes in these CNVRs gave significant associations with molecular adaptation-related Gene Ontology (GO) terms. Most CNVR genes were significantly enriched for specific biological functions; signaling pathways, sensory responses to stimuli, and various cellular processes. In addition, QTL analysis of CNVRs described them to be linked with economically essential traits in cattle. The findings here provide crucial information for constructing a more comprehensive CNVR map for the indigenous cattle genome. [ABSTRACT FROM AUTHOR]

Natural fibers derived from diverse animal species have gained increased attention in recent years due to their favorable environmental effects, long‐term sustainability benefits, and remarkable physical and mechanical properties that make them valuable raw materials used for textile and non‐textile production. Domestication and selective breeding for the economically significant fiber traits play an imperative role in shaping the genomes and, thus, positively impact the overall productivity of the various fiber‐producing species. These selection pressures leave unique footprints on the genome due to alteration in the allelic frequencies at specific loci, characterizing selective sweeps. Recent advances in genomics have enabled the discovery of selection signatures across the genome using a variety of methods. The increased demand for 'green products' manufactured from natural fibers necessitates a detailed investigation of the genomes of the various fiber‐producing plant and animal species to identify the candidate genes associated with important fiber attributes such as fiber diameter/fineness, color, length, and strength, among others. The objective of this review is to present a comprehensive overview of the concept of selection signature and selective sweeps, discuss the main methods used for its detection, and address the selection signature studies conducted so far in the diverse fiber‐producing animal species. [ABSTRACT FROM AUTHOR]

The present broad range of sheep phenotypic variation is the consequence of selection for various production characteristics such as wool, milk, meat, and natural adaptability to diverse situations. In the current study, the genomic data of 79 animals from three Indian sheep breeds (Changthangi, Deccani, and Garole) were explored to decipher regions under positive selection for various productive traits using various statistical tools. We found 61, 102 regions using Tajima's D, CLR and 58, 38, and 71 regions using FST, FLK, and hapFLK, respectively, under selective sweep. Significant candidate genes related to various important traits, such as KLHL for fibre diameter and the OMA1 gene for feed-induced thermogenesis in Changthangi, were identified. In addition, the SYCP2 and NAPAS3 genes were found to be associated with seasonal reproductivity, and BMPR1B for fertilization capacity in Garole. In a previous study, the HSPA6 gene (Garole) was found to be associated with thermo-tolerance in the Angus sheep breed. The outcomes discussed here provide a basis for detecting selective sweeps that underlie genetic variations of traits that have functional importance. [ABSTRACT FROM AUTHOR]

The present study was undertaken to identify the microRNAs (miRNAs) expressed in the mammary tissue of a bubaline heifer. Small RNAs were isolated from the mammary gland tissue and enriched for miRNA fraction. The linker-ligated small RNAs were reverse transcribed to synthesize cDNA and amplified by PCR. The PCR products were ligated to the pGEM-T Easy vector; cloned into DH5 alpha cells and sequenced. Sequencing of 40 clones, randomly chosen from this library, produced 115 concatemerized short sequences. The short sequences were checked for their matches with the help of refseq_rna database, EST database (NCBI) and Ensembl. The analysis was performed for more than 90% identity with miRNAs across different species in miRBase. Alignment of putative small RNA sequences with the bovine genome was attempted in GenBank (NCBI) and Ensembl using BLAST. The small RNA sequences with a partial matches within the bovine genome and/or with flanking sequences (upstream or downstream) were analyzed for hairpin structures using the Mfold web server. Reverse complements were also assessed for the homology search. miRNA sequences showing only a partial match with already reported sequences were considered as a putative bubaline miRNAs. Six developmentally important putative miRNA precursors were identified from this study using cloning and sequencing followed by the Bioinformatics approach. This study will help in the elucidation of pathways involving miRNAs in bubaline species at the heifer stage. [ABSTRACT FROM AUTHOR]

• "Inter-calving intervals reflect cattle reproductive capacity, influencing the sustainability of livestock production through impacts on lactation dynamics." • "Identification of numerous Quantitative Trait Loci (QTLs) associated with reproductive phenotypes in dairy cattle offers valuable insights for enhancing breeding strategies and genetic selection." • "Studying QTLs linked to reproductive traits not only informs livestock breeding practices but also contributes to advancements in biotechnology and broader fields like human health and conservation." From an economic standpoint, reproductive characteristics are fundamental for sustainable production, particularly for monotocous livestock like cattle. A longer inter-calving interval is indicative of low reproductive capacity. This issue changes the dynamics of current and future lactations since it necessitates more inseminations, veterinary care, and hormone interventions. Various reproductive phenotypes, including ovulation, mating, fertility, pregnancy, embryonic growth, and calving-related traits, are observed in dairy cattle, and these traits have been associated with several QTLs. Calving ease, age at puberty, scrotal circumference, and inseminations per conception have been associated with 4437, 10623, 10498, and 2476 Quantitative Trait Loci (QTLs), respectively. This data offers valuable insights into enhancing and comprehending reproductive traits in livestock breeding. Studying QTLs associated with reproductive traits has far-reaching implications across various fields, from agriculture and animal husbandry to human health, evolutionary biology, and conservation. It provides the foundation for informed breeding practices, advances in biotechnology, and a deeper understanding of the genetic underpinnings of reproduction. [ABSTRACT FROM AUTHOR]

