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

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.

Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds

“…Similar to our results, F ST values of 1.2% (Dadi et al, 2008) and 1.1% (Zerabruk et al, 2011) from microsatellite markers, and 1.2% from a low-density taurine-derived chip (Edea et al, 2013), were reported among Ethiopian cattle populations. However, our F ST values were lower than those from previous studies of West African cattle breeds (6%; IbeaghaAwemu and Erhardt, 2005) and six African cattle breeds (4%; Gautier et al, 2007).…”

“…A higher average F ST value (0.09) between Nellore and Northern Ethiopian cattle breeds was also observed (Zerabruk et al, 2011), compared with our finding of 0.07 for Ethiopian and Asian zebu. The lowest genetic differentiation and genetic distance observed among the Ethiopian cattle populations might be a result of their common ancestral origin and strong gene flow (Dadi et al, 2008;Zerabruk et al, 2011;Edea et al, 2013), a conclusion that is supported by our PCA and STRUCTURE analysis. The F ST estimates between Bangladeshi zebus and Ethiopian cattle were considered moderate (0.05 to 0.15), whereas estimates for Asian zebu and Hanwoo were very large (>0.25) (Wright, 1978).…”

“…Here, for the first time, we used indicinederived SNPs to investigate genome-wide diversity, relationships and admixture in cattle originating from Africa and Asia. The observed levels of polymorphism were higher than those reported for Ethiopian cattle populations (83.96%) (Edea et al, 2013) and those from a low-density bovine SNP chip assay (47.4% in Lagune and 71.0% in Borgou) (Gautier et al, 2007). The higher levels of polymorphism, MAF and heterozygosity in Ethiopian cattle and Asian zebu populations compared with Hanwoo (taurine) could be related to ascertainment biases, as we demonstrated here and as noted in previous reports (Gauiter et al, 2010).…”

A disparate trace element metabolism in zebu (Bos indicus) and crossbred (Bos indicus × Bos taurus) cattle in response to a copper-deficient diet1

“…Zebu cattle (Bos indicus) are the most common type of cattle in Ethiopia and renowned for their robustness under tough conditions (Edea et al, 2013). Moreover, they seem to have adapted to their environment very well, with reports indicating an ability to cope with dietary antagonists, such as tannins (Yisehak et al, 2012).…”

Genetic diversity in Zimbabwean Sanga cattle breeds using microsatellite markers

“…In addition, there are anecdotal reports that these genotypes harbour great genetic diversity and adaptive traits that make them potentially valuable resources for breeding programmes in regions facing similar biological stresses, and in response to the present and future needs of livestock production (Van Arendonk, 2011;Acosta et al, 2013;FAO, 2015). Local Sanga genotypes can be used in various pure and cross breeding systems, helping farms to cope with projected management, market and climate scenarios in the future (Wilson, 2009;Edea et al, 2013).…”