Genome wide association study of test days and 305 days milk yield in crossbred cattle

Abstract

The present study was conducted to identify SNPs associated with test days and 305 days milk production at genome level after correcting for the non-genetic factors affecting these traits in crossbred (Vrindavani) cattle. Crossbred cattle (96) were genotyped using double digestion genotyping-by-sequencing technique for genome wide association study (GWAS) with first lactation milk production traits. The effect of season was significant on TD36, TD66 and TD96. Initial quality control for genotyping call rate, Hardy-Weinberg equilibrium and minor allele frequency were achieved by using PLINK tool. SNPs (9638) were retained for ascertaining GWAS with first lactation milk production traits and was accomplished by regressing SNPs on first lactation milk traits using PLINK. Total 23, 28, 112, 3, 13 and 5 SNPs were found to be significantly associated with AVDY, PY, TD36, TD66, TD96 and FL305MY, respectively. Most of the SNPs were located within KIRREL3 or near to it on chromosome 29, followed by LRRC3 and TSPEAR on chromosome 1. Three SNPs (NC_007299.6_145850854, NC_007328.5_26544467 and NC_007328.5_26544511) were significantly associated with all milk production traits. Our findings revealed majority of significant SNPs for milk traits were located within non-coding genomic regions.

Keywords

• Crossbred cattle
• Milk production traits
• Genome wide association study
• Genotyping-by-sequencing