Jerusalem artichokes are a perennial crop with high drought tolerance and high value as a raw material to produce biofuels, functional feed, and food. However, there are few comprehensive metabolomic studies on Jerusalem artichokes under drought conditions. Methods: Ultra-performance liquid chromatography and tandem mass spectrometry were used to identify differential metabolites in Jerusalem artichoke seedling leaves under polyethylene glycol (PEG) 6000-simulated drought stress at 0, 18, 24, and 36 h. Results: A total of 661 metabolites and 236 differential metabolites were identified at 0 vs. 18, 18 vs. 24, and 24 vs. 36 h. 146 differential metabolites and 56 common were identified and at 0 vs. 18, 24, and 36 h. Kyoto Encyclopedia of Genes and Genomes enrichment identified 236 differential metabolites involved in the biosynthesis of secondary metabolites and amino acids. Metabolites involved in glycolysis, phenolic metabolism, tricarboxylic cycle, glutamate-mediated proline biosynthesis, urea cycle, amino acid metabolism, unsaturated fatty acid biosynthesis, and the met salvage pathway responded to drought stress. Conclusion: A metabolic network in the leaves of Jerusalem artichokes under drought stress is proposed. These results will improve understanding of the metabolite response to drought stress in Jerusalem artichokes and develop a foundation for breeding drought-resistant varieties.

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.

Turnip (Brassica rapa ssp. rapa) is considered to be a highly nutritious and health-promoting vegetable crop, whose flesh color can be divided into yellow and white. It is widely accepted that yellow-fleshed turnips have higher nutritional value. However, reports about flesh color formation is lacking. Here, the white-fleshed inbred line, W21, and yellow-fleshed inbred line, W25, were profiled from the swollen root of the turnip at three developmental periods to elucidate the yellow color formation. Transcriptomics integrated with metabolomics analysis showed that the PSY gene was the key gene affecting the carotenoids formation in W25. The coding sequence of BrrPSY-W25 was 1278 bp and that of BrrPSY-W21 was 1275 bp, and BrrPSY was more highly expressed in swollen roots in W25 than in W21. Transient transgenic tobacco leaf over-expressing BrrPSY-W and BrrPSY-Y showed higher transcript levels and carotenoids contents. Results revealed that yellow turnip formation is due to high expression of the PSY gene rather than mutations in the PSY gene, indicating that a post-transcriptional regulatory mechanism may affect carotenoids formation. Results obtained in this study will be helpful for explaining the carotenoids accumulation of turnips.

Jerusalem artichoke (Helianthus tuberosus L.) is a characteristic crop in the Qinghai-Tibet Plateau which has rapidly developed and gained socioeconomic importance in recent years. Fructans are abundant in tubers and represent the foundation for their formation, processing and utilization of yield; and are also widely used in new sugar-based materials, bioenergy processing, ecological management, and functional feed. To identify key genes in the metabolic pathway of fructans in Jerusalem artichoke, high-throughput sequencing was performed using Illumina Hi Seq™ 2500 equipment to construct a transcriptome library. Qinghai-Tibet Plateau Jerusalem artichoke “Qingyu No.1” was used as the material; roots, stems, leaves, flowers and tubers of Jerusalem artichoke in its flowering stage were mixed into a mosaic of the Jerusalem artichoke transcriptome library, obtaining 63,089 unigenes with an average length of 713.6 bp. Gene annotation through the Nr, Swiss Prot, GO, KOG and KEGG databases revealed 34.95 and 46.91% of these unigenes had similar sequences in the Nr and Swiss Prot databases. The GO classification showed the Jerusalem artichoke unigenes were divided into three ontologies, with a total of 49 functional groups encompassing biological processes, cellular components, and molecular functions. Among them, there were more unigenes involved in the functional groups for cellular processes, metabolic processes, and single-organism processes. 38,999 unigenes were annotated by KOG and divided into 25 categories according to their functions; the most common annotation being general function prediction. A total of 13,878 unigenes (22%) were annotated in the KEGG database, with the largest proportion corresponding to pathways related to carbohydrate metabolism. A total of 12 unigenes were involved in the synthesis and degradation of fructan. Cluster analysis revealed the candidate 12 unigene proteins were dispersed in the 5 major families of proteins involved in fructan synthesis and degradation. The synergistic effect of INV gene is necessary during fructose synthesis and degradation in Jerusalem artichoke tuber development. The sequencing data from the transcriptome of this species can provide a reliable data basis for the identification and assessment of the expression of the members of the INV gene family.A simple sequence repeat (SSR) loci search was performed on the transcriptome data of Jerusalem artichoke, identifying 6635 eligible SSR loci with a large proportion of dinucleotide and trinucleotide repeats, and the most different motifs were repeated 5 times and 6 times. Dinucleotide and trinucleotide repeat motifs were the most frequent, with AG/CT and ACC/GGT repeat motifs accounting for the highest proportion. In this study, a database search of the transcriptome of the Jerusalem artichoke from the Qinghai Tibet Plateau was conducted by high throughput sequencing technology to obtain important transcriptional and SSR loci information. This allowed characterization of the overall expression features of the Jerusalem artichoke transcriptome, identifying the key genes involved in metabolism in this species. In turn, this offers a foundation for further research on the regulatory mechanisms of fructan metabolism in Jerusalem artichoke.

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.

In order to fully understand and effectively utilize the genetic diversity of Jerusalem artichoke accessions in China. 257 Jerusalem artichoke accessions were analyzed. Among them, 12 quantitative traits had 6%–50% of the coefficient of variation, with a mean of 24.75%, which was the highest in tuber weight per plant (50%) and the smallest in growth period (6%). The diversity index (H′) of these 12 traits was 1.24–1.53, with a mean of 1.44, which was the highest in tuber number per plant (1.53) and the lowest in leaf width (1.24). The diversity index of the eight quality traits was 0.85–1.08, with a mean of 0.98, which was the highest in tuber habit and the lowest in tuber uniformity, showing rich genetic diversity in most traits. The subordinate function of 257 Jerusalem artichoke accessions was 0.12–0.58, in which the highest was in JA1095 (0.58) with the obvious advantages of flower number and tuber weight per plant. The correlation analysis of 12 quantitative traits indicated that stem diameter, leaf length, flower and disk size could be used as the main target traits for high yield Jerusalem artichoke varieties breeding in the future. The results of principal component analysis showed that the cumulative contribution rate of the seven principal component factors was 66.794%. Among them, the number of flowers, the tuber number per plant, the number of tuber hairs and the smoothness of tuber epidermis were the main factors contributing to the phenotypic difference of Jerusalem artichoke. By cluster analysis, 257 accessions materials were divided into five categories based on 20 traits,among them class I and class II accounted for 85% of the total germplasm resources. This results can provide an important reference for the utilization of Jerusalem artichoke accessions and variety breeding.