SSR-marker assisted evaluation of genetic diversity in local and exotic pigeonpea cultivars in Benin for parental genotypes selection

Pigeonpea production is limited in Benin due to the undesirable agronomic and organoleptic characteristics of cultivated landraces. For a breeding program, some exotic cultivars were introduced for improving the available genepool in the country. The present study aims to assess the genetic diversity within a collection comprising of 32 local and 28 exotic cultivars, with the objective of selecting suitable parental lines for pigeonpea genetic improvement. All of the 60 accessions were genotyped with 14 SSR makers and a total of 38 alleles were detected with an average of 2.71 alleles per locus. The mean value of PIC (Polymorphism Information Content) and overall gene diversity were 0.37 and 0.43, respectively, while the mean value of heterozygosity was 0.11, indicating moderate genetic diversity within the 60 accessions with a deficit of heterozygous genotypes. As expected, the diversity was higher in exotic cultivars than in local landraces. Based on the genetic relationship among accessions, the entire collection formed 3 clusters, one of which comprised four specific exotic accessions. Population structure analysis using model-based and DAPC (Discriminant Analysis for Principal Components) methods subdivided the 60 accessions into two major groups reflecting their geographic origins with a minimal number (02) of admixtures. This indicates significant genetic divergence between local and exotic cultivars. Analysis of Molecular Variance (AMOVA) results with an overall Fst value of 0.13 confirmed the significant genetic divergence between the two collections. The findings of this study will significantly benefit for pigeonpea breeding programs in Benin. For practical applications, selected exotic cultivars, particularly those within the specific cluster can immediately serve as donor parents in crossbreeding schemes with the local landraces, for developing new varieties.