East-Belgian Red and White (EBRW): Assessing genetic and phenotypic diversity and developing practical recommendations for the management of genetic diversity at mating

Abstract

The objective of this study is to assess the genetic and phenotypic diversity of the East-Belgian Red & White (EBRW) cattle breed. First, pedigree and genomic data were used to have an insight of population structure and to the within-breed genetic diversity by estimating heterozygosity and inbreeding and relationship coefficients. Then, records from milk recording were used in parallel with pseudo-phenotypes, i.e. deregressed estimated breeding values, to display the (pseudo-)phenotypic diversity existing between animals and herds reflecting differences in breeding objectives. This was achieved through principal component analysis. Based on the limited pedigree information, 2% of the EBRW population studied appear to be inbred with an average pedigree inbreeding of 2.3%. The pedigree information also confirmed to use of introgression in the past decades. Turning to genomic data, the observed heterozygosity was 0.358 and more than 40% of the genotyped population was inbred with average inbreeding estimates ranging from 2.9 to 3.5%. Phenotypical variation mostly occurs in regards to the milk yield what might reflect different breeding objectives. This tendency was also confirmed in pseudo-phenotypes. To conclude, practical recommendations were also formulated to manage the EBRW genetic diversity through mating with a focus on the 13 EBRW bulls available for artificial insemination. Finally, the EBRW genetic diversity seems to be relatively high while presenting limited inbreeding level and the phenotypic diversity seems to reflect divergent breeding objectives.