Transcriptomic analysis reveals ameliorative effects of exogenous selenium in Brassica napus L. seedlings exposed to chromium stress

The ameliorative effects of nitric oxide on oilseed rape seedlings, Okapy cultivar, under drought condition were investigated. Water stress at 60% and 30% field capacity, increased lipid peroxidation and H2O2 content in oilseed rape leaves. Among the different concentrations ( 25, 50, 75 and 100 µM) of sodium nitroprusside used, spraying plants leaves with 25µM sodium nitroprusside a NO donor, reduced the damaging effects of water stress which was reflected by a decrease in malondialdehyde and hydrogen peroxide content in leaves. Drought stress enhanced leaves superoxide dismutase, peroxidase and ascorbate peroxidase activities but decreased catalase activity. Sodium nitroprusside treatment (25µM) had a positive effect on antioxidant enzymes under water stress. At higher sodium nitroprusside concentrations, its ameliorative effects on water stress were decreased and the oxidative damages to the leaves were sustained. The reduction in drought induced oxidative damages by NO in oilseed rape is most likely mediated by the NO ability to induce and increase the activity of reactive oxygen species scavenging enzymes.

BackgroundSilique number is an important component of yield in oilseed rape, which is largely determined by the number of flowers. Although many QTL for silique number have been identified in oilseed rape, none of these has been fine-mapped and further cloned, largely limiting their application in genetic improvement. In our previous study, a few-silique mutant (No.7931) caused by determinate inflorescence has been mapped to three close regions on C02 chromosome by bulked segregant analysis by sequencing (BSA-seq) of two pools of F2 individuals derived from this mutant and more-silique accession No.73290.ResultsIn the current study, the hybrid F1 between No.7931 and an indeterminate inflorescence accession No.73290 showed nearly determinate inflorescence. This supported that the determinate inflorescence of No.7931 was nearly dominant to the indeterminate inflorescence of No.73290, suggesting the dosage effect of the causal gene. In the BC3F2 near-isogenic lines with No.73290 background, the numbers of plants with determinate and indeterminate inflorescence displayed a segregating ratio of 3:1, suggesting that it should be controlled by a single dominant locus (named as SNPI.C2 thereafter). The first BSA region close to the end of C02 chromosome was validated and fine-mapped to 172 Kb region containing only 23 annotated genes. The RNA-seq of shoot apical meristem (SAM) at the initial stage of floral bud differentiation identified a total of 3196 differentially expressed genes (DEGs) between No.73290 and NIL-SNPI.C2, which were significantly enriched into 22 pathways (e.g., fermentation, glycolysis, polyamine metabolism and nitrogen-metabolism) that are highly associated with floral bud differentiation and flower number regulation. The results of fine-mapping, re-sequencing and transcriptome analysis were integrated, which identified two candidate genes that are involved in regulating meristem identity and have sequence and/or expression variation.ConclusionsThese results provide further insights and candidate genes for silique number in oilseed rape, which represent a significant advancement toward the cloning of causal genes and understanding of genetic mechanism for silique number in oilseed rape.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-026-08126-4.

Ovule number per ovary (ONPO) determines the maximum potential of seed number per fruit that is a direct component of seed yield in crops. This study aimed to dissect the genetic basis and molecular mechanism of ONPO using a newly developed doubled haploid (DH) population in oilseed rape. In all the four investigated environments, the ONPO of 201 DH lines exhibited normal distribution with a wide variation from 22.6 to 41.8, suggesting quantitative inheritance appropriate for mapping QTL. A skeleton genetic map of 2111 markers within 19 linkage groups was developed, with a total of 1715.71 cM in length and an average of 0.82 cM between markers. Linkage mapping identified ten QTLs that were distributed on eight chromosomes and explained 7.0-15.9% of the phenotypic variance. Among these, four were identical to the reported and two were repeatedly detected with relatively large effects, highlighting their potential for marker-assisted selection. Phytohormone quantification of ovaries (at the ovule initiation stage) from two pools of high and low ONPO lines showed significant differences in the levels of nine sub-types of phytohormones, suggesting their important roles in regulating ovule number. Transcriptomic analysis identified 7689 differentially expressed genes (DEGs) between the two pools, of which nearly half were enriched into functional categories of reported genes regulating ONPO, including protein, RNA, signalling, miscellaneous, development, hormone metabolism, and tetrapyrrole synthesis. Integration of linkage QTL mapping, transcriptome sequencing and BLAST analysis identified 15 homologues of reported ovule number genes and 327 DEGs in the QTL regions, which were considered as direct and potential candidate genes. These findings propose further insights into the genetic basis and molecular mechanisms of ONPO, which will facilitate future gene cloning and genetic improvement for enhancing seed yield in oilseed rape.

