Large‐scale genome‐wide association study, using historical data, identifies conserved genetic architecture of cyanogenic glucoside content in cassava (Manihot esculenta Crantz) root

• Published in: The Plant journal : for cell and molecular biology 2021-02, Vol.105 (3), p.754-770
• Main Authors: Ogbonna, Alex C., Braatz de Andrade, Luciano Rogerio, Rabbi, Ismail Y., Mueller, Lukas A., Jorge de Oliveira, Eder, Bauchet, Guillaume J.
• Format: Article
• Language: English
• Subjects: Adenosine triphosphatase; Alleles; Breeding; Cassava; cyanogenic glucosides; Diagnostic software; Diagnostic systems; Domestication; epistasis interaction; Field tests; Gene mapping; Gene sequencing; genetic architecture; Genome-wide association studies; Genomes; Genotyping; Germplasm; Glucosides; Herbivory; Heritability; Hydrogen cyanide; Loci; Manihot esculenta; Manihot esculenta Crantz; Mapping; MATE protein; MATE transporter; Original; phylogenetics; Roots; Tropical environments
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.15071

Significance Statement The high cyanogenic glucoside content in some cassava varieties prevents herbivory but can be toxic for human consumption. The identification of an intracellular transporter gene and its allelic variation allow us to identify cultivars with up to 30% reduced cyanogenic glucoside content in cassava root. Summary Manihot esculenta (cassava) is a root crop originating from South America that is a major staple in the tropics, including in 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 is also toxic for human consumption. We genotyped 3354 landraces and modern breeding lines originating from 26 Brazilian states and 1389 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 experiments 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 the domestication of sweet and bitter cassava. Fine genomic characterization revealed: (i) the major role played by vacuolar transporters in regulating HCN content; (ii) the co‐domestication of sweet and bitter cassava major alleles are dependent upon geographical zone; and (iii) the major loci allele for high HCN in M. esculenta Crantz seems to originate from its ancestor, M. esculenta subsp. flabellifolia. Taken together, these findings expand our insights into cyanogenic glucosides in cassava roots and its glycosylated derivatives in plants.