A Genome wide association study of carcass traits based on Real Time Ultrasound in South African Nguni cattle

Abstract

The purpose of this study was to identify genomic regions associated with carcass traits using real-time ultrasound measurements in South African Nguni cattle. The dataset contained measurements from 200 Nguni steers finished in a growth trial. The following carcass traits were measured: ultrasound measurements of eye muscle area (EMA), rump fat thickness (RF) and backfat thickness (BF), slaughter weight (SW), dressing percentage (DP). The ultrasound measurements were measured at two separate dates during the growth trial. The 150k GGP HD SNP array (Geneseek) was used for genotyping 141 of the 200 cattle from the trial. The technical quality of the genomic data was investigated using SNP and individual call rates of 90%. Thereafter a genome-wide association study (GWAS) was performed on the data without genotypic data quality control and after genotypic quality control with MAF = 0.02 and HWE = 0.0001. After technical (SNP and individual call rate) and genetic (MAF and HWE) quality control, 137 789 SNPs and 124 178 SNPs remained in each dataset, respectively, with 139 animals remaining in both datasets. PLINK as well as EMMAX software was used to perform the GWAS and a 5% confidence interval was applied. SNPs at a threshold of p<10-5 were identified for BF (BTA1, BTA16, BTA25); EMA (BTA2, BTA7, BTA8, BTA9, BTA13, BTA20, BTA25) and RF (BTA5, BTA9, BTA16) at 72 days on trial. Similar chromosomes were detected with putative SNPs for BF, EMA and RF at 91 days on trial. Additional SNPs were observed for BF on BTA2, BTA3, BTA5, BTA28 and X-chromosome and EMA on BTA12, BTA23, BTA29. Furthermore, SNPs with a threshold of p<10-5 were identified for SW (BTA4, BTA9, BTA19) and DP (BTA16, X-chromosome). Of the 14 genes associated with the traits, NIPA1, SYNE1, NT5C3B, SMYD3 were the most applicable to the traits studied and involved in binding function. This study is the first GWAS in SA Sanga cattle on carcass traits and provides insight on the genes involved in carcass traits. Novel SNPs were observed with associations for BF on BTA3, BTA5, BTA25, BTA28 and X-chromosome; SW on BTA9; EMA on BTA25; RF on BTA1, BTA16 and for DP on the X-chromosome. Further studies on larger datasets will be required for confirmation.