Understanding genetic architecture overcomes tradeoffs between seed quality and insect resistance.

The sunflower (Helianthus annuus) pericarp protects the seed within from both abiotic and biotic stresses. Achenes with stronger pericarps are less susceptible to damage from insect feeding. Complicating the genetic improvement of pericarp strength is the negative correlation between pericarp thickness (a component of strength) and oil content. As breeding efforts have increased oil content, there has been a concomitant decrease in pericarp thickness. One breeding goal is to improve oil content while preserving pericarp strength through genetic mechanisms independent of the tradeoffs with pericarp thickness. To determine the genetic basis of oil content, pericarp strength, and thickness, we identified QTL in two populations: the Sunflower Association Mapping panel (Mandel et al. in Theor Appl Genet 123:693-704, 2011) and a recombinant inbred line (RIL) population derived from a thin pericarp oilseed inbred (HA 467) crossed to a thick pericarp open-pollinated variety from Türkiye (PI 170415). A region on chromosome 15 was associated with neighboring QTL for banded moth resistance, oil content, and pericarp thickness, partially underlying the trade-offs among these traits. Additional QTL on chromosome 5 and 14 for pericarp strength provide fewer trade-offs with oil content. QTL for pericarp strength on chromosome 5 and pericarp thickness on chromosome 16 were associated with large structural variants on chromosome 5 and putative structural variation on chromosome 16, with candidate gene presence/absence variation between the haplotypes on chromosome 5. Understanding the origin and nature of phenotypic tradeoffs is beneficial to plant biologists and sunflower breeders as they seek to understand the origin and genetic architecture of adaptive and maladaptive traits.