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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #332003
Title: Genome-wide association and prediction analysis in African cassava (Manihot esculenta) reveals the genetic architecture of resistance to cassava mosaic disease and prospects for rapid genetic improvement

Author
item WOLFE, MARNIN - Cornell University
item RABBI, ISMAIL - International Institute For Tropical Agriculture
item EGESI, CHIEDOZIE - National Root Crops Research Institute (NRCRI)
item HAMBLIN, MARTHA - Cornell University
item KAWUKI, ROBERT - International Institute Of Tropical Agriculture (IITA)
item KULAKOW, PETER - International Institute For Tropical Agriculture
item LOZANO, ROBERTO - Cornell University
item DEL CARPIO, DUNIA PINO - Cornell University
item RUMU, PUNNA - Cornell University
item Jannink, Jean-Luc

Submitted to: Virus Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/11/2016
Publication Date: 3/13/2016
Citation: Wolfe, M.D., Rabbi, I.Y., Egesi, C., Hamblin, M., Kawuki, R., Kulakow, P., Lozano, R., Del Carpio, D., Rumu, P., Jannink, J. 2016. Genome-wide association and prediction analysis in African cassava (Manihot esculenta) reveals the genetic architecture of resistance to cassava mosaic disease and prospects for rapid genetic improvement. Virus Research. 9. doi: 10.3835/plantgenome2015.11.0118.

Interpretive Summary: Cassava (Manihot esculenta) is a crucial, under-researched crop feeding millions worldwide, especially in Africa. Cassava mosaic disease (CMD) has plagued production in Africa for over a century. Traditional linkage mapping in bi-parental families suggests primarily a single major gene mediates resistance. To potentially identify new loci we conducted the first genome-wide association mapping study in cassava with 6128 African breeding lines. We also assessed the accuracy of genomic prediction to improve CMD resistance. We found a single region on cassava chromosome 8 accounts for most resistance but also identified 13 other small effect regions. We found evidence that two interacting loci and/or that multiple resistance alleles exist at major locus on chromosome 8. Genomic prediction of additive and total genetic merit was accurate for CMD and will be effective both for selecting parents and identifying highly resistant clones as varieties.

Technical Abstract: Cassava (Manihot esculenta) is a crucial, under-researched crop feeding millions worldwide, especially in Africa. Cassava mosaic disease (CMD) has plagued production in Africa for over a century. Bi-parental mapping studies suggest primarily a single major gene mediates resistance. To be certain and to potentially identify new loci we conducted the first genome-wide association mapping study in cassava with 6128 African breeding lines. We also assessed the accuracy of genomic selection to improve CMD resistance. We found a single region on chromosome 8 accounts for most resistance but also identified 13 small effect regions. We found evidence that two epistatic loci and/or alternatively multiple resistance alleles exist at major QTL. We identified two peroxidases and one thioredoxin as candidate genes. Genomic prediction of additive and total genetic merit was accurate for CMD and will be effective both for selecting parents and identifying highly resistant clones as varieties.