Introduction: Biochemical and metabolic processes help plants tolerate the adverse effects of drought. In plants accumulating bioactive compounds, understanding the genetic control of the biosynthesis of biochemical pathways helps the discovery of candidate gene (CG)–metabolite relationships.Methods: The metabolic profile of flowers in 119 rapeseed (Brassica napus) accessions was assessed over two irrigation treatments, one a well-watered (WW) condition and the other a drought stress (DS) regime. We integrated information gained from 52,157 single-nucleotide polymorphism (SNP) markers, metabolites, and transcriptomes to identify linked SNPs and CGs responsible for the genetic control of flower phenolic compounds and regulatory elements.Results: In a genome-wide association study (GWAS), of the SNPs tested, 29,310 SNPs were qualified to assess the population structure and linkage disequilibrium (LD), of which several SNPs for radical scavenging activity (RSA) and total flavanol content (TFLC) were common between the two irrigation conditions and pleiotropic SNPs were found for chlorogenic and coumaric acids content. The principal component analysis (PCA) and stepwise regression showed that chlorogenic acid and epicatechin in WW and myricetin in DS conditions were the most important components for RSA. The hierarchical cluster analysis (HCA) showed that vanillic acid, myricetin, gallic acid, and catechin were closely associated in both irrigation conditions. Analysis of GWAS showed that 60 CGs were identified, of which 18 were involved in stress-induced pathways, phenylpropanoid pathway, and flavonoid modifications. Of the CGs, PAL1, CHI, UGT89B1, FLS3, CCR1, and CYP75B137 contributed to flavonoid biosynthetic pathways. The results of RNA sequencing (RNA-seq) revealed that the transcript levels of PAL, CHI, and CYP75B137 known as early flavonoid biosynthesis-related genes and FLS3, CCR1, and UGT89B1 related to the later stages were increased during drought conditions. The transcription factors (TFs) NAC035 and ERF119 related to flavonoids and phenolic acids were upregulated under drought conditions.Discussion: These findings expand our knowledge on the response mechanisms to DS, particularly regarding the regulation of key phenolic biosynthetic genes in rapeseed. Our data also provided specific linked SNPs for marker-assisted selection (MAS) programs and CGs as resources toward realizing metabolomics-associated breeding of rapeseed.

As an emerging field of life science, epigenetics plays a pivotal role in regulating gene expression. Epigenetic modifications including histone modifications, DNA methylation, chromatin remodeling, non-coding RNAs, and RNA modifications (particularly m⁶A methylation) play crucial roles in fine-tuning plant developmental processes. Among these, floral transition marks a key developmental switch from vegetative to reproductive growth, orchestrated by complex interactions between endogenous signals (such as age and hormones) and environmental cues (such as photoperiod and temperature). Recent advances have uncovered that epigenetic mechanisms act as molecular bridges integrating these signals to ensure flowering occurs under optimal conditions. This review synthesizes the current understanding of epigenetic control in the six canonical flowering pathways—photoperiod, vernalization, autonomous, thermosensory, gibberellin, and age-dependent pathways—with a particular emphasis on the emerging role of m⁶A RNA modification. We also discuss the crosstalk among epigenetic layers and highlight the translational potential of epigenetic engineering in optimizing flowering time and crop adaptation.

Suppressors of cytokine signaling (SOCSs) are negative feedback regulators of the JAK-STAT pathway and are often exploited by viruses to evade host antiviral immunity. Unlike other SOCS members, the role of SOCS2 in viral infection remains poorly understood. Here, we report that overexpression of silkworm SOCS2 isoforms, SOCS2L and SOCS2S, promotes Bombyx mori nucleopolyhedrovirus (BmNPV) replication at multiple stages, including viral DNA replication, late gene (VP39) transcription, and virion egress, while their knockdown suppresses these processes. Overexpression of SH2 domain mutants (R123Q in SOCS2S, R142Q in SOCS2L) reduced viral DNA replication to baseline and VP39 expression below baseline, drastically decreased infectious progeny titers, but unexpectedly increased viral DNA release to wild-type levels, suggesting that the SH2 domain may differentially regulate distinct steps of viral replication. Furthermore, SOCS2 isoforms, alone or cooperatively with BmNPV, modulate the mRNA levels of SOCS-STAT network members in an isoform-, dose-, and target-specific manner. Collectively, this study reveals for the first time the multiple proviral functions of silkworm SOCS2 isoforms, with differential effects on distinct stages of the viral life cycle, and highlights their potential as transcriptional modulators exploited by viruses for immune evasion.