Knowledge about genetic diversity is very essential for the management and sustainable utilization of livestock genetic resources. In this study, we presented a comprehensive genome-wide analysis of genetic diversity, ROH, inbreeding, linkage disequilibrium, effective population size and haplotype block structure in Tharparkar cattle of India. A total of 24 Tharparkar animals used in this study were genotyped with Illumina BovineSNP50 array. After quality control, 22,825 biallelic SNPs were retained, which were in HWE, MAF > 0.05 and genotyping rate >90%. The overall mean observed (HO) and expected heterozygosity (HE) were 0.339 ± 0.156 and 0.325 ± 0.129, respectively. The average minor allele frequency was 0.234 with a standard deviation of ± 0.131. We identified a total of 1832 ROH segments and the highest autosomal coverage of 13.87% was observed on chromosome 23. The genomic inbreeding coefficients estimates by FROH, FHOM, FGRM and FUNI were 0.0589, 0.0215, 0.0532 and 0.0160 respectively. The overall mean linkage disequilibrium (LD) for a total of 133,532 pairwise SNPs measured by D' and r2 was 0.6452 and 0.1339, respectively. In addition, we observed a gradual decline in effective population size over the past generations. [ABSTRACT FROM AUTHOR]

The analysis of genetic diversity is very essential to understand the evolution and adaptability of livestock species to different environmental conditions. Genetic variation is the raw material for selection and foundation for breed improvement programmes. The use of high throughput molecular marker technologies, advanced statistical and software tools have revolutionized the precision of animal genetic diversity analysis in a large number of populations with limited time and resources. SNP genotyping is one of the best methods to study genetic variation due to its abundance in livestock species, stability and cost-effectiveness. In this review, some of the most popularly used diversity analysis software programs in livestock genomics are discussed briefly. Microsatellite-based software such as Genepop, Fstat, Genetix, TFPGA, Stackpack, Arlequin and other multipurpose software such as PLINK, PowerMarker, TASSEL, BEAGLE, R software packages (GenABEL, SNPassoc, snpstats, SNP relate), Gemma, SNP Express, SVS, etc. can be utilized for diversity analysis. [ABSTRACT FROM AUTHOR]

In spite of increase in milk production, dairy farmers suffer huge economic losses due to mastitis even in very well organized and modern farms. It has been observed that with the increase in the ability of milk production, dairy animals become more susceptible to mastitis. One of the most common causes of mastitis is infection of the mammary gland caused by bacteria like Staphylococcus aureus and Escherichia coli responsible for invoking sub-clinical and clinical mastitis, respectively. The resistivity or susceptibility of species/breeds towards mastitis depends on mode and intensity of immune response to invading pathogens. Inflammation of the mammary tissue results in the release of several cytokines, among which release of interleukin 10 (IL-10) has been identified as an important cytokine for the control of immune response. The present study was undertaken to evaluate the level of IL-10 expression when Peripheral Blood Mononuclear Cells (PBMCs) isolated from Crossbred cattle, Tharparkar cattle and Murrah buffalo were stimulated by antigens obtained from Staphylococcus aureus and Escherichia coli. The results demonstrated deviations in the level of IL-10 expression among these breeds and species in response to the stimulation by the same dose of antigens. Abbreviation: CMT (California Mastitis Test); ELISA (Enzyme-Linked Immunosorbent Assay); LPS (Lipopolysaccharide); LTA (Lipoteichoic acid); PBMCs (Peripheral Blood Mononuclear cells); PGN (Peptidoglycan); SCC (Somatic Cell Count) [ABSTRACT FROM AUTHOR]

Domestication and selection are the major driving forces responsible for the determinative genetic variability in livestock. These selection patterns create unique genetic signatures within the genome. BovineSNP50 chip data from 236 animals (seven indicine and five taurine cattle breeds) were analyzed in the present study. We implemented three complementary approaches viz. iHS (Integrated haplotype score), ROH (Runs of homozygosity), and F ST , to detect selection signatures. A total of 179, 56, and 231 regions revealed 518, 277, and 267 candidate genes identified by iHS, ROH, and F ST methods, respectively. We found several candidate genes (e.g., NCR3 , ARID5A , HIST1H2BN , DEFB4 , DEFB7 , HSPA1L , HSPA1B, and DNAJB4) related to production traits and the adaptation of indigenous breeds to local environmental constraints such as heat stress and disease susceptibility. However, further studies are warranted to refine the findings using a larger sample size, whole-genome sequencing, and/or high density genotyping. • The combination of various statistical approaches could facilitate the wider spectrum of detection of both recent and ancient selection signatures. • The identified candidate genes provide insights into the adaptation and production performance of various cattle breeds. • Our observations can provide valuable knowledge for GWAS, genomic selection, implementing breeding schemes and conservation programmes. [ABSTRACT FROM AUTHOR]

In the present study, to analyze the genomic ROH fragments, haplotypes, inbreeding coefficient and effective population size (Ne), SNP50K data of 72 Vrindavani crossbred cattle strain were obtained. After a quality check, 24,449 biallelic SNPs were retained, which were in HWE, MAF > 0.01 and genotyping rate >95%. A total of 385 ROH were found, and chromosome 25 was mostly covered with 50.86%, while chromosome one was least with 12.42%. We classified ROH into <10Mb, 10-15Mb, 15-20Mb, >20Mb categories and observed a 3% inbreeding coefficient for the population in >20Mb category. Inbreeding from an excess of homozygosity was found to be 6% in the population. Ne was also estimated through Ne Estimator and SNeP and in the recent generation, it was found to be 40 for a census size of 464 cattle. The Ne/Nc ratio was found to be 0.086 and a decreasing trend of Ne was observed for over five generations. 45.95% of the autosomal genome was covered with haplotypic structure with highest total block length in chromosome one and lowest in 28. From all the observations made in this study, it can be concluded that Vrindavani is an admixed cattle strain but have an unstable population structure in the current period. [ABSTRACT FROM AUTHOR]

