Genetic diversity and population structure of cavy (Cavia porcellus L) in three agro ecological zones of Côte d'Ivoire

To investigate the genetic diversity and population structure of cavies (Cavia porcellus (Linnaeus, 1758) from three agro ecological zones (North, central, and South) of Ivory Coast, 14 microsatellites markers were used. A total of 131 cavies were genotyped. The measure of population diversity for the three populations revealed a mean allele frequency of 6.0, 5.5 and 6.429 (P<0,05) for the north, central and south populations respectively. The observed heterozygosity (Ho) was 0.511 ± 0.66, 0.505 ± 0.55 and 0.567 ± 0.064 (p < 0,05) for the north, central and south populations and in all cases lower than the expected heterozygosity (He) (0.577 ± 0.059 , 0.634 ± 0.051, 0.645 ± 0.052) respectively. This indicates low heterozygosity across the three populations in the whole population., The population specific inbreeding coefficients (FSt) were 0.1695, 0.2768 and 0.2245 (P < 0,01) for the three separate populations and a mean of 0.2257.There were no clear differences in the population structure with only 2.59 % variation among the three populations and 21.99 % variation among individuals within a population. There were high rates of inbreeding in all the three populations (mean 0.2257 (p < 0,01). Therefore the tree population would mix. It is difficult to select non-related animals and thus control inbreeding in the target populations or selection for particular traits of interest.