Background: Colletotrichum camelliae is an important fungal disease in tea plants (Camellia sinensis), and NLR gene family play a central role in plant disease resistance recognition. Analyzing the expression characteristics and regulatory network of NLR genes in tea plants in response to anthracnose infection can provide a theoretical basis for exploring key genes for tea plant resistance to anthracnose and elucidating the molecular mechanisms of disease resistance. Method: Using the tea tree reference genome Shuchazao 2 as the material, CsNLR genes were identified based on NB-ARC (Pfam ID: PF00931) and LRR (Pfam ID: PF00560) conserved domains; Conduct bioinformatics analysis using TBtools, MEME, and MEGA; Using quantitative real-time PCR (qRT-PCR) to detect the expression changes of CsNLR in the common variety Sucha 120 and the purple variety Ziying 2 after anthracnose infection, and constructing a protein prediction association network. Result: A total of 158 CsNLR genes were identified, and their physicochemical properties, phylogenetics, gene structure, and cis element analysis revealed differentiation among family members. The promoters generally contain stress and hormone response elements; CsNLR is highly expressed in roots, stems, and mature leaves. After 4 days of inoculation with anthracnose infection, the expression trends of CsNLR in the two tea tree varieties were opposite, with Sucha 120 upregulated and Ziying 2 downregulated; The predicted protein association network shows CsNLR as the central node of the network, with 77 CsNLR proteins were included in the predictive functional association network, and there were differences in the connectivity of different members. Conclusions: The CsNLR identified in this study is a potential NLR resistant gene for anthracnose in tea plants, laying the foundation for subsequent functional verification of disease resistant genes and analysis of resistance mechanisms.

Brassica napus L. (rapeseed), a member of the family Brassicaceae, is the world’s third most important oilseed crop for edible oil production, after soybean and palm. Quantitative trait locus (QTL) mapping is a powerful strategy for dissecting the genetic basis of seed weight. In this review, Previous studies summarized a total of 1905 candidate genes associated with seed weight in Brassica napus. Five candidate genomic regions harboring 204 seed-weight-related genes were identified, among which 21 genes were characterized as differentially expressed genes via transcriptomic analysis. Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) mutant libraries targeting genes related to silique and seed size have been constructed in Brassica napus, revealing that BnaHRD genes play critical roles in seed development. These differentially expressed genes are involved in developmental processes, cell division. and nutrient storage, supporting their functions in seed size regulation. SHB1 and HAIKU2 modulate endosperm proliferation through the IKU pathway, thereby affecting seed weight. BZR1 (brassinazole-resistant 1) acts as a master regulator of seed growth via maternal tissues. Thidiazuron (TDZ), a cytokinin analogue, simultaneously promotes cell proliferation and cell expansion, thereby increasing cell number and cell size. Multiple phytohormone signaling pathways, including auxin, gibberellin (GA), and brassinosteroid (BR), as well as transcription factors such as LEC2, participate in the regulatory network of seed size. Here, we review current advances in the genetic and molecular regulation of seed size and discuss future perspectives for rapeseed breeding.

Brassica napus L. is a member of the family Cruciferae. This species is also referred to as "rape," “oilseed rape," "rapa," "rappi," and "rapeseed." It is the third most important source of edible oil globally after soybean and palm oil. Quantitative trait loci (QTLs) analysis has proven to be a powerful tool to reveal the genetic mechanisms of seed weight regulation in this species. We identified and compiled a comprehensive list of 1,905 candidate genes associated with seed weight regulation in Brassica napus. Five candidate genomic regions with 204 seed weight–related genes were identified, including 21 differentially expressed genes from transcriptomic analysis. A CRISPR/Cas mutant library targeting silique- and seed size-related genes was generated in rapeseed, indicating a potential role of BnaHRDs in their development. DEGs were involved in developmental processes, cell division, and nutrient storage, indicating their role in regulating seed size in Brassica napus. HB1 and HAIKU2 also regulate seed weight by controlling endosperm proliferation through the IKU pathway. A total of 1,643 SNP markers were aligned to the pseudochromosomes of Brassica napus using BLAST to identify significant hits. Furthermore, BRASSINAZOLE-RESISTANT1 (BZR1) is an important regulator of seed growth acting through maternal tissues. TDZ treatment enhanced both cell size and number. Plant hormones, including auxin, gibberellin (GA), and brassinosteroid (BR) signaling pathways, have been reported to regulate seed size. Transcription factors including LEC2, WRI1, FUS3, MYB30, and ABI3 were active during early seed development, while LEC1, LEC2, ABI3, and FUS3 remained active during seed maturation. Physiological processes play a key role in yield variation and the selection of high-yielding genotypes. Currently, marker-assisted selection and transgenic approaches are commonly used in rapeseed breeding. Temperature and light are key environmental factors affecting oil production in rapeseed. The integration of genetic engineering, molecular marker technologies, and conventional selection is expected to be a key approach for improving high-oil-content rapeseed. These limitations highlight the need for further studies on rapeseed applications.