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ThesisItem Open Access INHERITANCE OF LINEAR TYPE TRAITS AND THEIR ASSOCIATION WITH BEHAVIOURAL AND PERFORMANCE TRAITS IN CROSSBRED CATTLE(ICAR-NDRI, KARNAL, 2022) ISHMEET KUMAR; Sabyasachi MukherjeeKaran Fries is a prominent milch breed of India. In order to bring about genetic improvement in indigenous cross breeds of cattle, we must adopt a holistic and balanced approach to selection as well as to breeding strategies. Including linear type traits for dairy cattle selection in our indigenous cross-breed cattle is scanty. Therefore, the present study was taken up with the objective to determine inheritance in cross-breed cattle such as Karan Fries on the basis of linear type traits. Other objectives were to estimate genetic parameters of behavioral, functional, and linear type traits, and their association with production performance in Karan Fries cattle. Using multi-trait selection procedure. Data was collected on adult Karan Fries (N=134), from our Institute herd and was analysed by using both Least Square Maximum Likelihood (LSMLMW) and Bayesian methods, considering either a fixed effect or a mixed animal model for the present study. Parity, season, period of calving, and stage of lactation were taken as non-genetic factors, and age at first calving as coverable Sire or animal was considered a random variable. The leastsquares means of objective linear type traits viz., Stature was 131.43±0.96 cm, Body length 145.20±1.13 cm, Chest girth 181.97±1.25 cm, Body depth 209.98±1.90 cm, Rump angle 12.89±0.47 cm, Rump width 19.75±0.27 cm, Udder depth 25.61±0.54 cm, teat length 5.20±0.17 cm, and Rear udder height 22.27±0.49 cm. On the other hand, least square mean scores of subjective linear type traits. Angularity 38.89±0.55-degree, (1-9 scale) viz. The rear leg side view was 6.73±0.19, Rear leg rear view was 5.82±0.23 score, Foot angle 6.65±0.24, Fore udder attachment 6.17±0.3, Central ligament 5.16±0.29, Front teat placement 3.95±0.27, and Rear teat placement was 5.35±0.25. It was observed that Parity has a significant (p˂0.05/ p< 0.01) effect on Stature, Chest girth, Body length as well as Rear udder height, while Season of calving had a significant (p˂0.05) effect on Rump angle and Rear udder height. For Stage of Lactation Rear udder height, Angularity and Front teat placement come out to be Significant at (p˂0.01) in Karan Fries cattle. Most of the linear type traits, milking temperament, and milking speed were found to be low to moderately heritable (ranging from 0.40±0.03 to 0.25±0 04, while days open was having low heritability (0.20±0.25) Among linear type traits, stature, body length, and chest girth were having high positive genetic correlation (ranging from 0.74±0.03 to (0.63±0.017) with total milk yield. Rear leg rear view, Central ligament was having a negative phenotypic correlation with total milk yield (-0.018± 0.081 and -0.050±0.099) respectively. Twelve Karan Fries sires from the present data set were selected for evaluation and ranking. Sires with three or more progenies were considered for estimation of breeding values in the present study. Sires were ranked based on estimates of breeding value on the basis of multiple traits (stature, body length, chest girth, body depth, Angularity first lactation 305 days milk yield, and total milk yield) Association of ranking of sites based on multiple traits were estimated by Spearman's Rank Correlation. Correlation between rankings of sizes was checked, for multiple traits viz., stature, body length, chest girth, body depth, Angularity, first lactation 305 day’s milk yield, and total milk yield and significance was tested using a 1-test. Top-ranked sires were recommended for further breeding. Our study showed that Karan Fries cows may be selected on the basis of a few important linear type traits (stature, body length, chest girth, body depth, and angularity) having a positive genetic correlation with production performance. The present study may be continued to include a larger data set for validation and better accuracy of