Cassava, a vital crop in sub-Saharan Africa, faces significant threats from diseases like cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). While CMD-resistant varieties have been developed, CBSD remains challenging due to the lack of durable resistance genes. CBSD, caused by cassava brown streak virus (CBSV) and Uganda cassava brown streak virus (UCBSV), leads to devasting foliar and root symptoms. Among these symptoms, root necrosis is the most devastating, as it renders the economically significant roots unstable for both human consumption and animal feed. Developing resistant varieties is crucial, but challenges include the absence of known durable resistance sources and complexities in breeding. Modern techniques like marker-assisted selection and genomic selection (GS), accelerate genetic gains. In addition, precise phenotyping including CBSD virus titer evaluation and root necrosis imaging aids high-throughput analysis. The first study focused on identifying genomic regions associated with CBSD severity scores from the 1-5 scoring method, emphasizing the role of genetics in CBSD resistance. An elite population of African cassava clones was used, selected through genomic selection. The study addresses the challenge of limited CBSD resistance alleles in African cassava populations. Valuable insights into CBSD resistance, along with the foundation for marker-assisted and genomic selection, were established. In the second study, CBSD root necrosis was examined through image analysis using PlantCV and Genome-Wide Association Studies (GWAS). Heritability estimates for these traits ranged from low to moderate, with the percentage of necrosis having the highest estimate while solidity of necrosis and convex hull area of root necrosis had lower estimates and GWAS led to the identification of unique genomic region and candidate genes. Interestingly, the results showed lower heritability and genomic associations with image analysis compared to the traditional 1-5 scoring method, contrary to expectations. Further research is needed to fully understand the genetic basis of these traits and their relevance to cassava breeding and disease management. The third study explored the dynamics of CBSV and UCBSV virus titers in cassava genotypes. Genetic factors predominantly influenced UCBSV titer, while CBSV titer was more affected by genotype-by-environment interactions. The research emphasized the independence of these viruses across different sites and years. Genome-wide studies identified unique genetic markers for each virus, offering insights into the genetic complexities of CBSD. Moving forward, it is recommended to validate identified SNPs, explore candidate gene functionality, and conduct multi-omics analyses to gain a holistic understanding of the genetic basis of CBSD. Moreover, replicating the research in diverse environments, investigating whitefly populations, and further genomic analyses are essential steps to enhance CBSD resistance breeding and ensure long-term food security in the region.