Mapping copy number variable regions correlated with reproduction and production traits in Karan Fries cattle mammalian genomics.

Abstract

Copy Number Variants (CNVs) are the structural variations influencing more nucleotides when compared to other types of variations, having a greater impact on the regulation of gene expression, dosage of a gene, altering the coding sequences, all of which might lead to phenotypic variations. Research in the areas of the characterizing CNVs, their discovery and genesis, and their functional effects is in infancy particularly in Indian cattle breeds. We hypothesized that due to the intensive selection for production traits carried out for a premium milch crossbred cattle Karan-fries, they might be characterized by unique CNVs. In order to discover and characterize the genome-wide CNVs and CNV Regions (CNVRs) using HD SNP genotypic array, the current study was carried out on 44 Karan-Fries Cattle. To take use of the complementing advantages of the various methodologies, three distinct approaches (PennCNV, QuantiSNP, and CNVPartition) to identify CNVs were chosen. The techniques mentioned above revealed 2989, 4088, 2316 CNVs, and 980, 1526 917 CNVRegions respectively. The study failed to find a consistent pattern for the number and size of CNV (either overestimation or underestimate by different algorithms). PennCNV algorithm results could be considered to be more accurate than others as there was higher overlapping of PennCNV results by other algorithms. BTA5, BTA12, and BTA17 were significantly enriched for CNVs. QTLs for milk beta-lactoglobulin percentage and interval from estrus to calving were considerably enriched. Using combination of various approaches, the entire CNVR map for Karan-Fries Cattle was developed. This map could be used as a guide for other native breeds and crossbreds.