results for the selection of Karen Fries cattle.ThesisItem Open Access IDENTIFICATION OF DIVERSIFIED SELECTIVE SWEEPS USING HIGH DENSITY SNP ARRAY IN SAHIWAL CATTLE(ICAR-NDRI, KARNAL, 2022) YASER MUSHTAQ WANI; Anupama MukherjeeBoth natural and artificial selection have resulted in cattle breeds that are specialized for particular uses. Several specific genomic regions have been under selection pressure, and it is widely accepted that these genomic sequences, or selection signatures, control or affect key phenotypes that are involved in some traits. Positive selection pressure can reduce or even eliminate the frequency of negative alleles in the offspring’s genome. Therefore, selection signatures in a population could provide genomic information to facilitate selection and provide insights into evolutionary history. The estimation of the population structure and genetic relatedness between individuals is important for uncovering the demographic history of the population under study. We analyzed 735636 autosomal single nucleotide polymorphisms (SNPs) which were shared by 48 randomly sampled individuals to determine the genetic structure of Sahiwal herd. STRUCTURE reported maximum LnK (Mean of. Ln prob of data) at k=2 also confirmed by minimum ADMIXTURE cross validation error at same k value. Thus appropriate k value for Sahiwal herd is 2 indicating farm born animals and purchased animals. The effective population size was estimated to be 54 at one generation ago using GONE and 75 using SNeP 13 generations ago. Estimates from SNeP, built on equation, were lower than GONE estimates with the genetic algorithm both utilizing linkage disequilibrium data. In addition, the most rapid decline of population size was observed between 8 and 12 generations ago which suggests that the reduction in the population of Sahiwal cattle breeds began with herd formation at NDRI. We scanned the genome of Sahiwal cattle for selection signatures with 777 K SNP panel. A total of 284 extreme iHS values exceeded the empirical threshold level of 3 were calculated, with highest value at BTA 9 (iHS=4.26). Annotating the regions harboring clustered iHS signals revealed a panel of interesting candidate genes like NOL10,CXCL8,PDIA6, ATP6V1C2 and HPCAL1, in the context of Oxidative phosphorylation, IL-17 signaling, RIG-I-like receptor signaling and Synaptic vesicle cycle. The QTL present in iHS regions include Milk kappa-casein percentage, Milk yield, Milk fat percentage, luteal activity and clinical mastitis. By performing LASSI (Likelihood-based Approach for Selective Sweep Inference) a composite likelihood ratio statistic, we compiled a list of 561 selection sweeps described across 29 cattle autosome, which we subsequently grouped according to number of sweeping haplotype “m” with “m” = 1 indicating hard sweep (198) and “m”> 1 indicating soft sweep (363).For each selective sweep, we performed a candidate gene survey that identified 102 genes within the hard sweeps and 273 genes within soft sweeps regions. Genes identified were linked to milk fat yield, Immunoglobulin G level, Milk betalactoglobulin percentage and Milk protein yield in hard sweeps and Milk yield, triglyceride level, feed conversion ratio, age at first calving in soft sweeps. A complementary functional enrichment analysis of the selective sweep candidates highlighted other genes related to pathways underlying behavior, immune response, and reproductive traits.ThesisItem Open Access GENETIC EVALUATION OF PRODUCTION AND LIFETIME TRAITS IN MURRAH BUFFALO THROUGH BAYESIAN APPROACH(ICAR-NDRI, KARNAL, 2022) ASHISH YADAV; RAJA, K.N.The aim of the present study was to genetically evaluate Murrah buffaloes for various production traits recorded throughout their lifetimes. The study relied on lactation records of Murrah buffalo, maintained at the record room (AGB Division) of ICAR-NDRI, Karnal from the period 1971 to 2020. Through Bayesian analysis utilising the BLUPF90 family of programmes, genetic analysis was carried out using animal models with a combination of random factors, such as the direct additive genetic