Genetic diversity and population structure of six ethiopian cattle breeds from different geographical regions using high density single nucleotide polymorphisms

Abstract

The aim of this study was to investigate the genetic diversity and population structure of six Ethiopian cattle breeds. Illumina's Bovine HD BeadChip was used to genotype 76 DNA samples from indigenous cattle breeds, which were named after their regions of origin, namely Benishangul (n = 12), Fogera (n = 11), Gindeberet (n = 19), Gofa (n = 10), Nuer (n = 13), and Sheko (n = 11). Additionally, two comparative European breeds, namely Holstein Friesian (n = 15) and Jersey (n = 15), were included in the analysis as outgroups. The relatively high within breed genetic diversity of the European and the Ethiopian indigenous cattle breeds was clearly evidenced by their allelic richness (1.747–1.879), effective number of alleles (1.437–1.522), observed heterozygosity (0.271–0.313), nucleotide diversity (0.264–0.315), and inbreeding coefficients (−0.025–0.051). Wright's fixation index FST and identity-by-state genetic distance revealed considerable genetic distinctiveness of the Ethiopian indigenous cattle compared to the European breeds. The FST values between Ethiopian cattle breeds were at the low side of the range (less than 0.03). The lowest FST values (0.002) were found between Benishangul, Fogera and Gindeberet, and the highest between Sheko and the other five Ethiopian breeds. Analysis of molecular variance (AMOVA) showed that the Ethiopian indigenous cattle breeds have maintained a high level of within-population genetic differentiation (explaining 97% of the molecular variability), the remainder being accounted for by differentiation among breeds (3%). The geographical distances and the FST values had a moderate positive correlation coefficient (0.283). The inter-breed comparisons and structure analysis clearly revealed that Sheko and Nuer were quite separate from the other indigenous breeds and that Benishangul, Fogera, Gindeberet and Gofa are genetically very closely related breeds. Their genetic closeness could be due to high within breed genetic variability, due to a common ancestor, or because of lack of selection intensity. Our results, particularly for the Benishangul, Gindeberet, Gofa and Nuer breeds, are to our knowledge the first of this kind and could be used as a foundation for further investigations of breed characterization or for the design of conservation strategies.