Genetic diversity, population structure and relationships in indigenous cattle populations of Ethiopia and Korean Hanwoo breeds using SNP markers

Kwan-Suk Kim,Jong-Joo Kim,Hailu Dadi,Sang-Wook Kim,Zewdu Edea,Heebal Kim,Taeheon Lee,Tadelle Dessie

doi:10.3389/fgene.2013.00035

Abstract

In total, 166 individuals from five indigenous Ethiopian cattle populations – Ambo (n = 27), Borana (n = 35), Arsi (n = 30), Horro (n = 36), and Danakil (n = 38) – were genotyped for 8773 single nucleotide polymorphism (SNP) markers to assess genetic diversity, population structure, and relationships. As a representative of taurine breeds, Hanwoo cattle (n = 40) were also included in the study for reference. Among Ethiopian cattle populations, the proportion of SNPs with minor allele frequencies (MAFs) ≥0.05 ranged from 81.63% in Borana to 85.30% in Ambo, with a mean of 83.96% across all populations. The Hanwoo breed showed the highest proportion of polymorphism, with MAFs ≥0.05, accounting for 95.21% of total SNPs. The mean expected heterozygosity varied from 0.370 in Danakil to 0.410 in Hanwoo. The mean genetic differentiation (FST; 1%) in Ethiopian cattle revealed that within individual variation accounted for approximately 99% of the total genetic variation. As expected, FST and Reynold genetic distance were greatest between Hanwoo and Ethiopian cattle populations, with average values of 17.62 and 18.50, respectively. The first and second principal components explained approximately 78.33% of the total variation and supported the clustering of the populations according to their historical origins. At K = 2 and 3, a considerable source of variation among cattle is the clustering of the populations into Hanwoo (taurine) and Ethiopian cattle populations. The low estimate of genetic differentiation (FST) among Ethiopian cattle populations indicated that differentiation among these populations is low, possibly owing to a common historical origin and high gene flow. Genetic distance, phylogenic tree, principal component analysis, and population structure analyses clearly differentiated the cattle population according to their historical origins, and confirmed that Ethiopian cattle populations are genetically distinct from the Hanwoo breed.

Highlights

Ethiopia, with its 49.33 million heads of cattle, has the largest cattle population in Africa (Central Statistical Authority (CSA), 2008)
Among Ethiopian cattle populations, the proportion of single nucleotide polymorphism (SNP) with a minor allele frequencies (MAFs) ≥0.05 ranged from 81.63% in Borana to 85.30% in Ambo, with a mean of 83.96% across all populations
GENETIC VARIABILITY WITHIN POPULATIONS Most SNPs identified in the Ethiopian and Hanwoo cattle populations exhibited a high degree of polymorphism

Summary

Introduction

With its 49.33 million heads of cattle, has the largest cattle population in Africa (Central Statistical Authority (CSA), 2008). The biological diversity of indigenous cattle populations/breeds is a key to sustaining the wellbeing of millions of farming and pastoral communities, predominantly inhabiting low-input production systems. There has been a rapid decline in population and identity of most indigenous cattle populations of East Africa through breed substitution, indiscriminate crossbreeding, the absence of breed development programs, and environmental changes (Rege and Gibson, 2003; Hanotte et al, 2010). Understanding of farm animal genetic diversity is required to contribute to meeting current production needs in various environments, to allow sustained genetic improvement, and to facilitate rapid adaptation to changing environments and breeding objectives (Notter, 1999; Köhler-Rollefson et al, 2009; Hanotte et al, 2010)

Methods

Results

Conclusion