effect of the animal, the direct maternal genetic effect, and the maternal permanent environmental effect. Using the most appropriate models (based on DIC value) that account for direct and maternal influences fitted to the majority of the traits, (co)variance components and genetic parameters were estimated. The heritability estimates of FL305MY, TMY, LL, PY, PL and 305 MYAP in the most appropriate models were 0.49 ± 0.007, 0.20 ± 0.011, 0.04 ± 0.001, 0.10 ± 0.001, 0.10 ± 0.009 and 0.21 ± 0.003 respectively with repeatability estimates of TMY, LL, PY, and 305MYAP as 0.40, 0.20, 0.21 and 0.34. In comparison to the animal model with only additive genetic effects of the animal in each trait, lower error variance and higher additive variance were found for production and lifetime traits through various models based on partition of variance, indicating that it is crucial to use the best statistical model for elucidating genetic parameters that incorporate suitable random and fixed effects. The comparison of sires based on their breeding value (obtained from AIREML as well as the Bayesian approach) and ranking them, the correlation of which obtained using spearman’s rank correlation revealed that both approaches provide similar results as these all were normally distributed traits, with the best BV estimates for FL305MY, TMY, LL, PY, PL and 305 MYAP as 404.40, 415.99, 20.43, 1.39, 221.89 and 398.19 respectively using Bayesian approach. AIREML revealed estimates of BV of the given traits as 401.22, 409.02, 18.11, 1.37, 111.82, and 393.55. In terms of the accuracy of breeding values based on the standard error predicted, the Bayesian method provides a slightly better outcome with relative efficiency over the AIREML method as 0.73 %, 1.2 %, 7.2 %, 1.2 %, 42.94 %, and 0.78 % in respective traits. It is recommended to use the Bayesian method to estimate the breeding values of Murrah sires for production traits, which in turn can be used for ranking and selection of bulls.ThesisItem Open Access CRISPR/CAS9 MEDIATED EDITING OF COX-2 GENE IN LUTEAL CELLS OF BUFFALO(ICAR-SRS-NDRI, KARNAL, 2022) ARTHIYA K; D. N. DASThe domestic water buffalo (Bubalus bubalis) plays an important role in the economy of India as well as other developing countries in Asia by providing milk, meat and draught power and it has great unexploited production potential. One of the major constraints in the exploitation of the production potential of buffalo in comparison to cattle has been its inherently poorer reproductive efficiency that is mainly due to fertilization failure and early embryonic mortality. In many cases early embryonic mortality occurs because of luteal insufficiency. Corpus luteum plays a central role in maintenance of pregnancy, therefore it is necessary to prevent regression of CL for successful completion of pregnancy. One of the Prostaglandin (PG) i.e. PGF2α is the primary luteolysin in ruminants which causes regression of corpus luteum. The production of PGs is mainly governed by the rate limiting enzyme viz., cyclooxygenase-2 (COX-2) which is responsible for the conversion of arachidonic acid into PGH2, a common precursor of the various forms of PGs including PGF2α and PGE2. The present study was designed to examine the mRNA expression of edited COX-2 gene in the luteal cells of buffalo and it was undertaken with three objectives. Under objective 1: The CL tissues were assigned to consecutive stages viz., early, mid and late. Total RNA was isolated from these targeted tissue samples of early, mid and late stage. A total of six qRT-PCR experiments were conducted using corpus luteum samples. In this experiments, 5 samples of each stage were analysed keeping early stage as control. The qRT-PCR results revealed the mRNA expression of COX-2 in CL during the early luteal phase was higher followed by a continuous and significant downregulation afterwards. Under objective 2 and 3: Two single guide RNA against exon 1 were designed for COX-2 gene located at chromosome 5. The sgRNAs were successfully cloned into CRISPR/Cas9 plasmid vector separately and validated by