Mediated pleiotropy drives the negative correlation of total carotenoid and dry matter contents in cassava (<i>Manihot esculenta</i>)

Plant breeders aim to increase provitamin A carotenoids in cassava (Manihot esculenta) storage roots to help combat vitamin A deficiency in sub-Saharan Africa, but a negative genetic correlation between total carotenoid and dry matter contents hinders progress. While genetic linkage between a major-effect variant in the phytoene synthase 2 (PSY2) gene and nearby candidate gene(s) has been thought to drive this correlation, molecular evidence suggests there may be a metabolic relationship between total carotenoid and dry matter, implying genome-wide pleiotropic effects. Bivariate genome-wide associations were used to examine the genetic architecture of the negative covariance between traits and test for pleiotropy. A population of 378 accessions in the yellow-fleshed cassava breeding program at the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria was genotyped with DArTseqLD and phenotyped in field trials over 10 yr across three locations in Nigeria. Mixed linear models controlling for the previously identified PSY2 causal variant were used to identify multiple new pleiotropic loci. Among 17 jointly associated loci at a relaxed significance threshold, most (11 of 17) affected total carotenoid and dry matter in opposite directions, although this pattern did not reach statistical significance in a binomial test. Even after accounting for these 17 loci as covariates, significantly negative polygenic covariance between total carotenoid and dry matter remained. These findings support the hypothesis that widespread mediated pleiotropy rather than genetic linkage drives the negative genetic correlation between total carotenoid and dry matter in cassava and demonstrate a new application of multivariate genome-wide association study for interrogating the genetic architecture of correlated traits.