Genome-wide estimates of effective population size in the Spanish Holstein population

Abstract Text: In this study, genomic estimates of inbreeding, coancestry and effective population size in the Spanish Holstein population were obtained. Genomic estimates of inbreeding included those obtained on a marker-by-marker basis and those based on runs of homozygosity. Genomic estimates were compared with those obtained from genealogical information. The results indicate that the regression coefficient of genomic inbreeding on genealogical inbreeding was higher than the regression coefficient of genealogical inbreeding on genomic inbreeding. Similar results were also observed for coancestry. Additionally, inbreeding estimates based on runs of homozygosity tend to reflect identity by descent status better than estimates obtained on a marker-by-marker basis. Estimates of effective population size obtained from genomic and genealogical information were consistent and ranged from about 66 to 79. These values highlight the need of controlling the rate of coancestry and inbreeding in Holstein selection programmes.

Keywords: dairy cattle; effective population size; runs of homozygosity