Contemporary hybridization among Arabis floodplain species creates opportunities for adaptation.

Hybridization between closely related species is increasingly recognized as a major source of biodiversity. Yet, whether it can create advantageous trait combinations while purging harmful alleles remains unknown. To address this question, we studied Arabis nemorensis and Arabis sagittata, two endangered species that currently hybridize in a single hotspot. We chose two representative individuals originating from the hotspot, generated high-quality annotated genome sequences, crossed them to form an F2 population, quantified segregation distortion along the genome, measured 22 phenotypic traits and mapped their genetic basis. Two genomic regions showed strong segregation distortion favoring A. sagittata alleles in the F2 and potentially accelerating their introgression. Fifty-eight quantitative trait loci (QTLs) were identified for 20 traits, with additive and dominance effects best fitting Gaussian and logistic distributions, respectively. It was found that 48% of QTLs were unlinked to reduced fitness or segregation distortion. A major QTL affecting flowering time implicated Terminal-Flower 1 (TFL1) as a candidate gene for life-history adaptation. QTLs did not overlap with recent selective sweeps, except for those controlling rosette size. Our findings offer unique insights into both the potential for adaptive trait combinations and the constraints imposed by hybrid fitness loss during incipient stages of hybridization.