A population based expression atlas provides insights into disease resistance and other physiological traits in cassava (Manihot esculenta Crantz)

Authors: OGBONNA, ALEX - Cornell University; RAMU, PUNNA - Cornell University; ESUMA, WILLIAMS - National Crops Resources Research Institute; NANDUDU, LEAH - Cornell University; MORALES, NICOLAS - Cornell University; POWELL, ADRIAN - Boyce Thompson Institute; KAWUKI, ROBERT - National Crops Resources Research Institute; BAUCHET, GUILLAUME - Boyce Thompson Institute; Jannink, Jean-Luc; MUELLER, LUKAS - Boyce Thompson Institute

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/22/2021
Publication Date: 12/7/2021
Citation: Ogbonna, A.C., Ramu, P., Esuma, W., Nandudu, L., Morales, N., Powell, A., Kawuki, R., Bauchet, G., Jannink, J., Mueller, L.A. 2021. A population based expression atlas provides insights into disease resistance and other physiological traits in cassava (Manihot esculenta Crantz). Scientific Reports. 11: Article e23520. https://doi.org/10.1038/s41598-021-02794-y.
DOI: https://doi.org/10.1038/s41598-021-02794-y

Interpretive Summary: Cassava, a food security crop in Africa, is grown throughout the tropics and subtropics. We carried out 3'RNA sequencing on 150 accessions from the National Crops Resources Research Institute, Uganda for 5 tissue types, providing gene transcription information to the research community in a web-based cassava expression atlas. Differential expression and gene co-expression network analysis were performed to detect 8820 significantly differentially expressed genes (DEGs), revealing similarity in expression patterns between tissue types and the clustering of detected DEGs into 18 gene modules. As a confirmation of data quality, differential expression and pathway analysis targeting cassava mosaic disease (CMD) identified 27 genes observed in the plant-pathogen interaction pathway and several previously identified CMD resistance genes. This data represents a new resource for understanding complex cassava traits at expression and molecular levels for the development of disease resistant and high-yielding cassava varieties.

Technical Abstract: Cassava, a food security crop in Africa, is grown throughout the tropics and subtropics. Although cassava can provide high productivity in suboptimal conditions, the yield in Africa is substantially lower than in other geographies. The yield gap is attributable to many challenges faced by cassava in Africa, including susceptibility to diseases and poor soil conditions. In this study, we carried out 3’RNA sequencing on 150 accessions from the National Crops Resources Research Institute, Uganda for 5 tissue types, providing population-based transcriptomics resources to the research community in a web-based queryable cassava expression atlas. Differential expression and weighted gene co-expression network analysis were performed to detect 8820 significantly differentially expressed genes (DEGs), revealing similarity in expression patterns between tissue types and the clustering of detected DEGs into 18 gene modules. As a confirmation of data quality, differential expression and pathway analysis targeting cassava mosaic disease (CMD) identified 27 genes observed in the plant–pathogen interaction pathway, several previously identified CMD resistance genes, and two peroxidase family proteins different from the CMD2 gene. Present research work represents a novel resource towards understanding complex traits at expression and molecular levels for the development of resistant and high-yielding cassava varieties, as exemplified with CMD.