Genetic diversity and phylogenetic relationships in local cattle breeds of Senegal based on autosomal microsatellite markers

Abstract

Aim:In Senegal, uncontrolled cross-breeding of cattle breeds and changes in production systems are assumed to lead to an increase of gene flow between populations. This might constitute a relevant threat to livestock improvement. Therewith, this study was carried out to assess the current genetic diversity and the phylogenetic relationships of the four native Senegalese cattle breeds (Gobra zebu, Maure zebu, Djakoré, and N’Dama).Methods:Genomic DNA was isolated from blood samples of 120 unrelated animals collected from three agro-ecological areas of Senegal according to their phenotypic traits. Genotyping was done using 11 specific highly polymorphic microsatellite makers recommended by Food and Agriculture Organization. The basic measures of genetic variation and phylogenetic trees were computed using bioinformatics’ software.Results:A total of 115 alleles were identified with a number of alleles (Na) at one locus ranging from 6 to 16. All loci were polymorphic with a mean polymorphic information content of 0.76. The mean allelic richness (Rs) lay within the narrow range of 5.14 in N’Dama taurine to 6.10 in Gobra zebu. While, the expected heterozygosity (HE) per breed was high in general with an overall mean of 0.76±0.04. Generally, the heterozygote deficiency (FIS) of 0.073±0.026 was relatively due to inbreeding among these cattle breeds or the occurrence of population substructure. The high values of allelic and gene diversity showed that Senegalese native cattle breeds represented an important reservoir of genetic variation. The genetic distances and clustering trees concluded that the N’Dama cattle were most distinct among the investigated cattle populations. So, the principal component analyses showed qualitatively that there was an intensive genetic admixture between the Gobra zebu and Maure zebu breeds.Conclusions:The broad genetic diversity in Senegalese cattle breeds will allow for greater opportunities for improvement of productivity and adaptation relative to global changes. For the development of sustainable breeding and crossbreeding programs of Senegalese local breeds, effective management is needed towards genetic selection and transhumance to ensure their long-term survival.

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

“…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).…”

“…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.…”

“…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).…”

Genetic diversity in Zimbabwean Sanga cattle breeds using microsatellite markers

“…In Mozambique, Bessa et al (2009) found allelic diversity of 5.9-6.4 alleles per locus. However, Ndiaye et al (2015) reported 10.5 alleles per locus among Senegalese cattle, and Sharma et al (2013) reported 9.0 alleles per locus in Indian cattle breeds. Although comparable with other studies, genetic variability in this study was moderate and similar between breeds.…”

“…In recent times, various types of DNA-based (molecular) markers have been utilized to evaluate genetic variability within and between African cattle breeds (Kugonza et al, 2011;Ngono-Ema et al, 2014;Ndiaye et al, 2015). Among them, microsatellite and single nucleotide polymorphism (SNP) markers are the most efficient molecular markers to evaluate genetic diversity, population differentiation and breed relationships, and determine parentage in animal populations (Yang et al, 2013).…”