Large-scale GWAS using historical data identifies a conserved genetic architecture of cyanogenic glucosides content in cassava (Manihot esculenta Crantz.) root.

Cassava is a root crop originating from South America and a major staple in the tropics, including marginal environments. This study focused on South American and African germplasm and investigated the genetic architecture of hydrogen cyanide (HCN), a major component of root quality. HCN, representing total cyanogenic glucosides, is a plant defense component against herbivory but also toxic for human consumption. We genotyped 3,354 landraces and modern breeding lines originating from 26 Brazilian states and 1,389 individuals were phenotypically characterized across multi-year trials for HCN. All plant material was subjected to high density genotyping using Genotyping-by-sequencing. We performed genome wide association mapping to characterize the genetic architecture and gene mapping of HCN. Field experiment revealed strong broad and narrow-sense trait heritability (0.82 and 0.41 respectively). Two major loci were identified, encoding for an ATPase and a MATE protein and contributing up to 7% and 30% of the HCN concentration in roots, respectively. We developed diagnostic markers for breeding applications, validated trait architecture consistency in African germplasm and investigated further evidence for domestication of sweet and bitter cassava. Fine genomic characterization indicate; (i) major role played by vacuolar transporter in regulating HCN content, (ii) co-domestication of sweet and bitter cassava major alleles to be geographical zone dependant, and (iii) major loci allele for high HCN in Manihot esculenta Crantz seems to originate from its ancestor, M. esculenta subsp. flabellifolia. Taken together these findings expand insights on cyanogenic glucosides in cassava roots and its glycosylated derivatives in plants.