Single nucleotide polymorphisms (SNPs) have now replaced microsatellite markers in several species for various genetic investigations like parentage assignment, genetic breed composition, assessment for individuality and, most popularly, as a useful tool in genomic selection. However, such a resource, which can offer to assist breed identification in a cost-effective manner is still not explored in cattle breeding programs. In our study, we have tried to describe methods for reducing the number of SNPs to develop a breed-specific panel. We have used SNP data from Dryad open public access repository. Starting from a global dataset of 178 animals belonging to 10 different breeds, we selected five panels each comprising of similar number of SNPs using different methods i.e., Delta, Pairwise Wright's FST, informativeness for assignment, frequent item feature selection (FIFS) and minor allele frequency–linkage disequilibrium (MAF-LD) based method. MAF-LD based method has been recently developed by us for construction of breed-specific SNP panels. The STRUCTURE software analysis of MAF-LD based method showed appropriate clustering in comparison to other panels. Later, the panel of 591 breed-specific SNPs was called to their respective breeds using Venny 2.1.0 and UGent web tools software. Breed-specific SNPs were later annotated by using various Bioinformatics softwares. [ABSTRACT FROM AUTHOR]

The present study was aimed at genetic characterization and diversity analysis of Pandharpuri buffalo population using the Food and Agriculture Organization (FAO) recommended bovine microsatellite markers. Genomic DNA was isolated from blood samples of 50 unrelated animals and a total of 23 microsatellite loci were amplified using polymerase chain reaction. Among 23 recommended microsatellite markers, 14 markers (BM2113, BM1818, CSSM66, HEL13, INRA037, ILSTS05, HAUT27, INRA023, INRA035, HEL5, ETH3, NRA063, MM12 and ETH10) were found to be highly polymorphic in Pandharpuri population. The amplified products were run on polyacrylamide gel electrophoresis (PAGE) apparatus along with a ladder; subsequently, the allele typing was done based on silver staining of the gel. The effective and observed number of alleles, heterozygosity (expected and unbiased) estimates and polymorphic information content (PIC) levels were estimated for each locus. A total of 87 alleles were secured for 14 polymorphic loci studied giving an overall average of 6.21 alleles per locus. The number of alleles ranged from 2 (INRA063) to 9 (BM1818 and HEL13). The mean effective number of alleles across all polymorphic loci was found to be 4.28. The overall mean expected heterozygosity and unbiased expected heterozygosity values were 0.77 and 0.76, ranging from 0.50 (INRA063) to 0.88 (BM1818) and 0.50 (INRA063) to 0.88 (BM1818), respectively. The average PIC estimate across all polymorphic loci was 0.73 ranging from 0.373 (INRA063) to 0.864 (BM1818). In the present study, the characterization and diversity estimates are reported for Pandharpuri population. It was found to maintain optimum diversity based on 14 polymorphic microsatellite markers. [ABSTRACT FROM AUTHOR]

The present study aimed to evaluate the efficiency of two Bovine SNP genotyping arrays (i.e., 50 K and HD) for breed clustering and stratification related studies in taurine and indicine breeds. The whole-genome SNP data at two densities were assembled into three datasets (A, B and C). Dataset A (N = 213) included 50 K genotypic data for five taurine (Holstein–Friesian, Guernsey, Brown Swiss, Angus and Jersey) and two indicine (Gir and Nellore) breeds. Dataset B (N = 241) included the same breeds with HD density data. Dataset C (N = 299) included 50 K SNP genotypic data for six taurine (Holstein–Friesian, Jersey, Guernsey, Brown Swiss, Angus and Hereford) and six indicine (Hariana, Kankrej, Brahman, Nellore, Sahiwal and Gir) breeds. The analysis was done using ADMIXTURE program (bioinformatics-based) and cross-validation errors and Principal Component Analysis (statistical analysis). The proportion of polymorphic markers and minor allele frequencies were assessed for each breed. The proportion of markers polymorphic was consistently higher in taurine breeds when compared with breeds from indicine group. Minor allele frequency estimates and ADMIXTURE results showed differential patterns for both the lineages. However, no significant increase in the accuracy of genomic clustering was found on moving from 50 K to HD density data. [ABSTRACT FROM AUTHOR]

The aim of the present study was to assess the population structure and admixture levels in the Vrindavani composite population in India by using Bovine50KSNP BeadChip data. Genotypic data were generated for randomly selected animals (n = 72) of Vrindavani population and the data for parental breeds i.e., Hariana (n = 10), Holstein-Friesian (n = 63), Jersey (n = 28) and Brown Swiss (n = 22) were retrieved from a public repository. The indices of population structure were calculated using PLINK software and R-program. The merged dataset was analysed for assessing admixture levels and population stratification using three different approaches i.e., principal component analysis (PCA), multi-dimensional scaling (MDS) approach and the model-based approach in STRUCTURE software. The average minor allele frequency (MAF) value for Vrindavani population was estimated to be 0.235. Vrindavani population was found to possess an average ancestry of 39.5, 22.9, 26.9, and 10.7% inheritance levels from Holstein Friesian, Jersey, Hariana and Brown Swiss cattle breeds, respectively. • We have got evidence of optimum applicability of Bovine 50 K SNP BeadChip data on crossbred population for admixture study • Admixture levels in Vrindavani crossbred population were calculated for the first time in the Indian context • The basic information generated in our study will help for characterization of other similar crossbreds of the country [ABSTRACT FROM AUTHOR]

