CSCD2: an integrated interactional database of cancer-specific circular RNAs.

The significant function of circRNAs in cancer was recognized in recent work, so a well-organized resource is required for characterizing the interactions between circRNAs and other functional molecules (such as microRNA and RNA-binding protein) in cancer. We previously developed cancer-specific circRNA database (CSCD), a comprehensive database for cancer-specific circRNAs, which is widely used in circRNA research. Here, we updated CSCD to CSCD2 (http://geneyun.net/CSCD2 or http://gb.whu.edu.cn/CSCD2), which includes significantly more cancer-specific circRNAs identified from a large number of human cancer and normal tissues/cell lines. CSCD2 contains >1000 samples (825 tissues and 288 cell lines) and identifies a large number of circRNAs: 1 013 461 cancer-specific circRNAs, 1 533 704 circRNAs from only normal samples and 354 422 circRNAs from both cancer and normal samples. In addition, CSCD2 predicts potential miRNA-circRNA and RBP-circRNA interactions using binding motifs from >200 RBPs and 2000 microRNAs. Furthermore, the potential full-length and open reading frame sequence of these circRNAs were also predicted. Collectively, CSCD2 provides a significantly enhanced resource for exploring the function and regulation of circRNAs in cancer.

Transcription factor WRKY28 curbs WRKY33-mediated resistance to Sclerotinia sclerotiorum in Brassica napus.

Sclerotinia sclerotiorum causes substantial damage and loss of yield in oilseed rape (Brassica napus). The molecular mechanisms of oilseed rape defense against Sclerotinia remain elusive. In this study, we found that in the early stages of B. napus infection a conserved mitogen-activated protein kinase (MAPK) cascade mediated by BnaA03.MKK5-BnaA06.MPK3/BnaC03.MPK3 module phosphorylates the substrate BnWRKY33, enhancing its transcriptional activity. The activated BnWRKY33 binds to its own promoter and triggers a transcriptional burst of BnWRKY33, thus helping plants effectively resist the pathogenic fungi by enhancing the expression of phytoalexin synthesis-related genes. The expression of BnWRKY33 is fine-tuned during defense. Ongoing Sclerotinia infection induces BnaA03.WRKY28 and BnaA09.VQ12 expression. BnaA09.VQ12 interacts physically with BnaA03.WRKY28 to form a protein complex, causing BnaA03.WRKY28 to outcompete BnWRKY33 and bind to the BnWRKY33 promoter. BnaA03.WRKY28 induction suppresses BnWRKY33 expression in the later stages of infection but promotes branch formation in the leaf axils by regulating the expression of branching-related genes such as BnBRC1. BnaA03.WRKY28 participates in the trade-off between defense and growth. These findings suggest that oilseed rape plants may modulate defense-response strength and develop alternative reproduction and survival strategies in the face of lethal pathogens.

Fine mapping of BnDM1-the gene regulating indeterminate inflorescence in Brassica napus.

KEY MESSAGE: A candidate gene Bndm1 related to determinate inflorescence was mapped to a 128-kb interval on C02 in Brassica napus. Brassica napus plants with determinate inflorescence exhibit improved traits in field production, such as lower plant height, improved lodging resistance, and consistent maturity. Compared to plants with indeterminate inflorescence, such features are favorable for mechanized harvesting techniques. Here, using a natural mutant 6138 with determinate inflorescence, it is demonstrated that determinate inflorescence reduces plant height significantly without affecting thousand-grain weight and yield per plant. Determinacy was regulated by a single recessive gene, Bndm1. Using a combination of SNP arrays and map-based cloning, we mapped the locus of determinacy to a 128-kb region on C02. Based on sequence comparisons and the reported functions of candidate genes in this region, we predicted BnaC02.knu (a homolog of KNU in Arabidopsis) as a possible candidate gene of Bndm1 for controlling determinate inflorescence. We found a 623-bp deletion in a region upstream of the KNU promoter in the mutant. This deletion led to the significant overexpression of BnaC02.knu in the mutant compared to that in the ZS11 line. The correlation between this deletion and determinate inflorescence was examined in natural populations. The results indicated that the deletion affected the normal transcription of BnaC02.knu in the plants with determinate inflorescence and played an important role in maintaining flower development. This study presents as a new material for optimizing plant architecture and breeding novel canola varieties suitable for mechanized production. Moreover, our findings provide a theoretical basis for analyzing the molecular mechanisms underlying the formation of determinate inflorescence in B. napus.

Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling biomass heterosis in Brassica napus.

BACKGROUND: Heterosis is an important biological phenomenon in which the hybrids exceed the parents in many traits. However, the molecular mechanism underlying seedling heterosis remains unclear. RESULTS: In the present study, we analyzed the leaf transcriptomes of strong hybrids (AM, HM) and weak hybrids (CM, HW) and their parents (A, C, H, M, and W) at two periods. Phenotypically, hybrids had obvious biomass heterosis at the seedling stage, with statistically significant differences between the strong and weak hybrids. The transcriptomic analysis demonstrated that the number of differentially expressed genes (DEGs) between parents was the highest. Further analysis showed that most DEGs were biased toward parental expression. The biological processes of the two periods were significantly enriched in the plant hormone signal transduction and photosynthetic pathways. In the plant hormone signaling pathway, DEG expression was high in hybrids, with expression differences between strong and weak hybrids. In addition, DEGs related to cell size were identified. Similar changes were observed during photosynthesis. The enhanced leaf area of hybrids generated an increase in photosynthetic products, which was consistent with the phenotype of the biomass. Weighted gene co-expression network analysis of different hybrids and parents revealed that hub genes in vigorous hybrid were mainly enriched in the plant hormone signal transduction and regulation of plant hormones. CONCLUSION: Plant hormone signaling and photosynthesis pathways, as well as differential expression of plant cell size-related genes, jointly regulate the dynamic changes between strong and weak hybrids and the generation of seedling-stage heterosis. This study may elucidate the molecular mechanism underlying early biomass heterosis and help enhance canola yield.

QTL Mapping and Diurnal Transcriptome Analysis Identify Candidate Genes Regulating Brassica napus Flowering Time.

Timely flowering is important for seed formation and maximization of rapeseed (Brassica napus) yield. Here, we performed flowering-time quantitative trait loci (QTL) mapping using a double haploid (DH) population grown in three environments to study the genetic architecture. Brassica 60 K Illumina Infinium™ single nucleotide polymorphism (SNP) array and simple sequence repeat (SSR) markers were used for genotyping of the DH population, and a high-density genetic linkage map was constructed. QTL analysis of flowering time from the three environments revealed five consensus QTLs, including two major QTLs. A major QTL located on chromosome A03 was detected specifically in the semi-winter rapeseed growing region, and the one on chromosome C08 was detected in all environments. Ribonucleic acid sequencing (RNA-seq) was performed on the parents' leaves at seven time-points in a day to determine differentially expressed genes (DEGs). The biological processes and pathways with significant enrichment of DEGs were obtained. The DEGs in the QTL intervals were analyzed, and four flowering time-related candidate genes were found. These results lay a foundation for the genetic regulation of rapeseed flowering time and create a rapeseed gene expression library for seven time-points in a day.

Comparison of dynamic 3D chromatin architecture uncovers heterosis for leaf size in Brassica napus.

