HIGH - THROUGHPUT GENOTYPE BASED POPULATION STRUCTURE ANALYSIS OF SELECTED BUFFALO BREEDS
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Date
2018
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Department of Animal Genetics & Breeding College of Veterinary Science and Animal Husbandry Anand Agricultural University, Anand
Abstract
A population structure study was performed in Indian buffalo populations using the Axiom® Buffalo Genotyping Array (90,000 SNPs). Blood samples were obtained from 280 female buffaloes from their respective home tract namely 1. Murrah (70), 2. Nili-Ravi (40), 3. Mehsana (75), 4. Jaffarabadi (41), 5. Banni (20) and 6. Pandharpuri (34). The average call rate was 98.58 per cent with 123,040 SNPs after genotyping. After removal of duplicates, markers of “0” chromosome and “X” chromosomes (38,219 SNPs), there were 84,820 markers (for 1-29 chromosomes) for further analysis. These markers further were filtered with missing genotypes (geno > 0.1) which removed 13,730 and none of individuals removed for low genotyping (mind > 0.1). There were 71,090 markers available for analysis. Furthermore discarded markers with lesser HWE values than 0.00001(10-5) which were 3,868 and 11,381 markers failed in missingness test. Finally, after filtration and quality control there were 69,571 remained for population structure analysis.
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