Whole genome SNPs and phenotypic characterization of cassava (Manihot esculenta Crantz) germplasm in the semi-deciduous forest ecology of Ghana

Abstract

Diversity assessment in crop germplasm is an essential component towards its improvement and conservation. This study was undertaken to determine the genetic diversity within 87 cassava accessions using agro-morphological traits and Diversity Array Technology by sequencing based SNP (DArTseq). Results indicated that, the accessions significantly vary for most traits. Principal component analysis further showed the extent to which height and levels of branching, petiole length and colour, yield, cassava mosaic severity and above ground biomass contribute to the variability among the genotypes. Cassava mosaic disease was also significantly negatively correlated with most of growth and yield traits including shoot biomass and tuber yield. High heritability estimates and genetic advance was obtained for most of the traits indicating a positive response to selection. The uniqueness of each genotype and enormous variability in accessions based on agro-morphological data were debunked by the DArT-based SNP markers as redundant accessions were obtained which goes to confirm the environmental sensitivity of genetically identical genotypes. SNP markers identified fifteen accessions as being redundant based on Gower's distance matrix with nine of these being landraces which shows the continuous exchange of planting materials among cassava growers hence their removal from the collection will enhance the management of the cassava germplasm. This has implication for cassava breeders to make informed choices in the selection of parental accessions for use in breeding programs. The narrow genetic base of the accessions as established by the SNPs necessitate the need to broaden the genetic base.