Abstract:

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
(Hl)] and one quality trait (amylose content) in S, 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 '1 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 S| families. The highest reduction in Hl was observed in
Si progeny from Bamunanika (83.3%), while the highest reduction in DMC (23.8%) was
observed in Si progeny from 192/00067. Amylose content varied significantly between
cassava families and Si progeny, with most of the variation recorded within progeny.