Quantitative trait loci for genetically correlated seed traits are tightly linked to branching and pericarp pigment loci in sunflower

The seed oil concentrations of large-seeded, low-oil and small-seeded, high-oil sunflower (Helianthus annuus L.; x = 17) cultivars differ by 180 to 280 g kg(-1). We identified quantitative trait loci (QTL) for seed oil and other seed traits in a low- x high-oil (RHA280 x RHA801) recombinant inbred line (RIL) mapping population segregating for apical branching (B), phytomelanin pigment (P), and hypodermal pigment (Hyp) loci. B, Hyp, and P mapped to linkage groups 10, 16, and 17, respectively. The seed oil concentrations of RHA280 and RHA801 were 254 and 481 g kg(-1), respectively. Composite interval mapping (CIM) identified 40 QTL for seed oil concentration, 100-seed weight, seed length, width and depth, kernel and pericarp weight, and kernel-to-pericarp weight ratio in 14 DNA marker intervals on 10 of 17 linkage groups. Twenty-four of the QTL were tightly linked to B, P, and Hyp and may have been partly or wholly caused by the pleiotropic effects of B, P, and Hyp. Multilocus QTL analyses were performed using B, P, Hyp, and four DNA marker loci as independent variables in mixed linear models. Seventy percent of the additive effects (39/56) and 42% of the additive x additive and additive x additive x additive effects (189/448) were significant (p < 0.05). The linked, pleiotropically acting, and epistatically interacting QTL identified for seed traits in RHA280 x RHA801 were presumably targeted by selection in the transition from large-seeded, low-oil to small-seeded, high-oil cultivars in sunflower.