Assessment of genetic diversity in Phaseolus lunatus varieties cultivated in Côte d’Ivoire through microsatellite markers

Phaseolus lunatus L. (lima bean) is a food legume that is widely appreciated in Côte d’Ivoire, but its genetic diversity and population structure are poorly documented. We assessed SSR-based genetic diversity among 87 accessions collected from 33 localities across the four main agroecological zones of Côte d’Ivoire. A total of 379 individuals were genotyped at ten polymorphic microsatellite loci, and diversity was compared across three levels of stratification: collection zone, seed-coat color and morphological group. Polymorphism information content ranged from 0.51 to 0.79, with a mean of 0.66. The mean number of alleles per locus ranged from 1.66 across seed-color classes to 2.33 across morphological groups, and the proportion of polymorphic loci from 56 to 92.5%, reaching 100% in groups G2 and G4 and in the southern collections. Observed heterozygosity was low in every stratum (means 0.06–0.10) and fixation indices were correspondingly high (means 0.59–0.83), as expected in a predominantly self-pollinating species. The Shannon index was highest for morphological groups (0.59). Analysis of molecular variance attributed 12% to 30% of the total variation to differences among strata. Bayesian clustering in STRUCTURE supported four gene pools (K = 4) corresponding to geographic zones and to morphological groups, with limited admixture. Morphological groups captured more genetic variation than either seed color or geographic origin, and therefore provide the most useful proxy for the underlying gene pools. Future collecting missions should concentrate on southern Côte d’Ivoire and sample across morphological groups and seed-coat types in order to maximise the diversity captured.