PHENOTYPIC AND MOLECULAR CHARACTERIZATION OF ETHIOPIAN EQUINES: THEIR GENETIC DIVERSITIES AND GEOGRAPPHICAL DISTRICUTIONS

Abstract

Nationwide survey was carried out with the objectives to characterize and describe native Ethiopian equines populations (horse and donkey) at both phenotypic and molecular levels. Standard breed identification procedures were employed to identify distinct populations in both species. Accordingly, we identified six distinct domestic donkey populations namely Abyssinian, Afar, Hararghe, Ogaden, Omo and Sinnar but rejected a previously misidentified Jimma donkey as it failed to meet standard breed identification criteria. Twelve morphometeric variables were measured on a total o f569 adult donkeys (289 jacks and 280 jennets) that belonged to the six identified populations. The result showed that Sinnar donkeys were significantly taller (P<0.05) (109.78 cm) for height at wither (HW) while Abyssinian donkeys were shorter (93.87 cm) than all the remaining donkey populations. Principal component analysis (PCA) showed that four of the morphometeric variables including HW, height at back (HB), height at rump (HR) and body length (BOL) accounted for about 87.5% of the total variations among the donkey populations. Percent assignment of discriminant function analysis showed that, on avera g e 64.83% of individuals w ere reclassified back to their respective populations. Based on squared Mahalanobis distances, the six indigenous Ethiopian donkey populations were clustered into four major morphological clusters viz. l)Abyssinian; 2) Sinnar; 3) Omo and 4) Afar, Hararghe and Ogaden. Using similar procedure, seven distinct domestic and one feral horse populations were identified in Ethiopia. These include Abyssinian, Bale, Bor an, Horro, Ogaden, Kafa, Selale and Kundido feral horse. Seventeen morphometeric variables were measured on a total of 503 native Ethiopian horses that belonged to five of the eight identified horse populations. Comparison of Least squares means showed that Selale horses were taller (P<0.05) (131.2 cm) and longer bodied (133.6 cm) than the rest o f native Ethiopian horse populations. PCA showed that HW, HB, HR, BOL, back length (BAL) and barrel length (BEL) jointly account for about 80% per cent of the total variations o f the 17 measured morphometeric variables. Percent discriminant function analysis showed that 77.05% of individuals were correctly classified into their respective populations. Cluster analysis based on squared Mahalanobis distances clustered the five Ethiopian horse populations into at most three and at least two major morphological groups viz. 1) Selale and Kafa; 2) Bale; and 3) Abyssinian and Horro. Molecular characterization on the basis o f maternally inherited mitochondrial DNA (mtDNA) D-loop sequence was carried out in 39 randomly selected donkeys sequenced for 378 base pairs (bp). The 39 sequences were characterized by 29 polymorphic sites that further collapsed into 19 different haplotypes. Average haplotype diversity was high (0.903±0.032) ranging from 0.400 in Ogaden to 0.933 in Omo donkeys. Average nucleotide diversity was also high (0.020±0.003) ranging from 0.002 in Ogaden to 0.029 in Sinnar donkeys showing the least and highest heterozygous population, respectively. Reynolds ’pair-wise genetic (Dp) distances between Ethiopian donkey populations showed that Sinnar donkeys were consistently distant from the rest of Ethiopian domestic donkey populations suggesting it might be descended from a different ancestral trunk than the progenitor/s that gave rise to the rest of Ethiopian donkey populations. Hence, based on mtDNA data, Ethiopian domestic donkeys are clustered into two major genetic groups: 1) Sinnar and 2) Abyssinian, Afar, Hararghe, Ogaden and Omo. On the other hand, genetic relationship studies based on microsatellite loci variation clusters Ethiopian donkeys into highland and lowland population, which is concordant with the traditional donkey classification systems in Ethiopia. Moreover, Reynolds' genetic distance estimate from mtDNA sequence polymorphism and population differentiation estimates based on Fst estimates obtained from microsatellite marker loci both support that donkeys descended from two ancestral lineages co-exist in Ethiopia. Phylogenetic analysis using the newly sequenced sequences and previously published worldwide sequences retrieved from the GenBank showed that Ethiopian donkey haplotypes formed the center of the network suggesting that Ethiopian haplotypes are the most likely founding lineage for most of the worldwide domestic donkeys. We also investigated the genetic diversity and relationship among eight native Ethiopian horse populations using 46 randomly selected mtDNA D-loop sequences sequenced for 454 bp. The 46 mtDNA D-loop sequences were characterized by only 15 variable sites that further shrunk into five distinct haplotypes. The average haplotype diversity was 0.706 ranging from 0.333 in Boran to 0.800 in Abyssinian, Ogaden and Selale horses. The average nucleotide diversity was 0.014 ranging from 0.0026 in Kundido feral horses to 0.0167 in Abyssinian horses. The average number of nucleotide differences was 6.320 ranged from 1.200 in Kundido feral to 7.600 in Abyssinian domestic horses. Only Boran domestic horses and Kundido feral horses were genetically distant from the rest o f native Ethiopian horse populations. This indicates that native Ethiopian horses have a narrow genetic background. Based on mtDNA diversity, native Ethiopian horses are clustered into three major genetic groups 1) Kundido feral horses; 2) Boran and Bale 3) Abyssinian, Horro, Kafa, Ogaden and Selale horse populations. Phylogenetic analysis carried out using network on the combined Eihio-Eurasian mtDNA D-loop sequences showed that haplotypes derived from native Ethiopian horses formed separate clusters indicating continental sequence grouping in domestic horses. This suggests that native Ethiopian horses may trace their matrilineal genetic origin back to other native horses that might had been independently domesticated in Africa or emerged from the interbreeding between native African and introduced Eurasian type horses. Thus, the genetic origin of native Ethiopian horses remained enigmatic. In any case however, African domestication of domestic horses cannot completely ruled out. This warrants further multidisciplinary studies.