Yanjing Ren

Yushuyuangen ( Brassica rapa ssp. rapa ) is a characteristic turnip landrace cultivated on the Qinghai–Tibet Plateau and valued for its nutritional and flavor qualities. However, the tissue-specific distribution of quality-related metabolites and the gene-expression patterns associated with their accumulation remain poorly understood. Here, metabolomics and transcriptomics were integrated with weighted gene co-expression network analysis (WGCNA) to investigate three root tissues in two varieties, YPW (purple-white) and YGW (green-white): the upper colored peel (purple in YPW and green in YGW), lower white peel, and root flesh. A total of 775 metabolites were identified, showing clear tissue-dependent metabolic differentiation. Sugar-phosphate intermediates and aromatic/aspartate-family amino acids accumulated mainly in root flesh (glucose-6-phosphate, fructose-6-phosphate, phenylalanine, and homoserine), whereas branched-chain amino acids were abundant in colored peel (valine and leucine). Purple peel accumulated higher levels of p- coumaric acid and ferulic acid, while flavonoids differed markedly between purple and green peel, represented by phloretin and diosmetin in purple peel and trifolin and kaempferol-7- O -glucoside in green peel. Integrated WGCNA and correlation analyses further identified tissue-associated relationships among metabolites, structural genes, and transcription factors. Four candidate transcription factor–structural gene–metabolite associations were highlighted: NAC22 – F16P2.1 –D-fructose-6-phosphate, bHLH65 / ARFD4 – TRBP2.2 –L-tryptophan, MYB62 / AGL63 – PAL1.2 / C4H.2 – p- coumaric acid, and MYB62 – FLS1 / F3′H1.2 –trifolin/kaempferol-7- O -glucoside. These associations were inferred from co-expression and correlation patterns and represent candidate relationships for further functional validation.

In cabbage, epidermal wax plays a key role in adaptation to abiotic and biotic stresses. The glossy green cabbage variety, which has less wax, is becoming increasingly popular on the market. In this study, the highly inbred waxy cabbage HQ2-1 and the glossy green cabbage Y2-1 were sampled for fine mapping and transcriptomics analysis. In the glossy green leaf cabbage, inheritance follows a simple dominant pattern. BSA-seq and interval targeted sequencing technology identified BoCER1 as the candidate gene controlling the leaf wax trait in Brassica oleracea. Downregulated genes in the α-linolenic acid metabolic pathway and upregulated genes in the wax synthesis pathway in HQ2-1 collectively promote wax formation in HQ2-1 leaves. Cold stress induced the upregulation of α-linolenic acid metabolic pathway genes in HQ2-1, and we speculate that the upregulation of these genes may promote jasmonic acid accumulation. Our study lays a solid foundation for further understanding the regulatory mechanism of leaf wax formation in cabbage and for the translational application of breeding new glossy cabbage varieties.

Our multi-omics investigation of pepper fruit coloration dynamics demonstrates that the coordinated regulation of flavonoid accumulation and chlorophyll retention underpins the distinct pigmentation patterns between dark green (XHB) and light green (QL2017) cultivars. Through the integrated analysis of three developmental stages (10–30 DPA), we identified 989 differentially accumulated metabolites (DAMs) and 810 differentially expressed genes (DEGs), with flavonoid biosynthesis, phenylpropanoid metabolism, and chlorophyll turnover pathways pinpointed as central regulatory hubs. Notably, key metabolites such as quercitrin, kaempferol-3-O-rhamnoside, and cinnamic acid were significantly enriched in dark green fruits (XHB), coinciding with enhanced antioxidant activity and delayed chlorophyll degradation. Transcriptomic data revealed the coordinated upregulation of chlorophyll biosynthesis genes (COX15, POR) and light-harvesting complex components (Lhcb1, Lhcb2), while PAO—a pivotal chlorophyll catabolism gene—also exhibited elevated expression. Co-expression network analysis highlighted scopoletin GTase, F5H, CCR, and CAD as hub genes regulating flavonoid biosynthesis. qRT-PCR validation confirmed high consistency with transcriptomic trends (r > 0.85, p < 0.01). Our findings propose a synergistic model wherein flavonoid accumulation and chlorophyll metabolic dynamics jointly orchestrate green fruit pigmentation, offering novel insights and molecular targets for the precision breeding of pepper fruit coloration.

