PSIII-15 Genetic diversity and population structure in nine beef cattle sub-populations using whole genome SNP markers

Abstract Commercial beef cattle populations are rarely purebred. Understanding genetic diversity and population structure of crossbreds is important for future genetic improvement programs. Currently, an admixed beef cattle population comprised of British, Continental and Australian origin is being used for long-term research goals in understanding longevity, efficiency (reproductive and nutritional), and their interaction. This experiment aimed to assess the levels of genetic diversity and population structure among purebred (n = 6) and admixed (n = 3) sub-populations. A total of 727 animals were genotyped using the GeneSeek Genomic Profiler 150K. After quality checking, expected heterozygosity (HE) and polymorphism were calculated using 108,249 markers by sub-population. After LD-pruning, the remaining 19,316 SNP were used for pairwise fixation index (FST), analysis of molecular variance (AMOVA), and principle component analysis. The call rate for each sub-population ranged from 0.9866 ± 0.0351 to 0.9994 ± 0.0006. The lowest proportion (0.8527) of polymorphism was in the American Aberdeen (AA) and the highest proportion (1) was in the admixed populations. By sub-population, HE ranged from 0.3490 ± 0.1482 in AA to 0.3935 ± 0.1315 in Angus. The average nucleotide diversity over loci varied from 0.2976 ± 0.1444 in AA to 0.3872 ± 0.1879 in unknown parentage sub-population. The highest genetic differentiation was observed between AA and Continental breeds (Gelbvieh and Simmental) as FST estimates ranged from 0.1757 to 0.1789, respectively. Differences within individuals explained 98.15% of the total variance, whereas only -2.33% was due to differences among individuals within sub-populations. The first and second principal components (PC) explained 37.77% and 24.29% of the total variance, respectively. These PC show that admixed individuals clustered with animals of their primary breed. Therefore, this study suggests that clustering individuals according to their primary breed will assist in future genetic studies with this population and potentially future commercial genetic improvement programs.