PCR amplification using U6 primers. Analysis of sequence confirmed the cloning of sgRNAs into the vector. The resultant CRISPR/Cas9-sgRNA constructs were subsequently used for Lipofectamine mediated transfection into in-vitro cultured buffalo luteal cells. The cells transfected without CRISPR/Cas9-sgRNA construct was used as control. Puromycin was used for screening of the transfected cells. CRISPR/Cas9 tool was used for editing COX-2 gene using each sgRNA separately. Total RNA was isolated from the puromycin selected cells to investigate the effect of CRISPR/Cas9 mediated editing of COX-2 gene on its mRNA expression. The qRT-PCR results revealed the significant decline in COX-2 mRNA expression in the edited samples in comparison to the control. Genomic DNA extracted from the edited cell samples transfected with CRISPR/Cas9-sgRNA 1 construct along with control samples were subjected to PCR amplification using COX-2 gene specific primers. PCR amplified product was cloned using Topo TA cloning vector and the E. coli (DH5α strain) transformants were screened by ampicillin resistance. A total of 2 colonies were observed and plasmid DNA was isolated from these colonies. PCR amplification of plasmid DNA was performed using M13 primers. Out of the two colonies observed one was found to be positive clone. On the basis of above findings, it is concluded that the targeted editing of COX-2 gene significantly declined the mRNA expression of COX-2 gene in in-vitro cultured buffalo luteal cells.ThesisItem Open Access GENOMIC SIGNATURES OF MEAT TYPE GOAT BREEDS(ICAR-NDRI, KARNAL, 2022) RAVINA; S.P. DIXITNatural and artificial selections are known to fix certain genomic regions with reduced heterozygosity, which is a steping stone in the process of breed development. Comprehensive information on genetic variants viz genome-wide single nucleotide polymorphisms (SNPs) and INDELs, offers valuable genomic insights linked to key Kanniadu goat traits, has not yet been investigated. Exploring the genomic signals under positive selection and the overlappng genes in the Kanniadu goat breed is the major goal of the current investigation. High throughput genomic sequence data of Kanniadu (n=10) and Jakhrana (n=10) were generated from whole genome re-sequencing (~10X) using 150 bp paired-end chemistry on the Illumina NOVASEQ 6000 platform, while Saanen samples (n=10) were downloaded. FastQC (version 0.11.9) was utilized to assess the read quality parameters. Fastp (http://opengene.org/fastp/fastp) was employed for adapter trimming and quality filtering. The samples were then aligned to the goat (Capra hircus) genome assembly ARS1 (GCF 001704415.1 ARS1 genomic.fna.gz) from USDA ARS using Burrows Wheeler Aligner (BWA). The picard tool was used to remove duplicate reads and the GATK tool to call variants (SNPs and INDELs). We generated around 202.7 million clean reads which covers an average of 99.5% percent of the reference genome (ARS1), suggesting that high-quality sequences are generated. We identified 22.5 million SNPs and 3.7 million INDELs in the Kanniadu goat. SNPs found in intronic, intergenic, and exonic regions were annotated. Within breed selection signatures of Kanniadu were identified by θπ and CLR methods while regions under divergent selection between Kanniadu vs Jakhrana, Kanniadu vs Saanen and Jakhrana vs Saanen were studied by Fixation Index (FST) analysis. In overlapping regions, two approaches (CLR and θπ) displayed outlier signals (top 1 percent), and these regions were thus regarded as possible selection regions. Within selection signatures of Kanniadu, a total of 262 (θπ) and 1700 (CLR) genes were identified. A total number of 51 overlapping genes between top 1% θπ and CLR signatures were identified. The top signatures were identified on chromosome 16, 25 and 23 harboring important genes like IPO9 (muscle growth formation), LMOD1 (smooth muscle), U6 (carcass marbling), 7SK (carcass traits), SNORA62 (carcass traits), DCN (carcass traits), PTPRR (carcass traits) etc. Consequently, we performed functional annotation, Gene Ontology (GO) and KEGG