The cost of SNP genotyping to screen different breeds and to estimate the exact proportion of ancestry level is quite high, which can be compensated through deriving a small panel of ancestry informative markers (AIMs). Hence, we carried out the present study to provide an insight into ancestry level inferred from a panel of informative markers in the crossbred Vrindavani population developed at ICAR-IVRI, India. We have performed a new method i.e., discriminant analysis of principal components (DAPC) for the first time on the dataset of Vrindavani cattle. To confirm our method, we had performed DAPC on two other well-known crossbred cattle, i.e., Frieswal and Beefmaster. Three sets of panels (500, 1000 and 2000 markers) were tested for clustering of individuals. Among all the panels, we found the panel (1000 markers) with DAPC based contribution method was of the smallest size and comparatively of the highest accuracy. • The present study was carried out to infer ancestry level from a panel of informative markers in the crossbred population • The 1000 markers panel selected through DAPC based contribution method was the smallest and comparatively accurate • The information generated in our study will pave the way for characterization of other crossbreds available in the country [ABSTRACT FROM AUTHOR]

The present study was aimed to assess parameters related to genetic diversity, population structure and admixture in the Frieswal crossbred cattle of India. A total of three datasets were analyzed during this study. Dataset A (n = 80) consisted of data on two purebred populations, i.e., Shorthorn (n = 35) and Brahman (n = 25) and one crossbred strain Santa Gertrudis (n = 20). The dataset B (n = 71) consisted of data on three populations that included Holstein-Friesian (n = 30), Sahiwal (n = 27) and Frieswal (n = 14) cattle. The dataset C included data on all the six breeds under study. Dataset C was used to assess the indices of population structure and genetic diversity of different breeds prior to and after LD pruning. For Frieswal cattle strain, the proportion of polymorphic SNPs and MAF levels was 84.54% and 0.24, respectively. Frieswal strain maintained appreciable genetic diversity with observed heterozygosity measure of 0.414. PCA plots for three datasets depicted effective stratification of different breeds in the respective datasets. The genomic clustering levels of Sahiwal and Holstein-Friesian were found to be 98.45 and 99.89%, respectively, while the admixture of Frieswal was estimated to be about 61.5 and 38.5% from Holstein-Friesian and Sahiwal breeds, respectively. [ABSTRACT FROM AUTHOR]

Subclinical mastitis, generally caused by Staphylococcus aureus, has a global economic impact all over the world. Hence, it needs to be resolved on higher priority which may be attained via. selection of mastitis resistant animals or inclusion of mastitis resistant trait into herd apart from management care. Diverse hosts with various genetic make-ups encounter pathogens in a diverse manner which in turn leads to contradicting outcome of the disease. Identification of species-wise or breed-wise differential expressed genes in response to S. aureus through relative evaluation of transcripts may be useful for judging the immuno-competency of a species or breed toward mastitis. The present study was undertaken to examine the stimulant effect of S. aureus peptidoglycan (PGN) and lipoteichoic acid (LTA) on Peripheral blood mononuclear cells (PBMC) harvested from blood samples of crossbred cattle, Tharparkar cattle, and Murrah buffaloes. After 6 h of in vitro stimulation qRT-PCR was used to measure the relative mRNA expression of TLR-2, TNF-α, IL-8, IFN-γ and IL-10 genes in stimulated and un-stimulated PBMC. The selected genes revealed significant differences in the pattern of immune response among crossbred cattle, Tharparkar cattle and Murrah buffalo in spite of the same stimulant dose. [ABSTRACT FROM AUTHOR]

Contents: Progesterone (P4) plays a key role in the establishment and maintenance of pregnancy in most mammals. Unravelling the expression of progesterone‐regulated genes can expand the understanding of the embryonic mortality. Accordingly, we studied the relative mRNA expression of the P4‐regulated genes in the buffalo. Uteri were collected from the abattoir and categorized into nonpregnant late luteal phase, stage I (28–38th days of gestation) and stage II (48–56th days of gestation) of pregnancy (n = 6/group). After extraction of total RNA from the endometrial tissues, we carried out qRT‐PCR for determining the relative mRNA expression of the P4‐regulated genes using nonpregnant late luteal phase as calibrator group. The expression of LGALS3BP (essential for maternal recognition of pregnancy) gene was found to be significantly upregulated (p < 0.05), while MUC1 (important for embryo attachment) gene was downregulated in stage I and II of pregnancy. We observed no significant change in the expression of LGALS1, LGALS9 and CTSL genes. The SLC5A11 and SLC2A1 genes (involved in the transport of glucose to endometrium) in early pregnancy were upregulated in the pregnancy stage I (p < 0.05) relative to nonpregnant late luteal phase. The CST3 gene was significantly upregulated in pregnancy stage II (p < 0.01). These results provide molecular insights into the specific pathways involved in foeto‐maternal communication during early pregnancy in buffaloes. [ABSTRACT FROM AUTHOR]

Molecular level information related to buffalo (Bubalus bubalis) reproduction and related genes is not present at appropriate level. If such exploration is made in the form of comparison between expression of genes is made between non-pregnant and pregnant phase, it may be helpful to aid manipulate the reproduction. Hence, the present study was carried out to reveal mRNA quantitative real time expression of oxytocin receptor (OTR) mRNA. IFN-τ is considered as the substance of maternal recognition of pregnancy and shut down the probable mechanisms which lead to luteolysis. Such mechanism includes shutting down of OTR. Therefore, relative expression of OTR was studied in endometrial tissue of three groups. The groups were non-pregnant late luteal phase, pregnancy stage I (pregnancy of <42 days) and pregnancy stage II (>42 days of pregnancy). With designed primer and GAPDH as house-keeping gene, relative mRNA expression was measured in Real-time PCR. After statistical analysis of results, the gene found to be expressed in all three stages with non-significant difference. [ABSTRACT FROM AUTHOR]

