Variation in cassava (Manihot esculenta Crantz) based on single nucleotide polymorphisms, simple sequence repeats and phenotypic traits

English: Science-driven interventions aimed at increasing cassava’s (Manihot esculenta Crantz), productivity will positively impart on communities that primarily depend on it. Data presented in this thesis contributed towards this goal. Specifically, this thesis examined phenotypic variation in cassava germplasm available within selected national breeding programmes, analysed patterns of allele frequency distribution in the cassava germplasm, characterised single nucleotide polymorphisms (SNPs) in the cassava genome and examined variation for two agronomic [root dry matter content (DMC) and harvest index (HI)] and one quality trait (amylose content) in S1 cassava inbreds. The 29 qualitantive traits provided limited discrimination of cassava germplasm from Uganda, Kenya, Tanzania, Rwanda, Democratic Republic of Congo and Madagascar. However, significant differences in root DMC, HI, leaf retention (LR) and root cortex thickess were observed in this germplasm. Highest average DMC was registered in Uganda (37.7%) and lowest in Tanzania (30.1%), with the elite genotypes having a relatively higher DMC than local genotypes. Similary, highest average HI was observed in Uganda (0.60) and lowest in Kenya (0.32). This germplasm (1401 local and elite cassava genotypes) were furthermore genotyped using simple sequence repeat (SSR) markers. Genotypes were assigned to three distinct populations, with no appreciable gene differentiation (FST = 0.089) observed. Most genetic variation (> 89%) was detected within individuals. A total of 26 SNPs were identified from quality sequences of nine genes, giving an estimated frequency of one SNP for every 121 nucleotides. Nucleotide diversity ranged from 7.8 x 10-4 to 5.63 x 10-3. Average haplotype-based polymorphism information content (PIC = 0.414) was higher than for individual SNP (PIC = 0.228). HI and DMC varied both within and between the cassava S1 families. The highest reduction in HI was observed in S1 progeny from Bamunanika (83.3%), while the highest reduction in DMC (23.8%) was observed in S1 progeny from I92/00067. Amylose content varied significantly between cassava families and S1 progeny, with most of the variation recorded within progeny.