Discovery and validation of single nucleotide polymor- phisms with phenotypic associations in beef cattle grazing endo- phyte-infected tall fescue
Bastin, B. C., C. Bagley, B. Campbell, A. Houser, C. J. Kojima, A. M. Saxton, J. C. Waller, and L. Wojackiewicz.  2013.  Journal of Animal Science2013 ASAS/ADSA Joint Annual Meeting, J. Anim. Sci. Vol. 91, E-Suppl. 2/J. Dairy Sci. Vol. 96, E-Suppl. 1 pg. 393.

Abstract:
Development of a multi-locus marker panel will allow for genetic selec- tion for improved production in cattle grazing endophyte-infected tall fescue. Tall fescue (Lolium arundinaceum Schreb.) is the most prevalent forage in the Mid-south United States due in part to the presence of the endophytic fungus Neotyphodium coenophialum. The fungus, while conferring hardiness to tall fescue, contributes to decreased production efficiency in cow-calf operations. A genome-wide association study was performed using the Illumina 50k bovine SNP chip. Twenty-four SNPs were found to be associated (P < 0.05) with adjusted birth weight and adjusted 205-d weights of calves from 48 beef cows at Ames Plantation. Taqman genotyping assays (Applied Biosystems) were subsequently designed to genotype each SNP in beef cattle located at Tennessee Tech University (n = 654), to validate associations in a large, independent herd. Genotype-phenotype associations were tested using mixed models (SAS 9.3, Cary, NC) accounting for variability in calving season in calf-related traits, and least squares means compared with Fisher’s least significant difference (P < 0.05). Eleven of the GWAS SNPs were informative for such phenotypes as hair coat (scored 1–5), body condi- tion (scored 1–9), weight per day of age (kg/d), adjusted 205-d weight (kg), and days to first calf (Table 1). These data indicate that genetic polymorphisms found to be informative in a small herd can be validated in a larger representative population in a cost-effective manner. Table 1. Significant associations for GWAS-detected SNPs Phenotypic association SNP P-value BTA9B 0.028 BTA9C <0.001 Genotype means A H 1.7B 1.8A 1.9A 1.6B 1.8A 1.7B 1.7B 1.7B 1.8B 1.6C 1.6B 1.8A 1.8A 1.7B 5.0A 4.8B 0.52A 0.44B 128A 116B 129AB 119B 749B 1185A 715B 1073A 989A 723B Hair coat score Body condition score Weight gained per day Adj. 205-d weight Days to first calf of BTA9F BTA9I BTA14J BTA19A BTA26 BTA11 age BTA11 BTA14B BTA23 BTA9H BTA11 BTA19A 0.009 0.045 0.001 0.003 0.001 0.037 0.002 0.032 0.033 0.002 0.024 0.001 B 1.8AB 1.7B 1.8AB 1.9A 2.0A 1.8A 1.6B 5.1A 0.52A 134A 725B 781B 709B