Natural variation in Arabidopsis lyrata vernalization requirement conferred by a FRIGIDA indel polymorphism

Species share homologous genes to a large extent, but it isnot yet known to what degree the same loci have been targetsfor natural selection in different species. Natural variationin flowering time is determined to a large degree by 2 genes,FLOWERING LOCUS C and FRIGIDA, in Arabidopsis thaliana. Here,we examine whether FRIGIDA has a role in differences in floweringtime between and within natural populations of Arabidopsis lyrata,a close outcrossing perennial relative of A. thaliana. We found2 FRIGIDA sequence variants producing potentially functionalproteins but with a length difference of 14 amino acids. Thesevariants conferred a 15-day difference in flowering time inan association experiment in 2 Scandinavian populations. Thedifference in flowering time between alleles was confirmed withtransformation to A. thaliana. Because the north European late-floweringpopulations harbor both late- and early sequence variants atintermediate frequencies and the late-flowering variant is mostfrequent in the southern early flowering European population,other genetic factors must be responsible for the floweringtime differences between the populations. The length polymorphismoccurs at high frequencies also in several North American populations.The occurrence of functional variants at intermediate frequenciesin several populations suggests that the variation may be maintainedby balancing selection. This is in contrast to A. thaliana,where independent loss-of-function mutations at the FRIGIDAgene are responsible for differences between populations andlocal adaptation.