Genome-wide association mapping and genomic prediction for CBSD resistance in Manihot esculenta

Authors: KAYONDO, ISMAIL - National Agricultural Research Organization - Uganda; PINO DEL CARPIO, DUNIA - Cornell University; LOZANO, ROBERTO - Cornell University; OZIMATI, ALFRED - Cornell University; WOLFE, MARNIN - Cornell University; BAGUMA, YONA - National Agricultural Research Organization - Uganda; GRACEN, VERNON - University Of Ghana; OFFEI, SAMUEL - University Of Ghana; FERGUSON, MORAG - International Institute For Tropical Agriculture; KAWUKI, ROBERT - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; Jannink, Jean-Luc

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/8/2018
Publication Date: 1/24/2018
Citation: Kayondo, I., Pino Del Carpio, D., Lozano, R., Ozimati, A., Wolfe, M., Baguma, Y., Gracen, V., Offei, S., Ferguson, M., Kawuki, R., Jannink, J. 2018. Genome-wide association mapping and genomic prediction for CBSD resistance in Manihot esculenta. Scientific Reports. 8:1549. https://doi.org/10.1038/s41598-018-19696-1.
DOI: https://doi.org/10.1038/s41598-018-19696-1

Interpretive Summary: Cassava (Manihot esculenta Crantz) is an important security crop in sub-Saharan Africa that faces severe yield loses due to cassava brown streak disease (CBSD). Motivated by the slow progress of conventional breeding, genomic selection (GS), aided by genome-wide association mapping (GWAS), is being evaluated in. In this study, two cassava breeding panels were scored with genomic markers and evaluated for foliar and CBSD root symptoms at five locations in Uganda. We found two regions associated with CBSD, one on chromosome 4 which co-localizes with a Manihot glaziovii introgression segment and one on chromosome 11, which contains a cluster of genes known to be involved in disease resistance. We evaluated the potential of GS to improve CBSD resistance by assessing the accuracy of seven prediction models. For all disease-related traits, two methods called “Random Forest” and “reproducing kernel Hilbert spaces regression” showed the highest predictive accuracies. Our results provide insight into the genetics of CBSD resistance to guide CBSD marker-assisted breeding and highlight the potential of GS to improve cassava breeding.

Technical Abstract: Cassava (Manihot esculenta Crantz) is an important security crop that faces severe yield loses due to cassava brown streak disease (CBSD). Motivated by the slow progress of conventional breeding, genetic improvement of cassava is undergoing rapid change due to the implementation of quantitative trait loci mapping, Genome-wide association mapping (GWAS), and genomic selection (GS). In this study, two breeding panels were genotyped for SNP markers using genotyping by sequencing and phenotyped for foliar and CBSD root symptoms at five locations in Uganda. Our GWAS study found two regions associated to CBSD, one on chromosome 4 which co-localizes with a Manihot glaziovii introgression segment and one on chromosome 11, which contains a cluster of nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes. We evaluated the potential of GS to improve CBSD resistance by assessing the accuracy of seven prediction models. Predictive accuracy values varied between CBSD foliar severity traits at 3 months after planting (MAP) (0.27–0.32), 6 MAP (0.40–0.42) and root severity (0.31–0.42). For all traits, Random Forest and reproducing kernel Hilbert spaces regression showed the highest predictive accuracies. Our results provide an insight into the genetics of CBSD resistance to guide CBSD marker-assisted breeding and highlight the potential of GS to improve cassava breeding.