pathways analysis for the top 1% genes. Overall, the present study highlights the genes under selection in Kanniadu goats, which will be useful in determining the genetic potential of this breed.ThesisItem Open Access WHOLE GENOME SEQUENCING OF CHANGTHANGI GOAT FOR IDENTIFICATION OF SELECTION FOOTPRINTS(ICAR-NDRI, KARNAL, 2022) S.T VANZAMPUII; INDRAJIT GANGULYThe goat (Capra hircus) is one of the earliest domesticated livestock species, primarily raised for milk, meat, hair, cashmere, and skin to suit basic human requirements. Comprehensive study about genomic variants and selection signals, which would provide valuable genomic insights linked to key Changthangi goat traits, has not yet been investigated. The study included 10 random samples of Changthangi goat breed, domesticated by nomadic pastoralists in the Ladakh area of Jammu and Kashmir, which is one of the most valuable livestock breeds because it produces the finest and most costly animal fiber in the world, with an average fineness of 11-12 microns. The current research aimed to detect genetic variations of Changthangi goat and to examine selection footprints related to hair/fibre quality. To explore genetic composition, whole genome resequencing (~10X) of 10 Changthangi goat samples were performed on the Illumina NOVASEQ 6000 platform using 150bp paired-end chemistry. Additionally, we downloaded ten Angora goat whole genome resequencing data to compare the genomic variants with Changthangi goat. We identified 22.5 million single nucleotide polymorphisms (SNP) and 3.5 million insertions and deletions (INDEL) in Changthangi goat. We examined the selection footprints that selection had left behind using the composite likelihood ratio (CLR), nucleotide diversity (θπ), and fixation index (FST) approaches, and by using the top 1% of selection signatures, we obtained 1276, 206, and 700 genes, respectively. Candidate genes that are under selection pressure include genes like FGF5, FGF9, KRT17, KRT71, STK3, TCF7L1, FGF20, SOX10, CUX1 and IGFBP7 that may have a role in qualities associated to hair or fibre, as well as adaptive traits (NOS2, PRKCB). Significant enrichment of KEGG pathways like Ras signaling pathway, MAPK signaling pathway and Focal adhesion, which are associated with skin hair follicle developments and hair follicle morphogenesis, were identified. The enrichment of the HSF-1 signalling pathway in the top selection signatures also draws attention to Changthangi goat adaptation to the hypoxic environment at high altitudes. Our findings offer a comprehensive overview of the genomic variants in the Changthangi goat genome, and analysis of selection footprints revealed positive sites that may be connected to important traits. The improvement of this breed may be anticipated in the future through targeted screening of verified selection signatures in larger populations.ThesisItem Open Access IDENTIFICATION, MAPPING, AND SCREENING OF HARMFUL DNA MUTATIONS IN SAHIWAL CATTLE(ICAR-NDRI, KARNAL, 2022) GAURAV PATEL; S.K. NIRANJANFor the identification of deleterious mutations in cattle, the use of high throughput sequencing technology and related computational algorithms has become more pertinent, specifically in absence of genetic disease records or in vivo trials. The present study was carried out to identify the harmful mutations and to screen selected harmful mutations through PCR-based tests in Sahiwal cattle. Genomic ddRAD sequence data of twelve Sahiwal cattle were analyzed for the identification of harmful mutations, in silico. After initial quality control and discarding poor quality reads or raw sequence data, a total of 91.10 million reads were obtained. These reads were further aligned with the cattle (Bos taurus) reference genome ARS-UCD1.2 for variant calling and SNP identification in the Sahiwal genome with an average alignment rate of 97.5 percent. In the downstream analysis, a total of 1,62,377 SNPs and 14056 Indels were identified at read depth (RD10) in the Sahiwal cattle genome. The SNPs obtained at RD10 were further annotated with Ensemble - Variant Effect Predictor (VEP) and a total of 430 missense variants were identified. A total of 45 missense variants were found to be deleterious based on SIFT score obtained from the VEP. For further validation of the deleteriousness, all 45 deleterious nsSNPs, predicted with high confidence by SIFT, were analysed by PANTHER, PROVEAN, and PolyPhen-2. Total 18, 21, and 32 were found to be damaging through PANTHER, PROVEAN (Score ≤ -2.5), and PolyPhen-2.0, respectively. Further, using the consensus classifier of PredictSNP, the predictions of PredictSNP, MAPP, PhD-SNP, and SNAP were also obtained to identify deleterious nsSNPs, showing 29, 21, 20, and 19 nsSNPs as deleterious, respectively by these tools. Based on the results from all tools, four nsSNPs- C40Y, A242D, N234K, and D416Y, mapped on WDR4, ZNF280B, CCT6A, and CYP2C87 genes, were filtered out as common. Through I-Mutant2.0 and MUpro tools, change in protein stability was assessed, which revealed decrease in protein stability in almost all deleterious mutations. Using Project Hope, the effect of missense mutation on the protein was assessed, which revealed steric interference in ligand binding in C40Y of WDR4, repulsion of ligands, or other residues in A242D (ZNF280B), N234K (CCT6A) and D416 (CYP2C87), possibly. Differences in size and hydrophobicity of amino acids were found between wild and mutant structures for all four deleterious nsSNPs. Further, five non-sense mutations, causing termination of amino acid chain and one start lost mutation were identified in Sahiwal. With help of the Mapgene2chrom tool, these identified variants were represented chromosome-wise and compared with Bos taurus variants documented on Online Mendelian Inheritance in Animal (OMIA). In Bos taurus, maximum missense and nonsense deleterious mutations were found to be located at BTA2, followed by BTA19. Based on the associated function and effect of mutations of that gene in humans, two mutations, C40Y in the WDR4 gene and A242D in the ZNF280B gene were selected for genotyping. For A242D (ZNF280B) and for C40Y (WDR4) variants, PCR-RFLP (AluI enzyme) and allele-specific PCR assays were developed. Using PCR based assays, screening of 120 Sahiwal cattle was carried out for these two nsSNPs. After screening of A240D (ZNF280B), 104 animals were homozygous for the wild allele, 14 heterozygous, and 2 homozygous for the altered allele. At C40Y (WDR4) locus, 113 animals were homozygous for the wild allele, 7 heterozygous, and zero homozygous for the altered allele. However, no significant difference was observed among observed and expected genotype frequencies for both genotyped mutations, using Chi-square based statistics, indicating the absence of any natural selection against these mutants in the Sahiwal cattle. The study predicts four deleterious SNPs in Sahiwal (Bos indicus) cattle, which may be further studied in vitro and in vivo to validate their deleterious effects. Further, a larger population of Sahiwal cattle may be genotyped for these mutants to assess their purifying selection and genetic load in the population, if any.ThesisItem Open Access FUNCTIONAL TRANSCRIPTOME ANALYSIS UNDER THERMAL STRESS THROUGH RNA SEQUENCING IN KARAN FRIES CATTLE(ICAR-NDRI, KARNAL, 2022) GAURAV DUTTA; RANI ALEXAnimal geneticists and breeders have the impending challenge of enhancing the resilience of Indian livestock to heat stress through better selection strategies. Climate change’s impact on livestock is more intense in tropical countries like India where prolific dairy cattle crossbreeds are more sensitive to heat stress. So, the present study was planned to identify global transcriptome variations in Karan Fries cattle during heat stress conditions in comparison to the thermo-neutral environment using RNA sequencing. Blood samples were collected from two and three animals, as control and treatment, respectively from two seasons and total RNA was isolated. Good quality RNA was used for library preparation and whole transcriptome sequencing. Quality assessment of the raw reads was carried out and trimming was done using Fastp. Further, good