Tribolium castaneum is a small and low maintenance beetle that has emerged as a most suitable insect model for studying developmental biology and functional genetic analysis. Diverse population genetic studies have been conducted using Tribolium as the principal model to establish basic facts and principles of inbreeding experiments and response to the selection and other quantitative genetics fundamentals. The advanced molecular genetic studies presently focused on the use of Tribolium as a typical invertebrate model for higher diploid eukaryotes. After a whole genome sequencing of Tribolium, many areas of functional genomics were unraveled, which enabled the use of it in many technical approaches of genomics. The present text reviews the use of Tribolium in techniques such as RNAi, transgenic studies, immune priming, immunohistochemistry, in situ hybridization, gene sequencing for characterization of microRNAs, and gene editing using engineered endonuclease. In contrast to Drosophila, the T. castaneum holds a robust systemic RNAi response, which makes it an excellent model for comparative functional genetic studies. [ABSTRACT FROM AUTHOR]

Prostaglandins (PGs) are the key mediators of several female reproductive functions, including luteolysis, ovulation, fertilization, implantation, pregnancy, and parturition. The present study was conducted in buffalo endometrial and luteal tissues between nonpregnant and two stages of pregnancy (29–38 days of pregnancy, 48–56 days of pregnancy) tissue samples. The genes involved from synthesis upto receptor level effect of PGs (PGF 2α and PGE 2 ) were studied for their relative mRNA expression. We have collected the endometrial and luteal tissues from slaughtered animals and confirmed the stages by external examination and crown vertebral rump length measurement of the foetus. The mRNA expression of COX-2 and PGFS genes revealed high significant rise in the transcript at pregnancy stage I as compared to the late luteal phase of nonpregnant. However, EP2 and EP3 genes were highly upregulated in pregnancy stage II. The expression of PLA2G4A and PGT genes showed difference in their transcripts in pregnancy, however, the difference was nonsignificant as compared to the nonpregnant stage. The findings emerged from this study also suggested the strict regulation at COX-2 mRNA level than at synthase enzyme's level. Among the four subtypes of EP gene, we have observed highly significant expression difference in EP2 followed by EP3 after implantation. [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]

• The review covers livestock genomics of South Asian cattle, buffalo, sheep, goat, pig, camel, horse, yak, mithun, and poultry. • Advancements in next-generation sequencing (NGS) technologies led to the discovery of numerous SNP arrays for different livestock species. • The application of genomics in animal breeding has had the biggest economic impact on livestock production. Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements. [ABSTRACT FROM AUTHOR]

[Display omitted] • The availability of genomic data enables a very rapid global follow-up of COVID-19 progression. • Genomic surveillance integrates epidemiological and genomic data to track SARS-CoV-2 variants and their spread. • Genomics plays a significant role in the development of molecular diagnostics, therapeutics, and vaccine candidates. The coronavirus disease 2019 (COVID-19) quickly swept over the world, becoming one of the most devastating outbreaks in human history. Being the first pandemic in the post-genomic era, advancements in genomics contributed significantly to scientific understanding and public health response to COVID-19. Genomic technologies have been employed by researchers all over the world to better understand the biology of SARS-CoV-2 and its origin, genomic diversity, and evolution. Worldwide genomic resources have greatly aided in the investigation of the COVID-19 pandemic. The pandemic has ushered in a new era of genomic surveillance, wherein scientists are tracking the changes of the SARS-CoV-2 genome in real-time at the international and national levels. Availability of genomic and proteomic information enables the rapid development of molecular diagnostics and therapeutics. The advent of high-throughput sequencing and genome editing technologies led to the development of modern vaccines. We briefly discuss the impact of genomics in the ongoing COVID-19 pandemic in this review. [ABSTRACT FROM AUTHOR]

The bovine TLR4 gene is an interesting candidate marker for mastitis resistance, since it is involved in neutrophil migration to and from the mammary gland during mastitis. TLR4 detects pathogen ligands, such as the Escherichia coli lipopolysaccharide (LPS) endotoxin and facilitates innate and adaptive immune responses. In the current study, a total of 130 crossbred cows (74 mastitis tolerant and 56 with clinical mastitis) kept at the Cattle and Buffalo Farm, IVRI, Izatnagar, were selected to explore the polymorphism in the co-receptor binding region 2 (CRBR2) fragment of the TLR4 gene. PCR-SSCP and sequence analysis showed two genotypes of the TLR4 gene's CRBR2 fragment, AA and AB, which were polymorphic in both the afflicted and tolerant groups. Sequencing revealed eight single nucleotide polymorphisms (SNPs) in allele A and ten SNPs in allele B. This genotype had no significant effect on the incidence of clinical mastitis according to the logistic regression model. Our study found insufficient evidence linking SNP variants in the CRBR2 region of the TLR4 gene to mastitis susceptibility in crossbred cattle. • A total of 130 crossbred cows were selected to explore the polymorphism in the CRBR2 fragment of the TLR4 gene. • No link found between the genotypes in the CRBR2 region of the TLR4 gene and clinical mastitis in crossbred cattle. • Sequencing results revealed eight single nucleotide polymorphisms (SNPs) in allele A and ten SNPs in allele B. [ABSTRACT FROM AUTHOR]

