Dairy Science Department
BS in Dairy Science
The objective of this project was to determine if copy number variation (CNV) at specific genes related to BST had an effect on milk production. Hair samples from 1000 fresh heifers from Maddox Dairy in Riverdale, CA were sent to Geneseek, a Neogen Company for DNA extraction and processing. The DNA was processed using the BovineSNP50 BeadChip and the data were loaded into the GenomeStudio software. The data were manipulated in GenomeStudio to estimate the CNV at each single nucleotide polymorphism (SNP) of which a vast majority was two. The SNPs with a copy number of two were excluded and all remaining copy number values were converted into a comma separated value file and loaded into an Excel spreadsheet for final processing. This resulted in 283,558 SNPs from 578 individuals. The genes studied were growth hormone (GH1), growth hormone receptor (GHR), growth hormone releasing hormone (GHRH), growth hormone releasing hormone receptor (GHRHR), insulin-like growth factor (IGF-1), and insulin (INS). SNPs located near the start and end of the gene sequences for those genes were found that had a copy number of three. PTAs of animals with SNPs located near these gene sequences were analyzed to determine if copy number had an effect on production. There were 138,411 total SNPs with a copy number of three. Of these 138,411 SNPs, 28 were intronic with the exception of IGF-1 which had no SNPs with CNV in the intron. For IGF-1, the closest exonic SNPs were used. Copy number variation did occur for SNPs that were in introns for all the genes previously mentioned except for IGF-1. No CNV was identified in the SNPs closest to IGF-1.
Key words: copy number variation, growth hormone, growth hormone releasing hormone, insulin-like growth factor, insulin, single nucleotide polymorphism