Microsatellite analysis reveals high genetic diversity but low genetic structure in Ethiopian indigenous cattle populations

Dadi, Hailu; Tibbo, Markos; Takahashi, Yusuke; Nomura, Kazutaka; Hanada, Hirofumi; Amano, Takashi

doi:10.1111/j.1365-2052.2008.01748.x

Cited by 67 publications

(69 citation statements)

References 26 publications

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“…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).…”

Section: Discussionsupporting

confidence: 78%

“…Recent molecular studies have characterized Ethiopian cattle breeds by using a limited number of low-density microsatellites, mitochondrial DNA (mtDNA) or Y-chromosome markers (Li et al, 2007;Dadi et al, 2008;Zerabruk et al, 2011). To date, Bangladeshi cattle populations have not been subjected to thorough molecular investigation; however, limited study of the Red Chittagong population has been conducted using mtDNA (Bhuiyan et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

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

Edea

Bhuiyan

Dessie³

et al. 2015

Animal

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Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69 903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.

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Section: Discussionsupporting

confidence: 78%

Section: Introductionmentioning

confidence: 99%

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

Edea

Bhuiyan

Dessie³

et al. 2015

Animal

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“…3). High levels of admixture in Niger cattle were strongly evident and consistent with the reports on other African cattle (Dadi et al, 2008;Ndiaye et al, 2015). A general point of view is that the B. indicus first entered the African continent via the Suez route from Arabia (Epstein and Mason, 1984) and maritime routes to the Horn of Africa (Hanotte et al, 2002).…”

Section: Individual Assignment In Niger Cattlesupporting

confidence: 71%

“…Similarly, the pairwise allele sharing distance varied from 0.223 (Zebu Arabe-Kuri) to 0.259 (Zebu Bororo-Kuri) ( Table 3). The overall F ST observed in Niger cattle was much lower than that reported for Sudanese (F ST = 0.084; Hussein et al, 2015), Cameroonian (F ST = 0.061; Ngono Ema et al, 2014) and other West African cattle (F ST = 0.06; Freeman et al, 2004), while the estimate was relatively higher than that of Ethiopian cattle (F ST = 0.013; Dadi et al, 2008). Further, to evaluate within-and between-population diversities, pairwise allele sharing distances were calculated for all possible pairs of individuals within and across populations.…”

Section: Genetic Differentiation Among Niger Cattle Breedsmentioning

confidence: 42%

“…The values observed in Niger cattle are understandable as the sample size varied across the breeds and low-frequency alleles normally contribute little to the effective number of alleles. Estimates of allelic diversity and heterozygosity in Niger cattle breeds were comparable to those of Cameroonian (Ngono Ema et al, 2014), Senegal (Ndiaye et al, 2015, Sahelian (Alvarez et al, 2014), Sudanese (Hussein et al, 2015), Ethiopian (Dadi et al, 2008) , 2004). In general, the indigenous cattle breeds of Niger showed high levels of genetic diversity, possibly due to admixture of zebu and taurine cattle that had formed the foundation stock of these populations in the past (Dadi et al, 2008).…”

Section: Genetic Variation In Niger Cattlementioning

confidence: 71%

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Short tandem repeat (STR) based genetic diversity and relationship of indigenous Niger cattle

et al. 2017

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Abstract. The diversity of cattle in Niger is predominantly represented by three indigenous breeds: Zebu Arabe, Zebu Bororo and Kuri. This study aimed at characterizing the genetic diversity and relationship of Niger cattle breeds using short tandem repeat (STR) marker variations. A total of 105 cattle from all three breeds were genotyped at 27 STR loci. High levels of allelic and gene diversity were observed with an overall mean of 8.7 and 0.724 respectively. The mean inbreeding estimate within breeds was found to be moderate with 0.024, 0.043 and 0.044 in Zebu Arabe, Zebu Bororo and Kuri cattle respectively. The global F statistics showed low genetic differentiation among Niger cattle with about 2.6 % of total variation being attributed to between-breed differences. Neighbor-joining tree derived from pairwise allele sharing distance revealed Zebu Arabe and Kuri clustering together while Zebu Bororo appeared to be relatively distinct from the other two breeds. High levels of admixture were evident from the distribution of pairwise inter-individual allele sharing distances that showed individuals across populations being more related than individuals within populations. Individuals were assigned to their respective source populations based on STR genotypes, and the percent correct assignment of Zebu Bororo (87.5 to 93.8 %) was consistently higher than Zebu Arabe (59.3 to 70.4 %) and Kuri (80.0 to 83.3 %) cattle. The qualitative and quantitative tests for mutation drift equilibrium revealed absence of genetic bottleneck events in Niger cattle in the recent past. High genetic diversity and poor genetic structure among indigenous cattle breeds of Niger might be due to historic zebu-taurine admixture and ongoing breeding practices in the region. The results of the present study are expected to help in formulating effective strategies for conservation and genetic improvement of indigenous Niger cattle breeds.

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Mitochondrial DNA variation reveals maternal origins and demographic dynamics of Ethiopian indigenous goats

Tarekegn

Tesfaye

Mwai

et al. 2018

Ecology and Evolution

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The Horn of Africa forms one of the two main historical entry points of domestics into the continent and Ethiopia is particularly important in this regard. Through the analysis of mitochondrial DNA (mtDNA) d‐loop region in 309 individuals from 13 populations, we reveal the maternal genetic variation and demographic dynamics of Ethiopian indigenous goats. A total of 174 variable sites that generated 231 haplotypes were observed. They defined two haplogroups that were present in all the 13 study populations. Reference haplotypes from the six globally defined goat mtDNA haplogroups show the two haplogroups present in Ethiopia to be A and G, the former being the most predominant. Although both haplogroups are characterized by an increase in effective population sizes (N e) predating domestication, they also have experienced a decline in N e at different time periods, suggesting different demographic histories. We observed seven haplotypes, six were directly linked to the central haplotypes of the two haplogroups and one was central to haplogroup G. The seven haplotypes were common between Ethiopia, Kenya, Egypt, and Saudi Arabia populations, suggesting common maternal history and the introduction of goats into East Africa via Egypt and the Arabian Peninsula, respectively. While providing new mtDNA data from a historically important region, our results suggest extensive intermixing of goats mediated by human socio‐cultural and economic interactions. These have led to the coexistence of the two haplogroups in different geographic regions in Ethiopia resulting in a large caprine genetic diversity that can be exploited for genetic improvement.

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Microsatellite analysis reveals high genetic diversity but low genetic structure in Ethiopian indigenous cattle populations

Cited by 67 publications

References 26 publications

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

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

Short tandem repeat (STR) based genetic diversity and relationship of indigenous Niger cattle

Mitochondrial DNA variation reveals maternal origins and demographic dynamics of Ethiopian indigenous goats

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