• We merged extracted datasets of 11 cattle breeds with our own generated Tharparkar genotypic data to obtain a final dataset of 284 animals. • The PCA indicates the partitioning between Exotic and Indigenous cattle breeds on the two PC axis. • We used several statistical tools (eight) to find out and verify more genomic footprints. • More number of short ROHs in Tharparkar shows a more historical relationship. • Combined analysis of all the methods may provide refined information about selective sweep regions in different methods. • We extracted out various candidate genes associated with economically important traits. In the present study, the population genomic data of different cattle breeds were explored to decipher the genomic regions affected due to selective events and reflected in the productive, reproductive, thermo-tolerance, and health-related traits. To find out these genomic deviations due to selective sweeps, we used eight different statistical tools (Tajima's D, Fu & Li's D*, CLR, ROH, iHS, F ST , FLK, and hapFLK) on seven indigenous and five exotic cattle breeds. We further performed composite analysis by comparing their covariance matrix. Several candidate genes were found to be related to milk production (ADARB, WDR70, and CA8), reproductive (PARN, FAM134B2, and ZBTB20), and health-related traits (SP110, CXCL2, CLXCL3 , CXCL5 , IRF8, and MYOM1). The outcome of this investigation provides a basis for detecting selective sweeps that explain the genetic variation of traits. They may possess functional importance for multiple cattle breeds in different subcontinents. However, further studies are required to improve the findings using high-density arrays or whole-genome sequencing with higher resolution and greater sample sizes. [ABSTRACT FROM AUTHOR]

Crossbred cattle are more prone to mastitis in comparison to indigenous cattle. Toll-like receptor 4 (TLR4) recognizes pathogen ligands, for example, lipopolysaccharide (LPS) endotoxin fromEscherichia coliand mediates signaling to initiate innate and adaptive immune responses. Mutations in TLR4 can compromise the host immune response to certain pathogens, so it may be a potential candidate for marker assisted selection to enhance mastitis resistance in dairy cattle. Hence, in this study role of bovine TLR4 gene in mastitis resistance was investigated by association as well as expression profiling analysis in crossbred cattle. The animals were divided into mastitis affected and unaffected groups on the basis of history of animals and California Mastitis Test (CMT). PCR-SSCP and Sequence analysis revealed three genotypes of coreceptor binding region 1 (CRBR1) fragment of TLR4 gene namely AA, AB, and BB in both groups of cattle. The logistic regression model did not show any significant effect of these genotypes on the occurrence of clinical mastitis. Moreover, in vitro challenge of peripheral blood mononuclear cells (PBMCs) with LPS failed to show any association of the genotypes with TLR4 gene expression. In a nutshell, in the present study enough evidence was not found for association of the SNP variants of CRBR1 fragment of TLR4 gene with mastitis susceptibility in crossbred cattle. [ABSTRACT FROM PUBLISHER]

• Very few SNPs, when accurately selected, were sufficient to discriminate among the eight sheep breeds. • MAF-LD methodology unambiguously determines breed purity without pedigree data. • Breed-specific SNPs panels identified for three Indian sheep breeds. Recently DNA-based genetic purity determination tools have gained popularity, especially, in small ruminants like sheep. The objective of the present study was to select breed-specific SNPs for the three commercially important sheep breeds of India, i.e., Changthangi, Deccani, and Garole. Sheep genotype data (Ovine 50 K SNP array) from 344 individuals of eight sheep breeds (Garole, Deccani, Changthangi, Tibetan, Australian Merino, Dorset Horn, Rambouillet, and Irish Suffolk) were used as a reference population. Here, we used pre-selection statistics and the minor allele frequency–linkage disequilibrium (MAF-LD) method to analyze the reference population dataset. SNPs selection and breed assignment was executed with a panel of 768 markers for eight breeds near intermediate gene frequencies. We identified 95, 89, and 92 breed-specific SNPs for Changthangi, Deccani, and Garole, respectively. These informative SNPs were found to be associated with essential candidate genes associated with production and disease resistance. This methodology may be implemented in practice to identify individuals as being purebred or not. [ABSTRACT FROM AUTHOR]

With more and more Single Nucleotide Polymorphisms (SNPs) being identified throughout the genome, some of those SNPs will be found to be located within candidate genes, allowing the researchers to use the candidate gene approach on a genomewide scale. SNPs have some drawbacks but when compared to other markers they are more efficient and SNP consortium is growing to meet the requirements of genome-wide scans. Genomic selection should be able to at least double the rate of genetic gain in the dairy industry but the incorporation of genomic information into the breeding programs must be carefully considered. One needs to have around 2000 genotypes means a large reference population (population with both phenotype and genotype recorded) to achieve meaningful increases in accuracy. The available information, selection objectives, production circumstances and benefit/cost analysis must be evaluated in order to decide whether or not the population is suitable for GS implementation, and which would be the most convenient way, if any, for its implementation. Animal breeders will need to lead the way on the integration of genomic and phenotypic data into a new era of genome-enabled animal improvement and management. [ABSTRACT FROM AUTHOR]

