P1045 Determination of genome-wide linkage disequilibrium in the South African Bonsmara reference population

The largest beef breed in South Africa is the Bonsmara, a locally developed composite breed, consisting of approximately 81,000 registered cows. The Bonsmara was developed specifically for adaptability to sub-tropical conditions, using objective measurements between 1937 and 1963, and as a breed is subjected to mandatory performance recording. Biological samples have also been stored for the last 10 yr. The Bonsmara is therefore well placed to engage in genomic selection and is in the process of compiling a genomic reference population. To date, 583 Bonsmara cattle (388 bulls and 195 cows) were genotyped with the GeneSeek Genomic Profiler Bovine HD Chip (GGP-HD) 80K chip (Neogen, Lincoln, NE, USA) and the results of another approximately 990 Bonsmara cattle are pending, using the GeneSeek GGP-HD 150K chip. In this preliminary study, the genotypes of the initial 583 Bonsmara cattle were characterized for genome-wide linkage disequilibrium, as this may affect the accuracy of genomic estimated breeding values (GEBV). We used 56,248 autosomal SNPs to determine extent of LD in the current reference population. The software package PLINK was used in the analysis and the squared correlation of the alleles at 2 loci (r2) was used as a measure of LD. A 50 SNP sliding window was used with a 5 SNP increment between windows. Analysis of the marker pairs found that the level of LD in the current reference population decreased with physical distance between SNPs. Overall, the mean r2was 0.405. Genomic regions smaller than 420 kb and 815 kb displayed strong LD (r2> 0.8) and useful LD (r2> 0.2), respectively. These preliminary results indicate that some population stratification may be present in the reference population and should be taken into consideration during the estimation of GEBVs.