Genome-wide association mapping and genomic prediction unravels CBSD resistance in a Manihot esculenta breeding population

13 Cassava (Manihot esculenta Crantz), a key carbohydrate dietary source for millions of people in 14 Africa, faces severe yield loses due to two viral diseases: cassava brown streak disease (CBSD) 15 and cassava mosaic disease (CMD). The completion of the cassava genome sequence and the 16 whole genome marker profiling of clones from African breeding programs 17 (www.nextgencassava.org) provides cassava breeders the opportunity to deploy additional 18 breeding strategies and develop superior varieties with both farmer and industry preferred traits. 19 Here the identification of genomic segments associated with resistance to CBSD foliar symptoms 20 and root necrosis as measured in two breeding panels at different growth stages and locations is 21 reported. Using genome-wide association mapping and genomic prediction models we describe 22 the genetic architecture for CBSD severity and identify loci strongly associated on chromosomes 23 4 and 11. Moreover, the significantly associated region on chromosome 4 colocalises with a 24 Manihot glaziovii introgression segment and the significant SNP markers on chromosome 11 are 25 situated within a cluster of nucleotide-binding site leucine-rich repeat (NBS-LRR) genes 26 previously described in cassava. Overall, predictive accuracy values found in this study varied 27 between CBSD severity traits and across GS models with Random Forest and RKHS showing the 28 highest predictive accuracies for foliar and root CBSD severity scores. 29 30