Wuhong Wang

Clubroot, caused by the obligate biotrophic protist Plasmodiophora brassicae (P. brassicae), is a destructive soil-borne disease that severely threatens the production of radish (Raphanus sativus L.). Although chitinases are known to execute critical defense functions by degrading pathogen chitin, a comprehensive genome-wide characterization of the radish chitinase (RsChi) gene family and its specific role in clubroot resistance remains lacking. Here, we systematically identified 24 RsChi genes in the radish genome, characterizing their chromosomal distribution, structural organization, and promoter regulatory networks. These genes are unevenly distributed across seven chromosomes and cluster into four subfamilies, with tandem duplication driving family expansion, particularly on Chromosome 3. Promoter analysis revealed a significant enrichment of jasmonic acid- and abscisic acid-responsive cis-elements, implicating RsChi genes in hormone-mediated defense signaling. Using qRT-PCR to profile expression dynamics during P. brassicae infection across contrasting radish lines, we identified strong genotype- and stage-specific transcriptional responses. Notably, TRs0x1c000780 remained transcriptionally silent prior to infection but was specifically induced over 10-fold in the resistant line at 28 days post-inoculation. This infection-triggered induction positions TRs0x1c000780 as a promising candidate defense gene. Together, these findings provide structural and functional insights into the RsChi family and highlight candidate targets for breeding clubroot-resistant radish cultivars.

Seed dormancy is a vital adaptive mechanism regulated by the DELAY OF GERMINATION (DOG) gene family. Here, we present the first systematic genome-wide identification and expression profiling of the DOG gene family (RsDOGs) in radish (Raphanus sativus). Comprehensive analysis of physicochemical properties, chromosomal distribution, and phylogeny revealed strong evolutionary conservation alongside functional divergence. Notably, several RsDOG proteins harbor natural fusions of the DOG1 domain with a bZIP domain, suggesting potential transcription factor activity and novel regulatory functions. Promoter analysis identified abundant ABA-responsive and abiotic stress-responsive cis-acting elements. Quantitative real-time PCR (qRT-PCR) profiling across contrasting cultivars—dormant variety Rs275 and non-dormant variety Rs100—at 4 h and 28 h post-imbibition revealed distinct differential expression patterns. In particular, TRs0x5c022182.1 exhibited high expression levels in dormant seeds, suggesting its potential involvement in seed dormancy regulation in radish. This study provides key insights into the structural evolution and expression dynamics of RsDOG genes, laying a solid foundation for molecular breeding aimed at optimizing seed germination traits.

Eggplant (Solanum melongena) is a significant vegetable in the Solanaceae family. Significant progress has been made in genetic diversity analysis and fingerprinting construction for crops such as tomatoes and peppers within the same family, but research on eggplants in these aspects remains relatively limited. Current germplasm identification using fingerprinting primarily relies on traditional SSR markers, which suffer from limited polymorphism and labor-intensive workflows. This study aimed to identify high-quality single nucleotide polymorphisms (SNPs), develop reliable Kompetitive Allele-Specific PCR (KASP) markers for eggplant genotyping, and then conduct fingerprint construction and genetic diversity analysis. The ultimate goals were to achieve a precise identification of eggplant varieties and deeply explore the genetic background and evolutionary patterns of eggplant germplasm. In this study, 49 representative eggplant accessions were re-sequenced. After data quality control, sequence alignment, and multiple rounds of screening, 224 high-quality SNPs were identified. Based on these SNPs, 96 SNPs were selected to develop KASP markers. These markers can provide abundant genetic markers for eggplant genetic research, which are used to deeply explore the genetic background and conduct genetic diversity analysis. After multiple rounds of rigorous verification, 32 core candidate markers were finally screened out. The average polymorphic information content (PIC) and gene diversity (GD) values were 0.36 and 0.46, respectively. Phylogenetic tree, population structure, and principal component analyses divided the 280 eggplant accessions into eight distinct groups. Through the analysis of minimal core markers and core germplasm, 23 core SNP markers and a subset of 56 core germplasm accessions were identified, leading to the establishment of a comprehensive fingerprinting system for all 280 accessions. Our findings provide a foundational genetic resource for eggplant germplasm identification and offer significant support for future breeding efforts.