Low temperature is a significant abiotic stress factor that not only impacts plant growth, development, yield, and quality but also constrains the geographical distribution of numerous wild plants. Kohlrabi (Brassica oleracea L. var. caulorapa L.) belongs to the Brassicaceae family and has a short growing period. In this study, a total of 196,642 unigenes were obtained from kohlrabi seedlings at low temperatures; of these, 52,836 unigenes were identified as differentially expressed genes. Transcription factor family members ARR-B, C3H, B3-ARF, etc. that had a high correlation with biochemical indicators related to low temperature were identified. A total of nineteen BocARR-B genes (named BocARR-B1–BocARR-B19) were obtained, and these genes were distributed unevenly across seven chromosomes. Nineteen BocARR-B genes searched four conserved motifs and were divided into three groups. The relative expression level analysis of 19 BocARR-B genes of kohlrabi showed obvious specificity in different tissues. This study lays a foundation and provides new insight to explain the low-temperature resistance mechanism and response pathways of kohlrabi. It also provides a theoretical basis for the functional analysis of 19 BocARR-B transcription factor gene family members.

Kohlrabi is an important swollen-stem cabbage variety belonging to the Brassicaceae family. However, few complete chloroplast genome sequences of this genus have been reported. Here, a complete chloroplast genome with a quadripartite cycle of 153,364 bp was obtained. A total of 132 genes were identified, including 87 protein-coding genes, 37 transfer RNA genes and eight ribosomal RNA genes. The base composition analysis showed that the overall GC content was 36.36% of the complete chloroplast genome sequence. Relative synonymous codon usage frequency (RSCU) analysis showed that most codons with values greater than 1 ended with A or U, while most codons with values less than 1 ended with C or G. Thirty-five scattered repeats were identified and most of them were distributed in the large single-copy (LSC) region. A total of 290 simple sequence repeats (SSRs) were found and 188 of them were distributed in the LSC region. Phylogenetic relationship analysis showed that five Brassica oleracea subspecies were clustered into one group and the kohlrabi chloroplast genome was closely related to that of B. oleracea var. botrytis. Our results provide a basis for understanding chloroplast-dependent metabolic studies and provide new insight for understanding the polyploidization of Brassicaceae species.

Osmotic stress is a condition in which plants do not get enough water due to changes in environmental factors. Plant response to osmotic stress is a complex process involving the interaction of different stress-sensitive mechanisms. Differentially expressed genes and response mechanisms of kohlrabi have not been reported under osmotic stress. A total of 196,642 unigenes and 33,040 differentially expressed unigenes were identified in kohlrabi seedlings under polyethylene glycol osmotic stress. AP2/ERF, NAC and eight other transcription factor family members with a high degree of interaction with CAT and SOD antioxidant enzyme activity were identified. Subsequently, 151 AP2/ERF genes were identified and analyzed. Twelve conserved motifs were searched and all AP2/ERF genes were clustered into four groups. A total of 149 AP2/ERF genes were randomly distributed on the chromosome, and relative expression level analysis showed that BocAP2/ERF genes of kohlrabi have obvious specificity in different tissues. This study lays a foundation for explaining the osmotic stress resistance mechanism of kohlrabi and provides a theoretical basis for the functional analysis of BocAP2/ERF transcription factor family members.