• We have identified genes by GWAS which are involved in well-established MAPK and PI3K-AKT signalling pathways, affecting biochemical process of coat colour production. • Due to introduction of exotic blood to continue the process of development of Vrindavani cattle, a very low F ST value was observed suggesting outbreeding of the population. • This work provides a preliminary information to carry forward researches on genomic basis of coat colour patterns in crossbred cattle Coat colour and various patterns are the hallmarked qualitative traits studied in cattle as well as other livestock; however, variation in this trait is resultant of interactions and epistasis of a set of genes rather than being a product of a single gene. In this study, GWAS has been conducted from 50K SNP genotype data, with a stratified approach on Vrindavani cattle (n=48). The study was conducted in two sets of an experiment wherein set I treats all the solid colours (n=18) as controls and rest spotted or patchy types as cases (n=30), and set II treats brown and brown with white spots as controls (n=15), and rest as cases (n=33). After quality check (MAF>0.01, genotyping rate>90%, and H-W equilibrium at p≤ 0.001) of genotype data, 37247 SNPs were further used for accomplishing Genome-Wide Association Study (GWAS) with coat colour. The distinct phenotypes were classified into four different sub-groups that are solid black, black with white patches, solid brown, and brown with white patches along with greyish white. The allele frequency difference was checked in all sub-groups. The GWAS was conducted in PLINK v1.7 and for graphical representation R was used. Two SNPs in set I and 20 in set II were found to be significantly associated with coat colour in Vrindavani cattle. A ±500 Kb genome scan around the significant SNPs revealed gene BDNF for SNP DIAS-217 in set I and FGF18 for SNP ARS-BFGL-NGS-105192, and CACNA2D1 , and HGF for SNP BTB-01885061 in set II, are present around these SNPs. In KEGG-based pathway enrichment analysis, all the above-mentioned genes were found to be involved in well-established MAPK and PI3K-AKT signalling pathways, affecting the biochemical process of coat colour production. Genome-wide F ST values were low to moderate across the genome, however few associated SNPs had moderate to high F ST values indicating their power in differentiating the subgroups according to coat colour phenotype. This study provides a preliminary report of markers and genes involved in coat colour expression and revealed that the reported genes around the associated SNPs are involved in brown with white spotting phenotype. However, further researches in this field are essential for a more conclusive result. [ABSTRACT FROM AUTHOR]

• Combination of MAF-LD with Delta, F ST & FIFS methods enabled the selection of SNPs for breed purity. • 582 SNPs accurately assigned individuals to their respective breeds. • 63 Tharparkar-specific SNPs annotate to candidate genes of important phenotypic traits. Tharparkar cattle breed is widely known for its superior milch quality and hardiness attributes. This study aimed to develop an ultra-low density breed-specific single nucleotide polymorphism (SNP) genotype panel to accurately quantify Tharparkar populations in biological samples. In this study, we selected and genotyped 72 Tharparkar animals randomly from Cattle & Buffalo Farm of IVRI, India. This Bovine SNP50 BeadChip genotypic datum was merged with the online data from six indigenous cattle breeds and five taurine breeds. Here, we used a combination of pre-selection statistics and the MAF-LD method developed in our laboratory to analyze the genotypic data obtained from 317 individuals of 12 distinct breeds to identify breed-informative SNPs for the selection of Tharparkar cattle. This methodology identified 63 unique Tharparkar-specific SNPs near intermediate gene frequencies. We report several informative SNPs in genes/QTL regions affecting phenotypes or production traits that might differentiate the Tharparkar breed. [ABSTRACT FROM AUTHOR]

• The natural and artificial selection are expected to impose pressure on specific genomic regions and leave footprints called as "selection signatures" • We identified selective sweep regions based on Runs of Homozygosity (ROH) and Integrated Haplotype Score (iHS) • Highlighted candidate genes related to adaptation and production traits Knowledge about genetic diversity and selection signatures are very essential for the management and sustainable utilization of sheep genetic resources in India. In this study, we performed a comprehensive genome-wide analysis of genetic diversity and selection signatures using SNP data. A total of 79 animals from three Indian sheep breeds: Changthangi (n = 29), Deccani (n = 24), and Garole (n = 26) genotyped with Illumina Ovine SNP50 BeadChip were included in this study. The average minor allele frequency was 0.284 with a standard deviation of 0.129. The overall mean observed (H O) and expected heterozygosity (H E) were 0.369±0.141 and 0.373±0.118, respectively. The proportion of polymorphic SNPs (P N) ranged from 0.84 (Garole) to 0.93 (Changthangi). The average pairwise genetic distance (D) ranged from 0.301 (Garole) to 0.313 (Changthangi). We identified a total of 9244 ROH segments and the genomic inbreeding coefficients ranged from 0.0673 (Deccani) to 0.1779 (Garole). Two different statistical approaches (ROH and iHS) revealed selection signatures in 37 genomic regions mapping to 188 genes across 16 of the 26 autosomes in three sheep breeds. The selective sweeps provide new insights into the local adaptation and production potential of three Indian sheep breeds. Some notable candidate genes include the TRPM8 gene involved in cold adaptation, JADE2, PLEKHB2, SPP2, TSHR, and UBE2B genes associated with meat quality traits, and the PPP3CA gene associated with fecundity. [ABSTRACT FROM AUTHOR]

• Owing to developments in high-throughput technologies, the genome-wide detection of selection signatures has become more common in recent years • Various statistical methods have been developed for the identification of selection signatures based on site frequency spectrum, linkage disequilibrium, reduced local variability, and population differentiation. • In future, the advanced Machine Learning enabled neural networks can also be applied in livestock populations to handle large &complex data sets efficiently and to improve the accuracy of detection of selection signals. • In this review, we have discussed the results of significant studies done in the recent years. Livestock populations have been consistently improving in terms of performance and productivity by selective breeding over the centuries. These selection strategies are expected to leave footprints in the genome that are identified as selection signatures. Due to advances in high-throughput technologies, the genome-wide detection of selection signatures has become more widespread in recent years. Such studies provide insights into the domestication and evolutionary processes that resulted in a huge number of livestock breeds able to live in diverse environments and production systems. Furthermore, these studies facilitate the identification of candidate genes under selection that are associated with economically important traits in livestock populations. Various statistical methods have been developed for the detection of selection signatures based on site frequency spectrum, linkage disequilibrium, reduced local variability, and population differentiation. The objectives of this review are to give a comprehensive overview of the general concept, various methodologies, and bioinformatics tools currently available for the detection of selective sweeps and to summarize the results of recent selection signature studies carried out in various livestock species. [ABSTRACT FROM AUTHOR]

