Genomics Confirm an Alarming Status of the Genetic Diversity of Belgian Red and Belgian White Red Cattle

Abstract

Genetic diversity is increasingly important for researchers and society. Small and local populations deserve more attention especially, as they may harbor important characteristics. Moreover, small populations are at greater risk and their genetic management is often more challenging. Likewise, European red cattle populations are threatened, as they are outcompeted by more specialized cattle breeds. In this study, we investigate the genetic diversity of two local Belgian red cattle breeds: Belgian Red and Belgian White Red cattle. A total of 270 animals were genotyped via medium density SNP arrays. Genetic diversity was assessed using runs of homozygosity screening, effective population size estimation and F_st analyses. Genomic inbreeding coefficients based on runs of homozygosity were estimated at 7.0% for Belgian Red and 6.1% for Belgian White Red cattle, and both populations had a low effective population size (68 and 86, respectively). PCA, F_st and admixture analyses revealed the relationship to 52 other international breeds, where they were closest related to some Belgian, French, Scandinavian and Dutch breeds. Moreover, F_st analyses revealed for Belgian Red cattle a signature of selection on BTA6, adjacent to the KIT gene. This study gains important knowledge on the genetic diversity of these two small local red cattle breeds, and will aid in their (genetic) management.

Keywords: Bos taurus; SNP; admixture; conservation; genetic diversity; genomics; inbreeding; red cattle; runs of homozygosity; single nucleotide polymorphism.

Figure 1

Genome-wide incidence plots of SNPs in runs of homozygosity (ROH) for both the Belgian Red (left) and Belgian White Red (right) populations.

Figure 2

A genome-wide view of F_st values per SNP between the Belgian Red meat-type (BRM) and dual-purpose (BRD) populations.

Figure 3

(Left) Neighbor joining tree of all 55 analyzed cattle populations positioning Belgian Red (meat-type: BRM; and dual-purpose: BRD) and Belgian White Red (BWR) in an international context. (Right) Neighbor net graph of BR (both BRM and BRD) and BWR compared to the 14 other selected breeds. Abbreviations as in Table S1.

Figure 4

ADMIXTRURE clustering based on 4 and 8 clusters (K). Breed abbreviations as in Table S1.

Figure 5

A genome-wide view of F_st values per SNP between the Belgian Red compared to 16 cattle populations (Belgian Blue, Belgian White Red, Maine Anjou, Charolais, Ringamåla, Norwegian Red, Swedish Red, Improved Red, Deep Red, Maas-Rhine-Ijssel, Holstein, Red Holstein, Normande, Campine and Swedish Holstein Friesian cattle).