Genome-wide assessment of genetic diversity, linkage disequilibrium and haplotype block structure in Tharparkar cattle breed of India. Issue 2 (1st April 2022)

• Record Type: Journal Article
• Authors: Saravanan, K.A.; Panigrahi, Manjit; Kumar, Harshit; Parida, Subhashree; Bhushan, Bharat; Gaur, G.K.; Kumar, Pushpendra; Dutt, Triveni; Mishra, B.P.; Singh, R.K.
• Is Part Of: Animal biotechnology. Volume 33:Issue 2(2022)
• Page Start: 297
• Page End: 311
• Publication Date: 2022-04-01
• Subjects: Tharparkar cattle -- SNP -- genetic diversity -- ROH -- linkage disequilibrium -- haplotype blocks; Animal biotechnology -- Periodicals; Animals, Domestic -- genetics -- Periodicals; Animals, Genetically Modified -- Periodicals; 660.6
• DOI: 10.1080/10495398.2020.1796696
• Languages: English
• ISSNs: 1049-5398

Abstract

Abstract: 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 r 2 was 0.6452 and 0.1339, respectively. In addition, we observed a gradual decline in effective population size over the past generations.