Introduction: Seed coat color is a significant agronomic trait in horticultural crops such as Brassica rapa which is characterized by brown or yellow seed coat coloration. Previous Brassica rapa studies have shown that BrTTG1 is responsible for seed coat proanthocyanidin formation, which is dependent on the MYB-bHLH-WD40 complex, whereas some studies have reported that TRANSPARENT TESTA GLABRA 1 (TTG1) directly interacts with the structural gene promoters of the flavonoid pathway. Methods: Herein, the brown-seeded inbred B147 and ttg1 yellow-seeded inbred B80 mutants were used as plant materials for gene expression level analysis, gene promoter clone and transient overexpression.Results: The analysis identified eleven structural genes involved in the flavonoid biosynthesis pathway, which are potentially responsible for BrTTG1- dependent seed coat proanthocyanidin formation. The promoters of these genes were cloned and cis-acting elements were identified. Yeast one-hybrid and dual-luciferase assays confirmed that BrTTG1 directly and independently interacted with proCHS-Bra008792, proDFR-Bra027457, proTT12-Bra003361, proTT19-Bra008570, proTT19-Bra023602 and proAHA10-Bra016610. A TTG1-binding motif (RTWWGTRGM) was also identified. Overexpression of TTG1 in the yellow-seed B. rapa inbred induced proanthocyanidin accumulation by increasing the expression levels of related genes. Discussion: Our study unveiled, for the first time, the direct interaction between TTG1 and the promoters of the flavonoid biosynthesis pathway structural genes and glutathione S-transferases in Brassica rapa. Additionally, we have identified a novel TTG1-binding motif, providing a basis for further exploration into the function of TTG1 and the accumulation of proanthocyanidins in seed coats.

Chili pepper (Capsicum annuum L.) is extensively cultivated in China, with its production highly reliant on regional environmental conditions. Given ongoing climate change, it is imperative to assess its impact on chili pepper cultivation and identify suitable habitats for future cultivation. In this study, the MaxEnt model was optimized and utilized to predict suitable habitats for open-field chili pepper cultivation, and changes in these habitats were analyzed using ArcGIS v10.8. Our results showed that the parameter settings of the optimal model were FC = LQPTH and RM = 2.7, and the critical environmental variables influencing chili pepper distribution were annual mean temperature, isothermality, maximum temperature of the warmest month, and precipitation of the warmest quarter. Under current climate conditions, suitable habitats were distributed across all provinces in China, with moderately- and highly-suitable habitats concentrated in the east of the Qinghai–Tibetan Plateau and south of the Inner Mongolia Plateau. Under future climate scenarios, the area of suitable habitats was expected to be larger than the current ones, except for SSP126-2050s, and reached the maximum under SSP126-2090s. The overlapping suitable habitats were concentrated in the east of the Qinghai–Tibetan Plateau and south of the Inner Mongolia Plateau under various climate scenarios. In the 2050s, the centroids of suitable habitats were predicted to shift towards the southwest, except for SSP126, whereas this trend was reversed in the 2090s. Our results suggest that climate warming is conductive to the cultivation of chili pepper, and provide scientific guidance for the introduction and cultivation of chili pepper in the face of climate warming.

The formation of fruit color in pepper is closely related to the processes of carotenoid metabolism. In this study, red wild-type pepper XHB, SP01, PC01 and their corresponding mutants H0809 (orange), SP02 (yellow), and PC02 (orange) were used as research materials. The Ggps, Psy, Lcyb, Crtz, Zep, and Ccs genes involved in carotenoid biosynthesis were cloned, and bioinformatics and expression analyses were carried out. The results showed that the full lengths of the six genes were 1110 bp, 2844 bp, 1497 bp, 2025 bp, 510 bp, and 1497 bp, and they encoded 369, 419, 498, 315, 169, and 498 amino acids, respectively. Except for the full-length Ccs gene, which could not be amplified in the yellow mutant SP02 and the orange mutant PC02, the complete full-length sequences of the other genes could be amplified in different materials, indicating that the formation of fruit color in the SP02 and PC02 mutants could be closely related to the deletion or mutation of the Ccs gene. The analytical results of real-time quantitative reverse transcription PCR (qRT-PCR) showed that the Ggps, Psy, Lcyb, Crtz, and Zep genes were expressed at different developmental stages of three pairs of mature-fruit-colored materials, but their patterns of expression were not consistent. The orange mutant H0809 could be amplified to the full Ccs gene sequence, but its expression was maintained at a lower level. It showed a significant difference in expression compared with the wild-type XHB, indicating that the formation of orange mutant H0809 fruit color could be closely related to the different regulatory pattern of Ccs expression. The results provide a theoretical basis for in-depth understanding of the molecular regulatory mechanism of the formation of color in pepper fruit.