PERSISTENCE OF LINKAGE DISEQUILIBRIUM PHASE AMONGST FIVE SOUTH AFRICAN BEEF CATTLE POPULATIONS

Abstract Text: Genomic selection relies on the assumption that phases of linkage disequilibrium between markers and quantitative trait loci are the same in selection candidate and the reference population. If marker phase are correlated across multiple breeds, it could be possible to pool several breeds into one common reference population. This study investigated persistence of linkage disequilibrium phase among five South African beef cattle including Afrikaner (44), Nguni (56), Drakensberger (47) Bonsmara (46) and Angus (31). Consistencies of SNP phase between breed pairs were correlated using the signed r values. The correlation of r values between populations did not reach high levels, the highest correlation was observed between Nguni-Bonsmara pair (0.6) for markers separated by 10 kb. This suggested the necessity of breed-specific reference populations or the need to include adequate representation of each breed in the reference population if a multi-breed reference is to be used.

Keywords: Genomic selection