Species-specific genetic routes to a shared phenotype: convergent adaptation of beans to European long days

The loss of photoperiod sensitivity was a key prerequisite for the adaptation of common bean ( Phaseolus vulgaris ) and scarlet runner bean ( P. coccineus ) to European environments. While the genetic architecture of this trait has been studied for decades, primarily through QTL mapping in RILs and NILs, its molecular basis remains incompletely resolved. Here, we combine whole-genome resequencing of over 200 P. vulgaris accessions spanning Mesoamerican, Andean, and European origins with 130 P. coccineus cultivars from Mesoamerica and Europe. Phenotyping under controlled long-day conditions revealed distinct distributions of photoperiod sensitivity across species and gene pools. Genome-wide association and haplotype analyses identified single nucleotide variants strongly linked to flowering under long days. Consistent with prior studies, signals of selection reflect independent domestication events in the Americas. Importantly, we detect species-specific selection on core photoperiod regulators, demonstrating that both species achieved similar adaptive outcomes via functionally convergent genetic routes. By explicitly accounting for major loci shaping growth habit in our analyses, we were able to unmask additional genomic regions contributing to flowering responses in European cultivars. Together, these results show that adaptation to long-day environments occurred through stepwise, species-specific genomic innovations, first during domestication in the Americas and later under European cultivation. Our findings highlight the role of pathway-level convergent evolution in shaping complex domestication traits and underscore the potential of parallel genomic strategies for crop adaptation.