Genome wide association study of udder type traits and milk production traits in Gir cattle

Abstract

This study investigated the association of genome wide association study of udder type traits and milk production traits in Gir cattle. Data for the current study were collected from 635 Gir cows reared by farmers in small-holder conditions, and blood samples were collected for the Genomic study. The data for the phenotypic correlation study on 305 day milk yield and udder type traits were analysed using the statistical software R (v3.4.0), and the genome wide association study was carried out using the PLINK (v1.90b4.4) software. The phenotypic correlation between udder type traits, such as central ligament, rear udder height, rear udder width, teat length, and teat thickness, and 305 day milk yield was low to moderate, but significant (p 0.05) and positive. Some traits, however, were negatively correlated, including fore udder attachment, fore teat placement, rear teat placement, and udder depth. A genome-wide association study using a customised SNP chip (INDUSCHIP1) with 45,024 SNPs distributed on 29 autosomes discovered 838 SNPs that were significantly related to nine udder type traits and 305 day milk yield. The majority of SNPs were under MAF class of 0.3-0.5 from 45,024 SNPs spread over 29 Bos Indicus autosomes. Thus, present study on udder type traits and 305 day milk yield and their GWAS in Gir cattle using INDUSCHIP1 a customised SNP chip has provided the base line data for incorporation of udder type traits in Genomic selection for overall genetic improvement of Gir cattle.