Drought stress triggers complex and multilayered physiological, biochemical, and molecular responses contributing to plant stress adaptation mechanisms. In this study, we performed comparative transcriptomic and biochemical analyses between drought-tolerant and drought-sensitive rapeseed (Brassica napus) cultivars to identify candidate early response regulatory genes and molecular pathways associated with enhanced response to drought at the seedling stage. Under drought stress, the tolerant cultivar exhibited higher relative water content, greater proline accumulation, elevated antioxidant enzyme activities, and reduced membrane damage compared to the sensitive cultivar. Transcriptomic profiling revealed distinct early-response gene expression signatures between the cultivars. The cultivar-specific expression patterns of the candidate regulatory genes encoding transcription factors (DREB2A, ABI5, NAC019, ZAT10, MYB15, MYB44), protein kinases (SRK2E, SRK2I), calmodulin-like proteins (CML37, CML40), components of the ubiquitin-proteasome system (RDUF2, PUB23), along with drought-responsive effector genes (NCED3, RD29B, HAI1) may facilitate early activation of abscisic acid (ABA) and calcium signaling pathways, enhance activities of antioxidant enzymes and reactive oxygen species (ROS) detoxification, promote proline accumulation, and potentially improve the efficiency of protein degradation and turnover in the drought-tolerant cultivar. Together, these findings provide valuable insights into candidate genes and regulatory pathways associated with enhanced early drought responses in rapeseed, offering potential targets for genetic improvement through molecular breeding technologies.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-30408-4.

BackgroundIncreasing seed oil content is one of the most important targets for rapeseed (Brassica napus) breeding. However, genetic mechanisms of mature seed oil content in Brassica napus (B. napus) remain little known. To identify oil content-related genes, a genome-wide association study (GWAS) was performed using 588 accessions.ResultsHigh-throughput genome resequencing resulted in 385,692 high-quality single nucleotide polymorphism (SNPs) with a minor allele frequency (MAF) > 0.05. We identified 17 loci that were significantly associated with seed oil content, among which 12 SNPs were distributed on the A3 (11 loci) and A1 (one loci) chromosomes, and five novel significant SNPs on the C5 (one loci) and C7 (four loci) chromosomes, respectively. Subsequently, we characterized differentially expressed genes (DEGs) between the seeds and silique pericarps on main florescences and primary branches of extremely high- and low-oil content accessions (HO and LO). A total of 64 lipid metabolism-related DEGs were identified, 14 of which are involved in triacylglycerols (TAGs) biosynthesis and assembly. Additionally, we analyzed differences in transcription levels of key genes involved in de novo fatty acid biosynthesis in the plastid, TAGs assembly and lipid droplet packaging in the endoplasmic reticulum (ER) between high- and low-oil content B. napus accessions.ConclusionsThe combination of GWAS and transcriptome analyses revealed seven candidate genes located within the confidence intervals of significant SNPs. Current findings provide valuable information for facilitating marker-based breeding for higher seed oil content in B. napus.

