The Structural Variations of Rapeseed BnaC3.LEAFY with Agronomic Effects on the Timing of Inflorescence Formation and Flower Opening
Rapeseed (Brassica napus L.) is a globally significant oil-producing crop, and its structural variations (SVs) are fundamental to the enhancement and domestication of important agronomic traits. However, the effects of SVs on agronomic traits in allotetraploid rapeseed are still largely unexplored. Here, we conducted a whole-genome identification of SVs based on 300 re-sequenced rapeseed accessions and found 42,384 high-quality SVs consisted of 34,442 deletions, 6,653 insertions, 828 duplications and 461 inversions. Onset of inflorescence formation and subsequent flower opening at the proper time is crucial for successful propagation. To uncover significant SVs associated with inflorescence development, we performed genome-wide association study based on SVs (SV-GWAS) and identified seven significant SVs. Through analysis of each SV and referencing previous studies, we explored the SV in the second intron of LEAFY on Chromosome C3 (BnaC3.LFY), which is one of homologs of Arabidopsis floral identification gene LFY (AtLFY). BnaC3.LFY Hap1 is significantly related to early inflorescence development due to increased gene expression of BnaC3.LFY. By the CRISPR/Cas9 application in the wild-type spring accession Westar, multiple deletions in intron 2 region of BnaC3.LFY were received and the phenotype of delayed flowering opening was observed. Additionally, we discovered the conserved function of the second intron in Arabidopsis. This study demonstrates the whole-genome layout of SVs in Brassica napus genomes and highlights the conserved role of the second intron of BnaC3.LFY in influencing the timing of inflorescence formation and flower opening, with significant agronomic implications. Overall design: To compare the two distinct haplotypes of BnaC3.LFY, we selected 3 representative Hap 1 (R5044, R5159 and R5161) and Hap 2 (R4168, R4210, R4817) accessions for transcriptome analysis.