Genetic analysis of cassava brown streak disease root necrosis using image analysis and genome-wide association studies

Authors: NANDUDU, LEAH - Cornell University; STROCK, CHRISTOPHER - Cornell University; OGBONNA, ALEX - Cornell University; KAWUKI, ROBERT - National Agricultural Research Laboratories; Jannink, Jean-Luc

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/7/2024
Publication Date: 3/17/2024
Citation: Nandudu, L., Strock, C., Ogbonna, A., Kawuki, R., Jannink, J. 2024. Genetic analysis of cassava brown streak disease root necrosis using image analysis and genome-wide association studies. Frontiers in Plant Science. Voulume 15. https://doi.org/10.3389/fpls.2024.1360729.
DOI: https://doi.org/10.3389/fpls.2024.1360729

Interpretive Summary: Cassava brown streak disease (CBSD) is a serious threat to food security. To tackle this, researchers used a tool called PlantCV to analyze images of diseased cassava roots from 320 different plants. They aimed to find specific regions in the cassava genome linked to the disease. They discovered that some traits, like the size and shape of the necrotic (damaged) areas in the roots, were strongly related to each other. However, the usual method of scoring the disease on a scale of 1 to 5 didn't match well with the detailed image analysis. The researchers found that certain genetic markers (SNPs) on chromosomes 1, 7, and 11 were connected to these root traits. They identified 24 potential genes in one region that might be involved in the disease. Although they expected that using image analysis would give better results for predicting how these traits are inherited, the results were not as strong as they hoped. More research is needed to fully understand the genetics behind these traits and how they can help improve cassava breeding and disease management.

Technical Abstract: Cassava brown streak disease (CBSD) poses a substantial threat to food security. To address this challenge, we used PlantCV to extract CBSD root necrosis image traits from 320 clones, with an aim of identifying genomic regions through genome-wide association studies (GWAS) and candidate genes. Results revealed strong correlations among certain root necrosis image traits, such as necrotic area fraction and necrotic width fraction, as well as between the convex hull area of root necrosis and the percentage of necrosis. Low correlations were observed between CBSD scores obtained from the 1-5 scoring method and all root necrosis traits. Broad-sense heritability estimates of root necrosis image traits ranged from low to moderate, with the highest estimate of 0.42 observed for the percentage of necrosis, while narrow-sense heritability consistently remained low, ranging from 0.03 to 0.22. Leveraging data from 30,750 SNPs obtained through DArT genotyping, eight SNPs on chromosomes 1, 7, and 11 were identified and associated with both the ellipse eccentricity of root necrosis and the percentage of necrosis through GWAS. Candidate gene analysis in the 172.2kb region on the chromosome 1 revealed 24 potential genes with diverse functions, including ubiquitin-protein ligase, DNA-binding transcription factors, and RNA metabolism protein, among others. Despite our initial expectation that image analysis objectivity would yield better heritability estimates and stronger genomic associations than the 1-5 scoring method, the results were unexpectedly lower. Further research is needed to comprehensively understand the genetic basis of these traits and their relevance to cassava breeding and disease management.