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Vol. 11, Special Issue 12 (2022)

Mitochondrial genetic diversity analysis of cattle using high density SNP array

Author(s):
Hemal B Patel, SP Dixit, Jeevan C, Indrajit Ganguly and Anand Nagaleekar
Abstract:
Background: Animal mitochondrial DNA is small, extra chromosomal genome and self-replicating. The mtDNA has proved to be valuable in the study of genetic diversity as it shows maternal inheritance and changes rapidly than single copy nuclear DNA in mammals.
Aim: This study aim to analyse mitochondrial diversity and Lineage of diverse cattle breeds of India.
Method: Total 132 individuals DNA samples of seven diverse Indian native cattle breeds (Gir, Sahiwal, Tharparkar, Vechur, Hariana, Kangayam and Ongole) distributed over various geographical regions as well as covering different utility purposes (Milch/Dual/Draught/) were included in the present study. 132 mitochondrial DNA were isolated and SNP genotyping was done by Illumina Bovine HD chip.Data were analyzed by using Genome Studio software (Illumina). The data were filtered by using different parameters like SNP call rate (≤ 95%), and minor allele frequency (≤ 0.05) using PLINK version 1.07.Analysis of After pruning the data using above mentioned quality control parameters, various software’s were used for SNP data analysis as per the need. data were analyzed based on, different haplotypes and their frequencies, haplotype diversity (XD), Nucleotide Diversity (Pi) and pairwise differences (K value) between all the possible sets for each population. AMOVA and Global Fixation index were done.
Result: Analyses revealed 81 haplotype with the haplotypic diversity range from 0.9333±0.0477 to 0.9883±0.0210, Nucleotide diversity was ranging from 0 to 0.0862+/- 0.0446. AMOVA shows 2.61% variation among population and 97.39% variation within population. FST value is significantly different from 0 for all pair wise combinations representing significant amount of Genetic differentiation between populations. FST estimates between the population shows that Sahiwal and Vechur are more genetically closer (-0.00477) while animals from Gir and Kangayam are genetically more differentiated (0.06601). Multidimensional Scaling indicate milch breeds are in same lineage as compare to dual and draft.
Pages: 81-87  |  307 Views  90 Downloads
How to cite this article:
Hemal B Patel, SP Dixit, Jeevan C, Indrajit Ganguly and Anand Nagaleekar. Mitochondrial genetic diversity analysis of cattle using high density SNP array. The Pharma Innovation Journal. 2022; 11(12S): 81-87.
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