Genetic Diversity Assessment of Hydrocyanic Acid, Total Carotenoid, and Dry Matter Content in Biofortified Cassava Using SNP Markers

This study seeks to determine the genetic diversity among two cassava populations for total carotene content, dry matter, and hydrogen cyanide using single nucleotide polymorphic (SNP) markers. 376 cassava genotypes from two populations were assayed with nine trait-linked SNP markers. Data collected were subjected to marker (Minor Allele Frequency-MAF; Gene Diversity-GD; Heterozygosity-He; and Polymorphic Information Content-PIC) and principal components (PCA) analyses. A high call rate of 96 to 100% was observed across the populations. Discriminate analysis of PCA and hierarchical cluster dendrogram using the SNP markers categorized the genotypes into three clusters with 257, 88 and 15 genotypes in clusters 1, 2, and 3, respectively. The variation explained by the first two PCs was 39.1%. The level of genetic diversity observed in this study indicates sufficient variation in the two populations, hence promising for the pyramiding of genes for the three traits. The SNP markers used for this study were highly informative and polymorphic and revealed good estimates of genetic diversity. Clustering patterns of the genotypic backgrounds along the PC axis reflect an intense exchange of genetic backgrounds among the populations studied. Results from this study may contribute significantly to cassava breeding and germplasm conservation programs.