Atmospheric CO2 concentrations and temperatures have significantly increased, accompanied by substantial changes in precipitation patterns. These changes are anticipated to intensify in the future. In Nordic regions, increasing temperatures can improve growing conditions for some crops by extending the growing season and expanding cultivation northward. Climate changes may also favour some weed species, potentially reducing crop yield and affecting herbicide efficacy. To assess glyphosate efficacy under future climate conditions, we conducted two dose-response experiments on barnyard grass (Echinochloa crus-galli- C4 plant), oilseed rape (Brassica napus- C3 plant) and wild oat (Avena fatua- C3 plant). Plants were grown under ambient conditions (400ppm CO2 at 18/12°C (day/night)) and predicted future conditions (800ppm CO2 at 20.5/14.5°C (day/night)). Glyphosate was applied at 3-4-leaf-stage in doses of 0, 8.75, 17.5, 35, 70, 140, 420, 1260, and 2520g active ingredient (a.i.) ha-1, with the highest dose only included in the second experiment. Chlorophyll fluorescence was measured 48h after spraying. Two days after spraying, oilseed rape exhibited stress symptoms under both growing conditions, while barnyard grass showed symptoms only under future conditions and doses exceeding 6g a.i. ha-1. Plants were harvested 72h after spraying for transcriptome analysis and two weeks after spraying to determine dry weight, C%, N% and C/N ratio. The ED50 and ED90 values did not significantly differ between the two environments for each grass species. However, oilseed rape required significantly higher glyphosate doses to reduce dry weight by 50 and 90% at ambient growing conditions, likely due to the faster translocation of glyphosate. This suggests that glyphosate doses can be reduced in a warmer climate with an elevated CO2 level. No apparent differences in the C%, N%, or C/N ratio were observed between environments for any species. Transcriptome analysis indicated that all species respond differently to glyphosate and climate change.

BackgroundThe exchangeable aluminum (Al), released from the acid soils, is another addition to the environmental stress factors in the form of Al toxicity stress. Al stress affects the normal crop development and reduces the overall yield of rapeseed (Brassica napus L.). The response mechanism of plants to Al toxicity is complicated and difficult to understand with few QTL related studies in rapeseed under Al toxicity stress.ResultUsing 200,510 SNPs developed by SLAF-seq (specific-locus amplified fragment sequencing) technology, we carried out the genome-wide association analysis (GWAS) in a population of 254 inbred lines of B. napus with large genetic variation and Al-tolerance differences. There were 43 SNPs significantly associated with eight Al-tolerance traits in the seedling stage were detected on 14 chromosomes, and 777 candidate genes were screened at the flanking 100 kb region of these SNPs. Moreover, RNA-seq detected 8291 and 5341 DEGs (the differentially expressed gene) in the Al -tolerant line (ATL) and -sensitive line (ASL), respectively. Based on integration of GWAS and RNA-seq analysis, 64 candidate genes from GWAS analysis differentially expressed at least once in 6 h vs 0 h or 24 h vs 0 h conditions in ATL or ASL. Moreover, four out of sixty-four candidate genes (BnaA03g30320D, BnaA10g11500D, BnaC03g38360D and BnaC06g30030D) were differentially expressed in both 6 h and 24 h compared to 0 h (control) conditions in both lines. The proposed model based on the candidate genes excavated in this study highlighted that Al stress disturb the oxidation-redox balance, causing abnormal synthesis and repair of cell wall and ABA signal transduction, ultimately resulting in inhibition of root elongation.ConclusionsThe integration of GWAS and transcriptome analysis provide an effective strategy to explore the SNPs and candidate genes, which has a potential to develop molecular markers for breeding Al tolerant rapeseed varieties along with theoretical basis of molecular mechanisms for Al toxicity response of Brassica napus plants.

Genome-wide association study integrated with transcriptome analysis to identify boron efficiency-related candidate genes and favorable haplotypes in Brassica napus L.

