Genetic diversity and relationships among indigenous Borgou and White Fulani cattle breeds based on milk protein loci: Implications for breed improvement and conservation in Benin

Genetic diversity in a population is a prerequisite for implementing genetic selection. The aim of the study was to assess the genetic diversity, the gene flow and phylogenetic relationships among Borgou and White Fulani cattle breeds in Benin using the β-Lactoglobulin (MBLG), α-Lactalbumin (LALBA), αS1-Casein (CSN1S1 ) and κ-Casein (CSN3) genetic polymorphisms. Thus, 94 Borgou and 96 White Fulani indigenous cattle breeds were genotyped using polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) and Sanger sequencing methods. The results showed that all the studied loci were polymorphic. Borgou presented higher (p <0.01) observed heterozygosity (Hob) and unbiased gene diversity (H ex) (0.33, 0.36) than White Fulani (0.31, 0.33). The mean number of observed (MNA) alleles per locus was 2±0.000 in both breeds. The means expected number of alleles (MNE) were similar (p>0.05) in Borgou (1.59 ± 0.27) and White Fulani (1.50 ± 0.33). The f (within population inbreeding) and F (total inbreeding) were respectively 0.11 and 0.13 and were not different from zero (p>0.05). The population differentiation (q) was 0.02 and different from zero (p <0.01). High level of gene flow (Nem=16.44), a low Nei’s DA genetic distance (0.014) and a very close phylogenetic relationship were observed between both breeds. The high genetic exchange observed between the two indigenous cattle breeds is a big concern. There is therefore a need to develop a sustainable breeding program aiming to improve cattle productivity as well as their conservation in Benin. However, further studies with high density SNP chips are needed to better understand the genome-wide diversity of the studied breeds.