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Genome-wide assessment of genetic diversity, linkage disequilibrium and haplotype block structure in Tharparkar cattle breed of India.
- Source :
-
Animal Biotechnology . Apr2022, Vol. 33 Issue 2, p297-311. 15p. - Publication Year :
- 2022
-
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 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]
Details
- Language :
- English
- ISSN :
- 10495398
- Volume :
- 33
- Issue :
- 2
- Database :
- Academic Search Index
- Journal :
- Animal Biotechnology
- Publication Type :
- Academic Journal
- Accession number :
- 156189005
- Full Text :
- https://doi.org/10.1080/10495398.2020.1796696