MYB transcription factors (TFs) represent one of the largest gene families in plants, and previous studies have demonstrated their involvement in regulating anthocyanin synthesis. Eggplant is an important anthocyanin-rich solanaceae vegetable crop. In this study, a total of 219 MYB gene-family members were identified using the complete and high-quality eggplant genome, comprising 105 1R-MYBs, 107 R2R3-MYBs, 5 3R-MYBs, and 2 4R-MYBs. Using phylogenetic analysis, we divided them into 33 subfamilies. Members of the SmeMYB gene family are unevenly distributed on 12 chromosomes, but are mainly concentrated at the upper and lower ends of the chromosomes. In addition, the expression levels of R2R3-MYBs in differently colored eggplant tissues (peel, calyx, stem, flower, and leaf) were investigated with RNA-seq (RNA sequencing). A total of 13 differentially expressed R2R3-MYB transcription factors related to the synthesis of anthocyanins in different eggplant tissues were screened out. SmeMYB110, SmeMYB175, and SmeMYB182 were also found to play significant roles in this process. Furthermore, 10 MYB TFs were identified as potential genes regulating anthocyanin synthesis in different tissues. The quantitative real-time PCR (qRT-PCR) analysis results showed that SmeMYB175 was regarded as the most likely key transcription factor regulating anthocyanin synthesis in calyx. These results not only deepen our understanding of the MYB gene family in eggplant but also lay a solid foundation for further research on the regulation of SmeR2R3-MYBs in anthocyanin synthesis across diverse eggplant tissues.

Fusarium wilt in eggplant caused by F. oxysporum f. sp. melongenae is a major devastating soil-borne disease on a worldwide scale. Effectors play important roles in the interactions in pathogen–plant interactions. Identifying effectors is essential for elucidating the pathogenic mechanisms of phytopathogenic fungi. In this study, bioinformatic prediction approaches, including SignalP v5.0, TMHMM v2.0, WoLF PSORT, PredGPI, and EffectorP, were employed to screen for candidate secreted effector proteins (CSEPs) in F. oxysporum f. sp. melongenae. A total of 1019 proteins exhibiting characteristics typical of classical secretory proteins were identified, 301 of which demonstrated carbohydrate activity, and 194 CSEPs were identified. Furthermore, a total of 563 proteins from F. oxysporum f. sp. melongenae under induced conditions were identified using mass spectrometry-based label-free quantitative proteomics. These findings suggest a potential role of these CSEPs in the interaction between F. oxysporum f. sp. melongenae and eggplant, thereby contributing to a deeper understanding of the pathogenic mechanisms of F. oxysporum f. sp. melongenae and strategies for disease management.

Seed dormancy is a life adaptation trait exhibited by plants in response to environmental changes during their growth and development. The dormancy of commercial seeds is the key factor affecting seed quality. Eggplant seed dormancy is controlled by quantitative trait loci (QTLs), but reliable QTLs related to eggplant dormancy are still lacking. In this study, F₂ populations obtained through the hybridization of paternally inbred lines with significant differences in dormancy were used to detect regulatory sites of dormancy in eggplant seeds. Three QTLs (dr1.1, dr2.1, and dr6.1) related to seed dormancy were detected on three chromosomes of eggplant using the QTL-Seq technique. By combining nonsynonymous sites within the candidate regions and gene functional annotation analysis, nine candidate genes were selected from three QTL candidate regions. According to the germination results on the eighth day, the male parent was not dormant, but the female parent was dormant. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify the expression of nine candidate genes, and the Smechr0201082 gene showed roughly the same trend as that in the phenotypic data. We proposed Smechr0201082 as the potential key gene involved in regulating the dormancy of eggplant seeds. The results of seed experiments with different concentrations of gibberellin A₃ (GA₃) showed that, within a certain range, the higher the gibberellin concentration, the earlier the emergence and the higher the germination rate. However, higher concentrations of GA₃ may have potential effects on eggplant seedlings. We suggest the use of GA₃ at a concentration of 200–250 mg·L⁻¹ to treat dormant seeds. This study provides a foundation for the further exploration of genes related to the regulation of seed dormancy and the elucidation of the molecular mechanism of eggplant seed dormancy and germination.