quality reads were mapped into Bos taurus genome (ARS-UCD1.2) using HISAT2 package. The aligned reads were quantified using feature count and further differentially expressed genes (DEGs) were identified using the DESeq2 R package. A total of 2741 genes were found to be dysregulated in heat stress on the basis of the minimum log2 fold change and false discovery rate of 1 and 0.05, respectively, of which 468 were up-regulated. Functional annotation and pathway analysis of these DEGs were done on the basis of Gene Ontology (Biological process), KEGG and Reactome pathways using g: Profiler, ShinyGO v0.76, and iDEP.951. The most over-represented pathways from upregulated genes were neuronal and sensory organ development, collagen formation, MAPK and Rap 1 signaling pathways, apoptosis, and oxidative stress. Similarly, mRNA processing, immune system, B-cell receptor signaling pathway, ribosome, and Nonsense-mediated decay (NMD) pathway were identified from downregulated genes. Further co-expression network analysis revealed CHD4, RPS14, EIF4A3, HNRNPH1, DENND5A, EDEM1, HNRNPH1, and MSN as top genes. So, the results of the present study indicated the susceptibility of Karan Fries cattle to heat stress due to altered gene expression levels in pathways such as neuron and sensory development, apoptosis, and oxidative stress. Further, a detailed study on the upregulated pathways is suggested for better understanding of the systems biology of Karan Fries cattle under heat stress.ThesisItem Open Access COMPARATIVE GENOME ANALYSIS OF INTERNATIONAL TRANSBOUNDARY CATTLE BREEDS(ICAR-NDRI, KARNAL, 2022) ANUKA YADAV; SANJEEV SINGHSelection of the animals has resulted in differentiation of breeds exhibiting a wide range of phenotypic variation in a short amount of time. Gir and Ongole are International transboundary breeds of cattle of Indian origin, bred for dairy and meat production across different countries viz Brazil, USA, Mexico, Malaysia, Panama etc. These breeds are well adapted to Brazilian ecological niche and have undergone significant genetic differentiation in recent years. 90 cattle samples belonging to Indian Gir (n=15), Ongole (n=17), Brazilian Gyr (n=27) and Nellore (n=31) genotyped using Illumina BovineHD BeadChip were included in the current investigation. All the samples were quality checked using Plink software and after quality filtration 5.5 lakhs SNPs were retained for downstream analysis. Three complementary approaches viz., Runs of homozygosity (ROH), Integrated haplotype score (iHS) and Fixation index (FST) were implemented and these samples were analysis further, for the identification of the selection signatures. The present investigation revealed that the Pairwise FST differences between Gir versus Gyr and Ongole versus Nellore were 2.856 % and 2.354 %, respectively. Genomic regions under selection within (iHS and ROH) and among breeds (FST) were identified. A total of 4004, 3322, 3437 and 3485 genes were identified in Gir, Gyr, Ongole and Nellore, respectively under top 1% of the selected regions using the integrated haplotype score (iHS) approach. ROH method based selected regions (ROH consensus ≥20%) revealed 4285, 1768, 1663 and 1466 genes in Gir, Gyr, Ongole and Nellore cattle, respectively. FST based approach identified 1966 genes for Gir-Gyr pair and 1897 genes for Ongole-Nellore pair under top 1% selected regions. Several candidate genes were identified under top selected regions viz. IER5, MILR1, ARAP3 in Gir and PCDH9 in Ongole. These genes are responsible for immunity and body shape traits in Indian breeds of cattle. Gene related to mammary gland development, udder size and carcass (MYO16, AGAP2, MYO1B, ABCA7) in Gyr and carcass traits (PARP2, ATP10D and KCNJ11) were identified in Nellore breed of cattle. These findings suggests that selection in Indian population (Gir and Ongole) is more towards immunity and adaptation traits while Brazilian population is more selected towards carcass and milk production traits. Further studies on larger sample size using GWAS will be helpful in the validation of the present results.
