Abstract: Cassava (Manihot esculenta Crantz) is a crucial staple crop in Kenya, but its genetic diversity has not been fully exploited in breeding programs. This study compares phenotypic and molecular characterisation methods for cassava germplasm to assess its efficacy in reflecting genetic relationships. A total of 131 cassava genotypes were collected and characterised using morphological traits, which grouped the accessions into four major clusters with a similarity index of 0.5. From these, 40 samples were selected for molecular characterisation using the unweighted pair group method with arithmetic means (UPGMA) at a similarity coefficient of 0.35. The study found significant discrepancies between phenotypic and molecular classifications. While phenotypic characterisation categorised accessions into four clusters based on observable traits, molecular analysis revealed two main genetic clusters. Phenotypically distinct accessions from clusters #1, 2, and 4 were grouped together in molecular cluster #1(a), indicating closer genetic relationships. Accessions with similar observable traits, such as "Nyarkogutu-002," were found to be genetically distinct. Additionally, the study found a low correlation (0.0423) between phenotypic and molecular characterisations of cassava germplasm. Therefore, the study recommends using molecular markers to select genetically distant parents, even if they appear phenotypically similar, to enhance allele diversity and heterosis in breeding efforts. Thus, there is a need for a combined approach of phenotypic and molecular characterisation to improve the accuracy of cassava germplasm classification, thus supporting more effective breeding and conservation strategies.
Keywords: Cassava germplasm, Genetic diversity, Molecular characterization, Phenotypic characterization, Kenya