Panax ginseng C.A. meyer (family: Araliaceae) is a perennial crop that has been widely used as a traditional medicine in Korea. Various P. ginseng cultivars exhibit a range of morphological and physiological traits as well as genetic diversity. To elucidate the differences of primary metabolism underlying such genetic diverstiy, we performed primary metabolite profiles in adventitious roots from five Panax ginseng cultivars using gas chromatography-mass spectrometry (GC-MS). The GC-MS analysis revealed eight primary metabolites as biomarkers and allowed us to classify the five cultivars into three groups. We selected three cultivars to represent each group and analyzed their transcriptomes by Illumina sequencing. We inspected 100 unigenes involved in seven primary metabolite biosynthesis pathways and found that 21 unigenes encoding 15 enzymes were differentially expressed among the three cultivars. Integrated analysis of transcriptomes and metabolomes revealed that the ginseng cultivars differ in primary metabolites as well as in the putative genes involved in the complex process of primary metabolic pathways. Our data derived from this integrated analysis provide insights into the underlying complexity of genes and metabolites that co-regulate flux through these pathways in ginseng.

Panax Ginseng is a perennial medicinal plant originated from North-east asia. Because of its well-known tonic effects mainly from ginsenosides, various types of processed ginseng products have been distributed around the world. Here, we analyzed secondary metabolite profiling of adventitious roots of 5 korean ginseng cultivars, Chunpoong (CP), Sunhyang (SH), Gopoong (GO), Sunun (SU), and Cheongsun (CS). At the same time, the profiles of relative gene expressions related to ginsenoside biosynthesis pathway were compared among ginseng cultivars. Secondary metabolite profiles were revealed by UPLC/Q-TOF-MS from extracts of bioreactor derived adventitious roots of five ginseng cultivars. Using principal component analysis, secondary metabolite profiles of ginseng cultivars were categorized into three groups. Metabolites with high VIP values were annotated using known database and standards compounds. Relative gene expression of ginsenoside related gene were analyzed using realtime PCR. The three groups had distinct metabolite contents. Furthermore, gene expression profiles related to ginsenoside were also different, which might contribute diverse secondary metabolite composition of ginseng cultivars. Further integrated analysis would provide a relationship between genetic background of ginseng cultivars and secondary metabolite profiles.

The generation and analysis of genomic resources information are essential to understand genomic features of crops. Even though medicinal component and its effect of Panax ginseng was well studied, the genomic study has been recently started. The ginseng genome has been known to undergo two rounds of whole genome duplication (WGD), therefore we investigated an evidence of WGD in ginseng draft sequence for understanding current ginseng genome structure. Four paralogous gene-rich genome blocks were found, consisted by eight scaffolds, using about 3.0 Gb whole genome draft sequence and 48,821 unigenes of P. ginseng generated by whole genome shotgun sequencing. The eight scaffold sequences were ordered and connected into four genomic blocks, using zig-zag extension within scaffold sequences recently duplicated. The paralogous scaffold pairs that were recently duplicated showed high sequence conservation in genic and non-genic regions. However, paleo duplicated paralogue scaffold sequences showed little conservation only in genic regions. Finally, a total of 110 paralogous gene pairs and its expression were identified from recently and paleo duplicated scaffold pairs, which were co-linear among four genomic blocks. This study provides the first insight into duplicated genome structure of ginseng and will be a valuable information for further ginseng genomics including improvement of draft sequence quality, chromosome anchoring of scaffolds, and genetic mapping.

Chinese cabbage (Brassica rapa ssp. pekinensis) is one of the most important vegetables and widely cultivated in Asia countries including Korea and China. Recently, whole genome sequence and full-length cDNA information of this species became available, which are encouraging genetic studies of this species to characterize agricultural important traits. Orange-colored (Or) cultivar of Chinese cabbage has inner leaves in orange, whereas other cultivars generally cultivated have yellow (Ye)- or white-colored inner leaves. In this study, we investigated phenotypes and carotenoid biosynthesis genes related to color variation in the Or cultivar. Firstly we compared the carotenoid content and composition between the Or and Ye cultivars by HPLC analysis. The inner leaves of Or cultivar contained approximately 9-fold high β-carotene content, whereas content of both lutein and violaxanthin was decreased to less than 30%, compared to Ye cultivar. Or cultivar was segregated with ratio of 3:1 in F2 population derived from crossing between Or and Ye inbred lines, indicating that Or phenotype is controlled by single recessive gene. To identify this gene, we investigated the expression of several genes involved in carotenoid biosynthesis by RT-PCR analysis. Among genes tested, two encoding putative carotenoid isomerase (CRTISO) and phytoene desaturase (PDS) were identified to show different expression between Or and Ye cultivars. Through further analysis of genomic DNA regions of these two genes, we could expect that several mutations such as InDel and base-substitution occurred and then affected expression of these genes in Or cultivar. In this presentation, I will introduce more detailed results for Or cultivars.