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

Moustapha Grema,Maaouia Abdou,Albert Soudré,Moumouni Issa,Marichatou Hamani,Yenikoye Alhassane,Amadou Traoré,Hamidou H Tamboura,Rudolf Pichler,Kathiravan Periasamy,Moumouni Sanou

doi:10.5194/aab-60-399-2017

Abstract

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.

Highlights

Niger is a landlocked sub-Saharan country in West Africa that primarily depends on agriculture and livestock
235 alleles were amplified across 27 short tandem repeat (STR) loci in all three www.arch-anim-breed.net/60/399/2017/
The present study reports high genetic diversity and moderate levels of estimated inbreeding in three important breeds of Niger cattle

Summary

Introduction

Niger is a landlocked sub-Saharan country in West Africa that primarily depends on agriculture and livestock. The livestock sector contributes about 40 % of the country’s agricultural gross domestic product (GDP) and 14 % of the national GDP (Apaa-Okello et al, 2015). The rural livelihood is essentially dependent on livestock with four out of every five households rearing animals. Each of these households owns about 2.8 Tropical Livestock Units (TLU) that are predominantly made up of cattle (55 %) and small ruminants (33 %) (World Bank, 2012). Cattle in Niger play a vital role in rural subsistence and possess significant cultural importance, during the performance of religious rites and celebrations.

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