Genetic diversity assessment of the indigenous goat population of Benin using microsatellite markers

Habib Rainier Vihotogbe Whannou; Martin Spanoghe; Guiguigbaza-Kossigan Dayo; Dominique Demblon; Deborah Lanterbecq; Luc Hippolyte Dossa

doi:10.3389/fgene.2023.1079048

Genetic diversity assessment of the indigenous goat population of Benin using microsatellite markers

Front Genet. 2023 Mar 17:14:1079048. doi: 10.3389/fgene.2023.1079048. eCollection 2023.

Authors

Habib Rainier Vihotogbe Whannou¹, Martin Spanoghe², Guiguigbaza-Kossigan Dayo³, Dominique Demblon⁴, Deborah Lanterbecq², Luc Hippolyte Dossa¹

Affiliations

¹ Ecole des Sciences et Techniques de Production Animale, Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, Cotonou, Benin.
² Laboratory of Biotechnology and Applied Biology, Haute Ecole Provinciale de Hainaut-Condorcet, Hainaut, Belgium.
³ Centre International de Recherche-Développement sur l'Elevage en Zone Subhumide (CIRDES), Bobo-Dioulasso, Burkina Faso.
⁴ Haute Ecole Provinciale de Hainaut-Condorcet, Hainaut, Belgium.

Abstract

Improved knowledge of the diversity within and among local animal populations is increasingly necessary for their sustainable management. Accordingly, this study assessed the genetic diversity and structure of the indigenous goat population of Benin. Nine hundred and fifty-four goats were sampled across the three vegetation zones of Benin [i.e., Guineo-Congolese zone (GCZ), Guineo-Sudanian zone (GSZ), and Sudanian zone (SZ)] and genotyped with 12 multiplexed microsatellite markers. The genetic diversity and structure of the indigenous goat population of Benin were examined using the usual genetic indices (number of alleles Na, expected and observed heterozygosities He and Ho, Fixation index F_ST, coefficient of genetic differentiation G_ST), and three different methods of structure assessment [Bayesian admixture model in STRUCTURE, self-organizing map (SOM), and discriminant analysis of principal components (DAPC)]. The mean values of Na (11.25), He (0.69), Ho (0.66), F_ST (0.012), and G_ST (0.012) estimated in the indigenous Beninese goat population highlighted great genetic diversity. STRUCTURE and SOM results showed the existence of two distinct goat groups (Djallonké and Sahelian) with high crossbreeding effects. Furthermore, DAPC distinguished four clusters within the goat population descending from the two ancestry groups. Clusters 1 and 3 (most individuals from GCZ) respectively showed a mean Djallonké ancestry proportion of 73.79% and 71.18%, whereas cluster 4 (mainly of goats from SZ and some goats of GSZ) showed a mean Sahelian ancestry proportion of 78.65%. Cluster 2, which grouped almost all animals from the three zones, was also of Sahelian ancestry but with a high level of interbreeding, as shown by the mean membership proportion of only 62.73%. It is therefore urgent to develop community management programs and selection schemes for the main goat types to ensure the sustainability of goat production in Benin.

Keywords: Capra hircus; genetic structure; indigenous farm animal genetic resources; molecular genetic characterization; phytogeographic zones.

Grants and funding

This work is financially supported by the Government of Belgium through the “Académie de Recherche et d’Enseignement Supérieur (ARES)”. ARES-PRD Project entitled “Amélioration des systèmes traditionnels d’élevage de petits ruminants (ovins et caprins) dans un contexte de mutation environnementale et sociétale au Bénin” https://www.ares-ac.be/fr/cooperation-au-developpement/pays-projets /projets-dans-le-monde/item/150-prd-amelioration-des-systemes-tradi tionnels-d-elevage-de-petits-ruminants-ovins-et-caprins-dans-un-cont exte-de-mutation-environnementale-et-societale-au-Benin.