INTRODUCTION: Heterosis is the major event driving plant development and promoting crop breeding, but the molecular bases for this phenomenon remain elusive. OBJECTIVES: We aim to explore the effect of three-dimensional (3D) chromatin architecture on the underlying mechanism of heterosis. METHODS: Here, we constructed the North Carolina II (NC-II) population to select superior and inferior heterosis sets by comparing mid-parent heterosis (MPH) in Brassica napus. To decipher the impact of 3D chromatin architecture on the underlying mechanism of heterosis, we combined genetics, transcriptomics and 3D genomics approaches. RESULTS: We suggest that F1 hybrids with superior heterosis tend to contain more transcriptionally active A compartments compared with F1 hybrids with inferior heterosis, and approximately 19-21% compartment significantly altered in the F1 hybrids relative to the parental lines. Further analyses show that chromatin compartments correlate with genetic variance among parents, which may form the basis for differentially active chromatin compartments. Having more A compartments in F1 hybrids confers a more accessible chromatin circumstance, which promotes a higher proportion of highly expressed ELD (expression level dominance) genes in superior heterosis F1 hybrids (46-64%) compared with inferior heterosis F1 hybrids (22-31%). Moreover, genes related to hormones which affect plant growth, are more up-regulated with changes of 3D genome architecture, and we validate that increased hormone content contributes to cell proliferation and expansion by influencing the key genes of cell cycle thereby promoting leaf size. CONCLUSION: Dynamic 3D chromatin architecture correlates with genetic variance among parents and contributes to heterosis in Brassica napus.

Brassica evolution of essential BnaFtsH1 genes involved in the PSII repair cycle and loss of FtsH5.

The PSII repair cycle is an important part of photosynthesis and is essential for high photosynthetic efficiency. The study of essential genes in Brassica napus provides significant potential for the improvement of gene editing technology and molecular breeding design. Previously, we identified a B. napus lethal mutant (7-521Y), which was controlled by two recessive genes (cyd1 and cyd2). BnaC06.FtsH1 was identified as a CYD1 target gene through functional verification. In the present study, we employed fine-mapping, genetic complementation, and CRISPR/Cas9 experiments to identify BnaA07.FtsH1 as the target gene of CYD2, functioning similarly to BnaC06.FtsH1. By analyzing CRISPR/Cas9 T1 generation plants of the Westar variety, we found that the copy number of FtsH1 was positively correlated with its biomass accumulation. Transcriptome analysis of cotyledons revealed differences in the expression of photosynthesis antenna and structural proteins between the mutant and complementary seedlings. Phylogenetic and chromosome linear analyses, based on 15 sequenced cruciferous species, revealed that Brassica alone had lost FtsH5 during evolution. This may be related to the fact that FtsH5 was located at the end of chromosome ABK8 in the ancestor species. Cloning and identification of BnaFtsH1s provide a deeper understanding of PSII repair cycle mechanisms and offer new insights for the improvement of photosynthetic efficiency and molecular breeding design in B. napus.

BnaA03.MKK5-BnaA06.MPK3/BnaC03.MPK3 Module Positively Contributes to Sclerotinia sclerotiorum Resistance in Brassica napus.

Brassica napus (oilseed rape) is one of the most important oil crops worldwide, but its growth is seriously threatened by Sclerotinia sclerotiorum. The mechanism of oilseed rape response to this pathogen has rarely been studied. Here, it was identified that BnaA03.MKK5 whose expression was induced by S. sclerotiorum infection was involved in plant immunity. BnaA03.MKK5 overexpression lines exhibited decreased disease symptoms compared to wild-type plants, accompanied by the increased expression of camalexin-biosynthesis-related genes, including BnPAD3 and BnCYP71A13. In addition, two copies of BnMPK3 (BnA06.MPK3 and BnC03.MPK3) were induced by Sclerotinia incubation, and BnaA03.MKK5 interacted with BnaA06.MPK3/BnaC03.MPK3 in yeast. These interactions were confirmed using in vivo co-immunoprecipitation assays. In vitro phosphorylation assays showed that BnaA06.MPK3 and BnaC03.MPK3 were the direct phosphorylation substrates of BnaA03.MKK5. The transgenic oilseed rape plants including BnaA06.MPK3 and BnaC03.MPK3 overexpression lines and BnMPK3 gene editing lines mediated by CRISPR/Cas9 were generated; the results of the genetic transformation of BnaA06.MPK3/BnaC03.MPK3 indicate that BnMPK3 also has a positive role in Sclerotinia resistance. This study provides information about the potential mechanism of B. napus defense against S. Sclerotiorum mediated by a detailed BnaA03.MKK5-BnaA06.MPK3/BnaC03.MPK3 module.