Genetic complexity of cassava brown streak disease: insights from qPCR-based viral titer analysis and genome-wide association studies

Authors: NANDUDU, LEAH - Cornell University; SHEAT, SAMAR - Institute For Plant Protection In Field Crops And Grassland; WINTER, STEPHAN - Institute For Plant Protection In Field Crops And Grassland; 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: 2/29/2024
Publication Date: 3/12/2024
Citation: Nandudu, L., Sheat, S., Winter, S., Ogbonna, A., Kawuki, R., Jannink, J. 2024. Genetic complexity of cassava brown streak disease: insights from qPCR-based viral titer analysis and genome-wide association studies. Frontiers in Plant Science. Volume 15. https://doi.org/10.3389/fpls.2024.1365132.
DOI: https://doi.org/10.3389/fpls.2024.1365132

Interpretive Summary: Cassava, an important food crop worldwide, is under threat from Cassava Brown Streak Disease (CBSD), which is caused by two viruses: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). The usual method of checking for the disease by looking at symptoms (using a 1-5 scale) isn’t always accurate. A more precise method called qPCR can measure the amount of virus in the plant, but it’s expensive. In this study, researchers used qPCR to measure the levels of these viruses in cassava plants. They wanted to see how these levels varied in different environments, how they related to the usual symptom scores, and which parts of the cassava genome are linked to these virus levels. They found that CBSV was much more common (50.2%) in the plants than UCBSV (12.9%), with some plants infected by both viruses. The study also showed that the genetics of the plants had a big impact on how much UCBSV was present, while environmental factors mostly affected CBSV levels. The researchers identified specific regions in the cassava genome associated with the levels of these viruses, with certain genetic markers explaining a large part of the variation in virus levels. These findings help us better understand how these viruses affect cassava and could lead to better breeding strategies to protect the crop.

Technical Abstract: Cassava, a vital global food source, faces a threat from Cassava Brown Streak Disease (CBSD). CBSD results from two viruses: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). These viruses frequently pose challenges to the traditional symptom-based 1-5 phenotyping method due to its limitations in terms of accuracy and objectivity. Quantitative polymerase chain reaction (qPCR) offers precise virus quantification, although high costs hinder its widespread adoption. In this research, we utilized qPCR to measure the viral titer/load of CBSV and UCBSV. The objectives were to evaluate titer variability within the Cycle 2 (C2) population in two different environments, establish connections between viral titers and CBSD severity scores from the 1-5 scoring method, perform Genome-Wide Association Studies (GWAS) to identify genomic regions associated with CBSV and UCBSV titers, and investigate the functional annotated genes. The results demonstrated a significantly higher prevalence of CBSV (50.2%) in clones compared to UCBSV (12.9%) with mixed infections in some cases. Genotypic effects, particularly concerning UCBSV, were significant, with genotype-by-environment effects primarily influencing CBSV titer. GWAS Studies identified genomic regions associated with CBSV and UCBSV titers. Twenty-one SNP markers on chromosomes 10, 13, 17, and 18 exhibited significant associations with CBSV titer, collectively explaining 43.14% of the phenotypic variation. Additionally, 25 SNP markers on chromosomes 1, 2, 4, 5, 8, 11, 12, 13, 16, and 18 were associated with UCBSV titer, and explained 70.71% of the phenotypic variation. No shared genomic regions were identified between CBSV and UCBSV viral titers. Gene ontology analysis also revealed diverse gene functions, especially in transport and catalytic activities. These findings enhance our understanding of virus prevalence, genetics, and molecular functions in cassava plants, offering valuable insights for targeted breeding strategies.