Assessing Genetic Relatedness of In Vitro Cassava Accessions Using Quantitative Morphological Traits and DarTseq Single Nucleotide Polymorphism (SNP) Markers

Genetic diversity is crucial for breeding progress and biodiversity. Genetic relatedness was assessed using quantitative morphological traits (plant height, root length, number of roots, number of leaves, leaf length, leaf width, and number of leaf lobes) and SNP markers of 101 in vitro cassava ( Manihot esculenta Crantz) accessions from the International Institute of Tropical Agriculture (IITA), Genetic Resources Centre, in 2023. Analysis of Variance (ANOVA) of morphological traits revealed significant differences (P < 0.01) of all traits across accessions and weeks. Root length and number of leaf lobes had significant differences (P < 0.01) across accessions and weeks. Cluster analysis identified four distinct clusters. Principal Component Analysis (PCA) revealed that the first three components explained 67.26% of the total variation among accessions. The leaf length (LL), Leaf width (LW), Number of roots (NR), Plant height (PH), and Root Length (RL) had the highest eigenvalues of -0.551, -0.531, -0.398, -0.383, and − 0.298 respectively in PC1. A strong positive correlation (r = 0.81***) was observed between leaf width and leaf length. Genome-wide SNP markers were generated using the DArTseq Genotype by Sequencing approach. Polygenic analysis using 19,467 SNPs identified four distinct genetic groups within cassava population. Phylogenetic and PCA analyses yielded consistent results. Molecularly, PCA revealed that the first three PCs explained 15%, 4.74%, and 3.7% of the genetic variation in the cassava population. SNP markers are effective for evaluating genetic diversity and identifying duplicates in the cassava collection. These results have important implications for cassava genebank management, quality control, conservation strategy, germplasm exchange, and future breeding efforts.