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Acta Agronomica Sinica ›› 2025, Vol. 51 ›› Issue (10): 2693-2704.doi: 10.3724/SP.J.1006.2025.55008

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Transcriptome-based identification of flowering candidate genes and functional characterization of BnaCOR27 in Brassica napus

WANG Chen1,2(), HE Dan1,2, YAO Min1,2, QIU Ping1,2, HE Xin1,2, XIONG Xing-Hua1,2, KANG Lei1,2, LIU Zhong-Song1,2, QIAN Lun-Wen1,2,*()   

  1. 1College of Agronomy, Hunan Agricultural University, Changsha 410128, Hunan, China
    2Yuelu Mountain Laboratory, Changsha 410082, Hunan, China
  • Received:2025-01-16 Accepted:2025-07-09 Online:2025-10-12 Published:2025-07-22
  • Contact: *E-mail: qianlunwen@163.com E-mail:1048162651@qq.com;qianlunwen@163.com
  • Supported by:
    Hunan Province Science and Technology Innovation Leading Talent Project(2023RC1063);Training Program for Excellent Young Innovators of Changsha(kq2107016)

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Abstract:

Flowering is a critical developmental transition in higher plants, marking the shift from vegetative to reproductive growth, and it directly influences biomass accumulation and seed yield. To elucidate the regulatory network underlying vernalization in Brassica napus and identify key candidate genes, we analyzed the transcriptomes of leaves from seven rapeseed varieties before and after vernalization. A total of 1305 differentially expressed genes (DEGs) were identified, including 554 upregulated and 751 downregulated genes. GO enrichment analysis showed that these DEGs were primarily involved in biological processes such as the vernalization pathway, photoperiod pathway, circadian rhythm, flower development, and response to cold. Further analysis revealed differential expression in 96 flowering-related genes, including BnaVIN3, BnaFLC, BnaCOR27, among others. Additionally, genome-wide association studies (GWAS) indicated that BnaCOR27-C04 is significantly associated with flowering time. Integration with weighted gene co-expression network analysis (WGCNA) suggested that BnaCOR27 may interact with genes such as BnaFLC, BnaFT, and BnaVIN3, forming a potential regulatory network controlling flowering time in rapeseed. Furthermore, CRISPR/Cas9-mediated knockout of BnaCOR27 resulted in an early-flowering phenotype in T3 transgenic plants. These findings enhance our understanding of flowering regulation in B. napus and provide a genetic foundation for improving flowering-related traits in future breeding efforts.

Key words: Brassica napus, flowering, transcriptome analysis, GWAS, BnaCOR27

Fig. 1

Volcanic map of differentially expressed genes The vertical axis represents the significance of differential expression, the horizontal axis represents the fold change in gene expression level, the red dots represent upregulated differential genes, and the blue dots represent downregulated differential genes."

Fig. 2

GO enrichment analysis of differentially expressed gene A: GO enrichment analysis of up-regulated genes; B: GO enrichment analysis of down-regulated genes."

Fig. 3

Heat map shows the expression intensities (DEGs) of differentially expressed genes related to flowering A: heat map of the expression levels of up-regulated differential genes; B: heat map of the expression levels of down-regulated differential genes."

Fig. 4

Analysis of candidate genes in significantly associated genomic regions A: regional Manhattan plot surrounding the peak signals on C04: 16,048,376-16,594,153 bp. Red dot indicates the SNPs associated with FT from BnaCOR27, dashed line represents the significance threshold; B: phenotypic analysis of two alleles corresponding to BnaCOR27-C04 gene region. Differences between the allele locus were analyzed by t-test."

Fig. 5

Co-expression network analysis A: modular system tree diagram; B: correlation between modules and flowering; C: gene network diagram. According to functional labeling, co-expression networks are divided into vernalization pathway (pink nodes), photoperiod pathway (orange nodes), flower development (lavender nodes), hormone pathway (dark green nodes), low temperature pathway (turquoise nodes), circadian clock pathway (emerald nodes), autonomous pathway (purple nodes), and other genes related to flowering (grey nodes)."

Fig. 6

Target site mutations and flowering phenotype of transgenic plants A: schematic diagram of BnaCOR27 knockout vector and target mutation on A09 chromosome; B: schematic diagram of BnaCOR27 knockout vector and target mutation on A09 chromosome; C: knockout mutant CAS:BnaCOR27-T3 and control plant ZS6 flowering time phenotype picture; D: knockout mutant lines CAS:BnaCOR27-T3 and control lines ZS6 flowering time bar graph; **: P < 0.01. There is a large deletion on chromosome A09, and a single base is inserted on chromosome C09. Knockout mutant plant CAS:BnaCOR27-T3 blooms about 6.54 days earlier than the control plant ZS6. ZS6: Zhongshuang 6. Bar = 5 cm."

Fig. 7

Transcriptome analysis of differentially expressed genes in CAS: BnaCOR27-T3 transgenic plants A: volcanic map of transgenic material CAS: BnaCOR27-T3 differentially expressed genes; B: GO enrichment analysis of transgenic plants CAS: BnaCOR27-T3; C: analysis of differential gene expression in the transcriptome of transgenic material CAS:BnaCOR27-T3. ZS6: Zhongshuang 6."

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