Anthropozoonotic parasite Toxoplasma gondii causes widespread human and animal diseases, mostly involving central nervous system. Human acquires toxoplasmosis from cats, from consuming raw or undercooked meat and from vertical transmission to the fetus through placenta from mother during pregnancy. Socio-epidemiological as well as unique environmental factors also plays a significant role in transmission of this infection. Preventive measures should be taken into account the importance of culture, tradition, and beliefs of people in various communities more than solving poverty and giving health education. Therefore the focus of this article is to create public awareness regarding sense of responsibility of looking after pets to prevent such an important zoonotic disease. [ABSTRACT FROM AUTHOR]

Nanobiotechnology is an emerging field that is potentially changing the way we treat diseases through drug delivery and tissue engineering. Methods of targeting nanoparticles to specific sites of the body while avoiding capture by vital organs are major hurdles that need to be answered. Whether actual or perceived, the potential health hazards associated with the production, distribution and use of nanomaterial must be balanced by the overall benefit that nanobiotechnology has to offer biomedical science such as therapeutic and diagnostic applications. It would be difficult to deny the potential benefits of nanobiotechnology and stop development of research related to it since it has already begun to penetrate many different fields of research. However, nanobiotechnology can be developed using guidelines to insure that the technology does not become too potentially harmful. As Richard Feynmann has rightly predicted that "There is plenty of room at the bottom" to modify and enhance existing technologies by manipulating material properties at the nanoscale, therefore with sufficient time and research nanobiotechnology based early detection, diagnosis and treatment of various diseases may become a reality. Nanobiotechnology may bring immense paradigm shift that we would wonder that how did we live without it? [ABSTRACT FROM AUTHOR]

• Early pregnant buffalo endometrial transcriptome identifies 270 highly upregulated and 180 highly downregulated genes. • The most upregulated genes relate to the processes of transport, secretion and homeostasis. • The most downregulated genes relate to mitosis, neuronal development and negative regulation of viral processes. Buffalo reproduction struggles with a high incidence of early embryonic mortality. Effective treatment and prevention strategies for this condition are not available due to lack of understanding of molecular pathways in early pregnancy of this species. In the present study, we have attempted to understand these molecular pathways by characterizing the endometrial transcriptomic profiles of pregnant buffalos during early pregnancy. For the transcriptome profiling, buffalo endometrial tissues of 29–36 days of pregnancy and of nonpregnant luteal phase were collected from the local slaughterhouse. We confirmed the status of pregnancy based on the crown vertebral length of the foetus. Total RNA was isolated and sequencing was performed using the Illumina nextseq platform. The raw reads were filtered and mapped to the Bos taurus UMD 3.1 reference genome assembly. An average of 24,597 genes was investigated for differential expression between the two groups. Transcriptome data identified a total of 450 differentially expressed genes (using a cut off value of log 2 fold changes >2 and <−2) in early pregnancy in comparison to the nonpregnant group (P adj < 0.05). Among these, 270 genes were significantly upregulated and 180 genes were downregulated. The most impacted pathways were related to secretion, transport, ionic homeostasis, mitosis and negative regulation of viral processes. In conclusion, our study characterized a unique set of DEGs, during the early pregnancy of buffalo, which potentially modulate the endometrial environment to establish and maintain a successful pregnancy. [ABSTRACT FROM AUTHOR]

• Association of bovine MHC class I (BoLA-A) exons 2–3 and 4–5 allelic variants with immune response to B. abortus S19 is reported in the present study. • The association analysis of various BoLA-A alleles with the immune response revealed that calves with certain defined genotypes induced significantly higher cell-mediated immune responses in terms of lymphocyte proliferation, lymphocyte mediated cytotoxicity and nitrite production. • It is assumed that allelic variants of BoLA-A (exons 2–3 and 4–5) were associated with the differential immune response of calves to B. abortus S19 vaccination. In the present study, we analyzed the immune response of calves to Brucella abortus strain 19 vaccine (S19) and its association with MHC class I (BoLA-A) alleles (exons 2–3 and 4–5). Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used for typing of BoLA-A exon 2–3 with Dde I and Taq I restriction enzymes; and exon 4–5 with Hinf I in 45 crossbred calves. The PCR-RFLP analysis revealed five BoLA-A alleles each for exon 2–3 (A10/A19, A19, A18/19, A18 and A31) and exon 4–5 (A, B, C, D and E). Immune response against B. abortus S19 was assessed at the 4th week post vaccination; antibody response by standard tube agglutination test (STAT) and cell-mediated immunity by lymphocyte proliferation and lymphocyte-mediated cytotoxicity assays. Further, the macrophage function in terms of nitrite production was also analyzed. The association analysis of various BoLA-A alleles with the elicitation of immune response revealed that calves with certain defined genotypes induced significantly higher cell-mediated immune response in terms of lymphocyte proliferation with higher stimulation indices (S.I.) of 1.59 (BoLA-A19), 1.49 (A18/19) and 1.52 (Hinf I-D); lymphocyte mediated cytotoxicity (55.52 % in A19) and nitrite production (43.40 μM in A31). It is assumed that allelic variants of BoLA-A (exons 2–3 and 4–5) were associated with the differential immune response of calves to B. abortus S19 vaccination. Therefore, further studies on association analysis of MHC class-I genes in large number of cattle may generate more information and might be useful for adapting the alternative approach of exploring genetic resistance in the cattle herd against bovine brucellosis. [ABSTRACT FROM AUTHOR]

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]