Background: Brassica napus is one of the most important oilseed crops, and also an important biofuel plant due to its low air pollution and renewability. Growth period are important traits that affect yield and are crucial for its adaptation to different environments in B. napus. Results: To elucidate the genetic basis of growth period traits, genome-wide association analysis (GWAS) and linkage mapping were employed to detect the quantitative trait loci (QTL) for days to initial flowering (DIF), days to final flowering (DFF), flowering period (FP), maturity time (MT), and whole growth period (GP). A total of 146 SNPs were identified by association mapping, and 83 QTLs were identified by linkage mapping using the RIL population. Among these QTLs, 19 were pleiotropic SNPs related to multiple traits, and six (q18DFF.A03-2, q18MT.A03-2, q17DFF.A05-1, q18FP.C04, q17DIF.C05 and q17GP.C09) were consistently detected using both mapping methods. Additionally, we performed RNA sequencing to analyze the differential expression of gene (DEG) transcripts between early- and late-flowering lines selected from the RIL population, and the DEGs were integrated with association mapping and linkage analysis to confirm their roles in the growth period. Consequently, 12 candidate genes associated with growth period traits were identified in B. napus. Among these genes, seven have polymorphic sites in the coding sequence and the upstream 2-kb sequence based on the resequencing data. The haplotype BnaSOC1.A05-Haplb and BnaLNK2.C06-Hapla showed more favorable phenotypic traits. Conclusions: The candidate genes identified in this study will contribute to our genetic understanding of growth period traits and can be used as targets for target mutations or marker-assisted breeding for rapeseed adapted to different environments.

Alternative splicing (AS) is a post-transcriptional regulatory process that enhances transcriptome diversity, thereby affecting plant growth, development, and stress responses. To identify the new transcripts and changes in the isoform-level AS landscape of rapeseed (Brassica napus) infected with the fungal pathogen Leptosphaeria maculans, we compared eight RNA-seq libraries prepared from mock-inoculated and inoculated B. napus cotyledons and stems. The AS events that occurred in stems were almost the same as those in cotyledons, with intron retention representing the most common AS pattern. We identified 1892 differentially spliced genes between inoculated and uninoculated plants. We performed a weighted gene co-expression network analysis (WGCNA) to identify eight co-expression modules and their Hub genes, which are the genes most connected with other genes within each module. There are nine Hub genes, encoding nine transcription factors, which represent key regulators of each module, including members of the NAC, WRKY, TRAF, AP2/ERF-ERF, C2H2, C2C2-GATA, HMG, bHLH, and C2C2-CO-like families. Finally, 52 and 117 alternatively spliced genes in cotyledons and stems were also differentially expressed between mock-infected and infected materials, such as HMG and C2C2-Dof; which have dual regulatory mechanisms in response to L. maculans. The splicing of the candidate genes identified in this study could be exploited to improve resistance to L. maculans.

Hypersensitive-induced response protein (HIR) is a class of plant immune proteins that play pivotal roles in Sclerotinia sclerotiorum (Lib.) de Bary resistance. However, there has been no systematic investigation and identification of HIR genes in rapeseed (Brassica napus L.). Hence, we identified 50 BnHIR genes and classified them into four groups. Subcellular localization prediction suggested that HIR proteins are mainly localized in the mitochondria. Cis-acting elements involved in light and diverse abiotic stress were found in the promoter regions of BnHIR. The majority of BnHIR genes in Groups 1/3/4 were expressed in most examined tissues, especially in leaves and siliques pericarp, while the BnHIR genes in Group 2 were not or had low expression in all detected tissues. In the case of S. sclerotiorum inoculation, HIR genes in Groups 1/3/4 were strongly induced, especially homologous genes in Group 1, which exhibited different expression patterns. Moreover, overexpression of BnHIR2.7 in Arabidopsis thaliana illustrated its prominent resistance to S. sclerotiorum. Our study provides insight into the evolutionary relationships of the HIR family genes in B. napus and lays the foundation for their resistance to S. sclerotiorum in B. napus.

