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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]

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]

• 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]