Molecular characterization of cassava (Manihot esculenta Crantz) germplasm in Kenya

Abstract

Globally, as a staple food crop, cassava (Manihot esculenta Crantz) provides millions of people with a substantial amount of carbohydrates. Selection of the appropriate parental forms for breeding programs is the most crucial decision made by plant breeders in order to maximize genetic variability and produce superior recombinant varieties. However, insufficient genetic diversity and population structure data regarding Kenyan cassava accessions hinder the appropriate breeding parent selection process. Thus, this study sought to determine the genetic diversity and population structure among 40 sampled cassava accessions grown in Kenya by use of start-codontargeted (SCoT) molecular markers. The study utilized 15 SCoT molecular markers. A total of 119 fragments were amplified, of which 89.9% were polymorphic with an average of 7.13 polymorphic fragments per primer. The polymorphic information content (PIC) value and primer resolving power (Rp) of 0.35 and 3.44 respectively, revealed a moderate genetic diversity among the accessions. A dendrogram based on the unweighted pair group method of arithmetic means (UPGMA) grouped the 40 cassava accessions into two clusters at 0.35 genetic similarity coefficients. Bayesian structural analysis identified two subpopulations as well as a few admixed accessions. Analysis of molecular variance (AMOVA) revealed a variance of 84% within the subpopulations and 14% among the subpopulations. The moderate level of genetic variation in the cassava accessions that SCoT molecular markers were able to successfully identify, can serve as a tool for expanding the genetic base in cassava breeding initiatives. Cassava breeding and variety development may benefit from the selection and hybridization of parental lines from the various clusters and subclusters that have been established.