Rapeseed (Brassica napus) is the third-largest source of vegetable oil in the world with an edible, medicinal, and ornamental value. However, insufficient light or high planting density directly affects its growth, development, yield, and quality. Mitogen-activated protein kinases (MAPKs) are serine/threonine protein kinases that play key roles in regulating the responses to biotic and abiotic stresses in plants. In this study, we found that the promoter of BnaMAPK1 contained several light-responsive elements (including the AT1-motif, G-Box, and TCT-motif), consistent with its shading stress-induced upregulation. Compared with the wild type under shading stress, BnaMAPK1-overexpressing plants showed higher light capture efficiency and carbon assimilation capacity, enhancing their shading tolerance. Using RNA sequencing, we systematically investigated the function of BnaMAPK1 in shading stress on photosynthetic structure, Calvin cycle, and light-driven electron transport. Notably, numerous genes encoding light-harvesting chlorophyll a/b-binding proteins (BnaLHCBs) in photosystem II-light-harvesting complex (LHC) II supercomplex were significantly downregulated in the BnaMAPK1-overexpressing lines relative to the wild type under shading stress. Combining RNA sequencing and yeast library screening, a candidate interaction partner of BnaMAPK1 regulating in shading stress, BnaLHCB3, was obtained. Moreover, yeast two-hybrid and split-luciferase complementation assays confirmed the physical interaction relationship between BnaLHCB3 and BnaMAPK1, suggesting that BnaMAPK1 may involve in stabilizing the photosystem II–LHC II supercomplex. Taken together, our results demonstrate that BnaMAPK1 positively regulates photosynthesis capability to respond to shading stress in rapeseed, possibly by controlling antenna proteins complex in photosystem II, and could provide valuable information for further breeding for rapeseed stress tolerance.

E2F/DP (Eukaryotic Transcription Factor 2/Dimerization Partner) refers to a class of protein complexes that play a pivotal role in the regulation of gene transcription in eukaryotes. In higher plants, E2F/DP transcription factors are of vital significance in mediating responses to environmental stresses. Based on differences in their conserved structural domains, they can be categorized into three subgroups: E2F, DP, and DEL (DP-E2F-like). Studies on E2F/DP in plants are relatively scarce, and no research on E2F/DP in Brassica napus has been reported to date. Utilize bioinformatics approaches to identify the BnE2F/DP gene family in Brassica napus. Construct a phylogenetic tree for evolutionary relationship analysis, and analyze the chromosomal distribution, gene structure composition, types of cis-acting elements, as well as intragenomic and interspecific collinearity. Integrate transcriptome data with real-time quantitative PCR (RT-qPCR) technology to explore the expression patterns of BnE2F/DP gene family members across various tissues. Total 29 BnE2F/DP genes were identified in Brassica napus and classified into 8 sub-families. These genes were unevenly distributed across 15 chromosomes, with enrichment on chromosomes 3 and 13. Intragenomic collinearity analysis detected 35 pairs of collinear BnE2F/DP gene pairs. Interspecific analysis revealed that there were 9 pairs of orthologous gene pairs between Brassica napus and Arabidopsis thaliana. Cis-acting element analysis showed that members of the BnE2F/DP family harbored four types of cis-acting elements, which might be involved in multiple regulatory processes, including hormonal regulation, abiotic stress responses, light reactions, and growth and development. Transcriptome and quantitative PCR data analyses indicate that members of the E2FC subfamily are likely to actively regulate seed and embryo development and positively respond to various abiotic stresses.. The conserved motifs and gene structures within each BnE2F/DP subfamily are largely consistent, which indicates that BnE2F/DP plays a crucial role in the growth and development of rapeseed seeds and embryos, as well as in the response to various abiotic stresses.

Background Brassica napus (rapeseed) is an important oilseed crop and its leaves and stems can also be used as animal feed. Lignocellulose content is closely related to the nutritional quality and palatability of animal feed. However, quantitative trait loci (QTLs) associated with acid detergent fiber (ADF) and neutral detergent fiber (NDF) contents in rapeseed stems have not yet been mapped. Results In this study, we used 494 B. napus accessions to perform genome-wide association studies (GWAS) of ADF and NDF contents. Ninety-two single-nucleotide polymorphisms (SNP) and 35 simple-sequence repeat (SSR) loci were significantly correlated with ADF and NDF contents, respectively, and six genetic loci associated with ADF and NDF contents were detected using both types of markers. We identified three candidate genes on chromosome A05 related to ADF content, including genes encoding chitinase-like protein 2 (CTL2) and two trichome birefringence-like 41 s (TBL41s). Seven genes on chromosomes A03 and A04 were related to NDF content, including genes encoding glycosyl hydrolase (GH), reversibly glycosylated polypeptide 1 (RGP), irregular xylem 12 (IRX12), trichome birefringence-like 34 (TBL34), galacturonosyltransferase 7 (GAUT7), cytokinesis defective 1 (CYT1), and LOB domain-containing protein 15 (LBD15). These candidate genes encode factors that likely participate in secondary cell wall formation and lignocellulose biosynthesis. Conclusions These findings lay the foundation for identifying genes related to forage quality traits and improving the efficiency of forage utilization in rapeseed, which will be beneficial for breeding new varieties for high-quality forage with low lignocellulose content.