Lack of phosphorus (P) is a major environmental factor affecting rapeseed (Brassica napus. L) root growth and development. For breeding purposes, it is crucial to identify the molecular mechanisms of root system architecture (RSA) traits underlying low P tolerance in rapeseed. The natural variations in the glycine-rich protein gene, BnGRP1, were analyzed in the natural population of 400 rapeseed cultivars under low P stress through genome-wide association study (GWAS) and transcriptome analyses. Based on 11 SNP mutations in BnGRP1 sequence, ten types of haplotypes (Hap) were formed. Compared with the other types, the cultivar of BnGRP1Hap1 type in the panel demonstrated the longest root length and heaviest root weight. BnGRP1Hap1 overexpression in rapeseed depicted the ability to enhance its resistance in response to low P tolerance. CRISPR/Cas9-derived BnGRP1Hap4 knockout mutations in rapeseed can lead to sensitivity to low P stress. Furthermore, BnGRP1Hap1 influences the expression of phosphate transporter 1 (PHT1) genes associated with P absorption. Overall, the findings of this study highlight new mechanisms of GRP1 genes in enhancing low P tolerance in rapeseed.

Phoma stem canker is one of the most important diseases of winter oil seed rape (Brassica napus) world-wide and is caused by a complex that comprises at least two species: Leptosphaeria maculans and Leptosphaeria biglobosa. Screening a panel of field Leptosphaeria isolates from B. napus for the presence of mycoviruses revealed the presence of a novel double stranded (ds) RNA virus in L. biglobosa and no viruses in L. maculans. The virus forms isometric particles ca. 40–45 nm in diameter and has four genomic segments, each possessing a single open reading frame flanked by untranslated regions. Phylogenetic analysis revealed modest similarities to known and suspected members of the family Quadriviridaeand therefore the virus was nominated Leptosphaeria biglobosa quadrivirus-1. Following eradication of the mycovirus, virus-infected and virus-free isogenic lines of L. biglobosa were created. A direct comparison of the growth and virulence of these isogenic lines illustrated that virus infection caused hypervirulence and resulted in induced systemic resistance towards L. maculans in B. napus following lower leaf pre-inoculation with the virus-infected isolate. Analysis of the plant transcriptome suggests that the presence of the virus leads to subtle alterations in metabolism and plant defences. For instance, transcripts involved in carbohydrate and amino acid metabolism are enriched in plants treated with the virus-infected isolate, while pathogenesis-related proteins, chitinases and WRKY transcription factors are differentially expressed. These results illustrate the potential for deliberate inoculation of plants with hypervirulent L. biglobosa to decrease the severity of phoma stem canker later in the growing season.

Rapeseed (Brassica napus) is the third-largest oil crop globally, making it crucial to understand the molecular mechanisms behind the thousand-seed weight (TSW) for enhancing its yield and value. Previous studies have identified BnaKINβ1 (β1 subunit of SnRK1 complex) as a candidate gene for TSW. In this study, we employed CRISPR/Cas9-mediated editing of BnaKINβ1 and phenotypic analysis to confirm its role in seed size regulation, and electron microscopy further revealed its function at the cellular level. Integrated transcriptomic and metabolomic analyses revealed that BnaKINβ1 might regulates seed size by influencing sugar metabolism pathways. Protein interaction and ubiquitination assays elucidated the molecular mechanism by which BnaJUL1 (an E3 ubiquitin ligase) mediates the degradation of BnaKINβ1 and BnaKIN10. This study establishes a functional link between BnaKINβ1 and TSW regulation in rapeseed, providing novel insights into the molecular network controlling seed size and offering valuable genetic resources and theoretical foundations for high-yield rapeseed breeding.

