The structure of a cattle stud determined using a medium density single nucleotide polymorphism array

Genetic progress depends on accurate knowledge of the genetic composition of a population or herd including level of inbreeding and parentage. However, in many circumstances, such as at an individual property level, the relationships between animals may be unknown, or at best, only partly known. In this study, we used DNA from 938 animals and genotypes from ∼54000 single nucleotide polymorphisms (SNP) to determine the genetic structure of a stud from Central Queensland. Animals on the study were bred using multi-sire mating in mobs of composite tropically adapted cattle of the Senepol, Belmont and Bonsmara breeds. Following genotyping using an array of 54000 SNP, we were able to separate animals into breed groups using principal components and show that ∼400 SNP were sufficient to separate animals into stable groups if the sample was genetically diverse. However, precise principal component values were only achieved when a few thousand SNP were used. We characterised the pedigree relationships between individuals using a genome relationship matrix. At least 3000 SNP were required to calculate accurate relationship coefficients between individuals. Around 19% of paired comparisons between animals showed similarity equivalent to sharing a great-grandparent or 1/64 shared ancestry. Approximately 8% of the individuals showed more than 10% inbreeding. To demonstrate the utility of calculating the relationship coefficients, we counted the tick burden on each animal at more than one time and then calculated the heritability of tick burden of h2 ≤ = 0.46 (±0.08). There was no significant genetic difference in tick burden between Belmont and Bonsmara cattle compared with Senepol on this property once a genetic relationship matrix was included to account for co-ancestry of individuals. © 2012 CSIRO.