Identification and functional validation of the BcFPA, a candidate regulator of flowering time in pak choi

Abstract Background Flowering time is an essential complex quantitative agronomic trait in pak choi ( Brassica rapa ssp. chinensis ). It exerts decisive effects on crop yield, commercial quality and environmental adaptability throughout the whole cultivation cycle. Uncovering the key genes controlling flowering time is therefore critical for molecular genetic research and genetic improvement of pak choi. Results In the present work, we performed bulked segregant sequencing (BSA-seq) using an F 2 segregating population derived from a cross between late-flowering inbred line M1-006 and early-flowering line M2-001 to isolate and functionally characterize the flowering-related gene. Finally, a major-effect QTL governing flowering time was mapped to a 2.62 Mb genomic interval on chromosome A09, harboring a total of 440 annotated genes. Further gene function annotation pinpointed Brap0046500.1 (designated BcFPA ), an ortholog of the autonomous-pathway flowering regulator AtFPA from Arabidopsis thaliana , as the promising candidate gene within this target region, which was subsequently verified via polymorphic InDel molecular markers and genotype screening of F 2 individuals. Combined sequence comparison and functional assays demonstrated that a non-synonymous substitution in the coding region of BcFPA leads to delayed floral transition in pak choi. Consistently, transgenic complementation assays in Arabidopsis fpa-1 loss-of-function mutants verified that the wild-type BcFPA allele was sufficient to rescue the late-flowering phenotype and restore normal flowering. Moreover, overexpression of BcFPA in transgenic pak choi significantly accelerated flowering, further corroborating its positive regulatory role in floral initiation. Conclusions This research systematically reveals the genetic mechanism responsible for natural flowering time variation in Brassica rapa. The identified BcFPA gene and its linked molecular markers can serve as important genetic resources for marker-assisted selective breeding, facilitating the breeding of new pak choi varieties with optimal flowering traits.