Genome-wide association analysis revealed that BnaGRP3-A03 regulates flowering time in Brassica napus

Flowering time serves as the critical agronomic trait substantially affecting rapeseed (Brassica napus L.) production and adaptability. However, the genetic mechanisms related to flowering time modulation within rapeseed are not fully explored. The present work identified a new flowering time regulator, BnaGRP3-A03, through the genome-wide association study (GWAS) carried out using 157 Brassica napus accessions. Compared with those harboring BnaGRP3-A03-Hap1, those harboring BnaGRP3-A03-Hap2 at this locus flowered significantly earlier. Furthermore, CRISPR/Cas9-mediated knock-out (KO) of BnaGRP3 in the semi-winter cultivar Zhongshuang 6 consistently resulted in an early-flowering phenotype, confirming that it negatively regulated flowering. Comparative transcriptome analysis of CK and bnagrp3 mutant inbred lines revealed substantial alterations in the circadian clock and abscisic acid (ABA) response-related gene levels. Specifically, the mutants presented decreased expression of core morning element genes (BnaLHY and BnaCCA1) and increased expression of evening element genes (BnaTOC1 and BnaPRR5/7). Furthermore, exogenous ABA application rescued the early-flowering phenotype, suggesting that ABA acts as a key downstream component. Our results demonstrate that BnaGRP3 may negatively modulate B. napus flowering time through modulating ABA signaling and circadian clock. The above findings provide genetic insights into the molecular network that controls flowering time while identifying BnaGRP3 as the candidate molecular breeding target for early-maturing rapeseed species.

The online version contains supplementary material available at 10.1007/s11032-026-01696-z.