Dissecting flowering time and flower color in Carum carvi utilizing a long-read draft genome and a GBS-based QTL...

Caraway (Carum carvi L.) is a major essential oil crop with biennial and annual flowering types. As basic research resource, we developed a draft genome assembly using long-read ONT sequencing and provide a structural and functional gene annotation for an annual caraway inbred line. To elucidate the genetic control of flowering, a genotyping-by-sequencing (GBS) was conducted for an F₂ population (N = 187) generating 731 strictly filtered SNPs. A linkage map was constructed spanning 663 cM across 10 linkage groups with in total 634 (full map) or 259 (thinned map) SNPs. Contrary to its dominance in F₁, annual flowering occurred in only 36% of F₂ plants under late sowing conditions. Furthermore, the annual F₂ plants exhibited delayed flowering compared to the annual parent. QTL analysis identified five significant QTLs for (adjusted) flowering time (LG02, LG03, LG05, LG08 and LG10) explaining 6.1% to 10.5% (in total 42.7%) of phenotypic variance. The results support a polygenic predominately additive model for flowering induction in caraway. In addition, two QTLs for flower color (LG01, LG10) were detected explaining 10.9% and 26.0% of phenotypic variance, respectively. This study provides a comprehensive genomic resource for caraway, bridging the gap between traditional breeding and molecular improvement.