Grafting has a significant impact on the botany properties, commercial character, disease resistance, and productivity of eggplants. However, the mechanism of phenotypic modulation on grafted eggplants is rarely reported. In this study, a widely cultivated eggplant (Solanum. melongena cv. ‘Zheqie No.10’) was selected as the scion and grafted, respectively, onto four rootstocks of TOR (S. torvum), Sa (S. aculeatissimum), SS (S. sisymbriifolium), and Sm64R (S. melongena cv. ‘Qiezhen No. 64R’) for phenotypic screening. Physiological and biochemical analysis showed the rootstock Sm64R could improve the fruit quality with the increasing of fruit size, yield, and the contents of total soluble solid, phenolic acid, total amino acid, total sugar, and vitamin C. To further investigate the improvement of fruit quality on Sm64R, a transcriptome and a metabolome between the Sm64R-grafted eggplant and self-grafted eggplant were performed. Significant differences in metabolites, such as phenolic acids, lipids, nucleotides and derivatives, alkaloids, terpenoids, and amino acids, were observed. Differential metabolites and differentially expressed genes were found to be abundant in three core pathways of nutritional qualities, including biosynthesis of phenylpropanoids, phospholipids, and nucleotide metabolism. Thus, this study may provide a novel insight into the effects of grafting on the fruit quality in eggplant.

Root shape is an important characteristic that affects the commodity of radish (Raphanus sativus L.), which can be measured using the ratio of root length (RL) to root diameter (RD). Although it is known that root shape is controlled by quantitative trait loci (QTLs), reliable QTLs for radish root shape are still lacking. In the present study, we used three F₂ populations (1902, 1908 and 1909) derived from the crossing of five radish cultivars with highly divergent root shapes to perform QTL-seq. A total of 1282 individuals of the three F₂ populations were measured to determine the root length and maximum diameter. High-depth resequencing of six extreme pools and five parents was performed, and QTL-seq was used to detect the QTLs controlling the radish root shape. We identified seven QTLs for root shape distributing on five radish chromosomes (R1, R2, R4, R5 and R7), among which rs7.1 and rs7.2 had an overlap of 1.02 Mb (13.79–14.81 Mb). In addition, two QTLs, rs4.1 and rs4.2, were adjacent to each other on chromosome R4. In conclusion, this study provides an important foundation for the fine mapping and functional analysis of the QTLs controlling the root shape and breeding for root shape in radish.

Flowering time is an important agronomic trait in Brassica rapa and has a wide range of variation. The change from vegetative to reproductive development is a major transition period, especially in flowering vegetable crops. In this study, two non-heading Chinese cabbage varieties with significantly different flowering times, Pak-choi (B. rapa var. communis Tesn et Lee) and Caitai (B. rapa var. tsaitai Hort.), were used to construct segregated F₂ populations. The bulk-segregant approach coupled with whole genome re-sequencing was used for QTL sequencing (QTL-seq) analysis to map flowering time traits. The candidate genes controlling flowering time in B. rapa were predicted by homologous gene alignment and function annotation. The major-effect QTL ft7.1 was detected on chromosome A07 of B. rapa, and the FT family gene BrFT was predicted as the candidate gene. Moreover, a new promoter regional difference of 1577 bp was revealed by analyzing the sequence of the BrFT gene. The promoter region activity analysis and divergent gene expression levels indicated that the difference in the promoter region may contribute to different flowering times. These findings provide insights into the mechanisms underlying the flowering time in Brassica and the candidate genes regulating flowering in production.