Genome - wide association and prediction reveals the genetic architecture of 1 cassava mosaic disease resistance and prospects for rapid genetic 2 improvement 3 4

30 Cassava (Manihot esculenta) is a crucial, under-researched crop feeding 31 millions worldwide, especially in Africa. Cassava mosaic disease (CMD) has plagued 32 production in Africa for over a century. Bi-parental mapping studies suggest 33 primarily a single major gene mediates resistance. To be certain and to potentially 34 identify new loci we conducted the first genome-wide association mapping study in 35 cassava with 6128 African breeding lines. We also assessed the accuracy of genomic 36 selection to improve CMD resistance. We found a single region on chromosome 8 37 accounts for most resistance but also identified 13 small effect regions. We found 38 evidence that two epistatic loci and/or alternatively multiple resistance alleles exist 39 at major QTL. We identified two peroxidases and one thioredoxin as candidate 40 genes. Genomic prediction of additive and total genetic merit was accurate for CMD 41 and will be effective both for selecting parents and identifying highly resistant 42 clones as varieties. 43 44 . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/031179 doi: bioRxiv preprint first posted online Nov. 11, 2015;