Secondary metabolites, particularly alkaloids, are crucial for plant adaptation to abiotic stresses, including cold stress, which significantly hampers rapeseed (Brassica napus L.) productivity. Our previous research demonstrated that elevated alkaloid levels confer cold tolerance in Arabidopsis, but the precise molecular mechanisms underlying this function remain poorly understood. In this study, we investigated the role of scopolamine (SCOP; a "tropine alkaloid" and close to "neurotransmitters") in mediating cold tolerance in rapeseed. Exogenous application of TAs, using SCOP as an example, significantly mitigated cold-induced damage and improved seedling survival rate. To elucidate the underlying mechanisms, we performed an integrated transcriptomic and metabolomic analysis of SCOP-treated (150 nmol/plant) seedlings under cold stress. This analysis identified over 8000 differentially expressed genes (DEGs) and over 3000 primary differentially accumulated metabolites (DAMs). A combined analysis discovered a strong correlation between 11 DEGs and 12 DAMs, indicating that SCOP orchestrates a comprehensive response to cold stress at both transcriptional and metabolic levels. Further pathway enrichment analysis demonstrated that these key genes and metabolites are predominantly involved in amino acid and carbohydrate metabolism, as well as in phenylpropanoid and secondary metabolic pathways. Collectively, our results provide a deeper understanding of the TA-mediated cold response independent of the traditional CBF pathway, highlighting its role in carbon reallocation, cell wall reinforcement, and reactive oxygen species scavenging. In short, this study offers significant insights into the molecular mechanisms by which SCOP regulates cold tolerance in rapeseed, and identifies new targets for future engineering applications to fast-track stress-smart breeding for crop improvement.

Biochar solutions: Slow and fast pyrolysis effects on chromium stress in rapeseed roots

In higher plants, the structure of a flower is precisely controlled by a series of genes. An aberrance flower results in abnormal fruit morphology. Previously, we reported multi-silique rapeseed (Brassica napus) line zws-ms. We identified two associated regions and investigated differentially expressed genes (DEGs); thus, some candidate genes underlying the multi-silique phenotype in warm area Xindu were selected. However, this phenotype was switched off by lower temperature, and the responsive genes, known as thermomorphogenesis-related genes, remained elusive. So, based on that, in this study, we further investigated the transcriptome data from buds of zws-ms and its near-isogenic line zws-217 grown in colder area Ma’erkang, where both lines showed normal siliques only, and the DEGs between them analyzed. We compared the 129 DEGs from Xindu to the 117 ones from Ma’erkang and found that 33 of them represented the same or similar expression trends, whereas the other 96 DEGs showed different expression trends, which were defined as environment-specific. Furthermore, we combined this with the gene annotations and ortholog information and then selected BnaA09g45320D (chaperonin gene CPN10-homologous) and BnaC08g41780D [Seryl-tRNA synthetase gene OVULE ABORTION 7 (OVA7)-homologous] the possible thermomorphogenesis-related genes, which probably switched off the multi-silique under lower temperature. This study paves a way to a new perspective into flower/fruit development in Brassica plants.

Regional association analysis of 50 re-sequenced Chinese semi-winter rapeseed accessions in combination with co-expression analysis reveal candidate genes affecting oil accumulation in Brassica napus. One of the breeding goals in rapeseed production is to enhance the seed oil content to cater to the increased demand for vegetable oils due to a growing global population. To investigate the genetic basis of variation in seed oil content, we used 60K Brassica Infinium SNP array along with phenotype data of 203 Chinese semi-winter rapeseed accessions to perform a genome-wide analysis of haplotype blocks associated with the oil content. Nine haplotype regions harbouring lipid synthesis/transport-, carbohydrate metabolism- and photosynthesis-related genes were identified as significantly associated with the oil content and were mapped to chromosomes A02, A04, A05, A07, C03, C04, C05, C08 and C09, respectively. Regional association analysis of 50 re-sequenced Chinese semi-winter rapeseed accessions combined with transcriptome datasets from 13 accessions was further performed on these nine haplotype regions. This revealed natural variation in the BnTGD3-A02 and BnSSE1-A05 gene regions correlated with the phenotypic variation of the oil content within the A02 and A04 chromosome haplotype regions, respectively. Moreover, co-expression network analysis revealed that BnTGD3-A02 and BnSSE1-A05 were directly linked with fatty acid beta-oxidation-related gene BnKAT2-C04, thus forming a molecular network involved in the potential regulation of seed oil accumulation. The results of this study could be used to combine favourable haplotype alleles for further improvement of the seed oil content in rapeseed.