Do-Soon Kim

Progress in upscaling Miscanthus biomass production for the European bio-economy with seed-based hybrids

Field trials in Europe with Miscanthus over the past 25 years have demonstrated that interspecies hybrids such as M. × giganteus (M × g) combine both high yield potentials and low inputs in a wide range of soils and climates. Miscanthus hybrids are expected to play a major role in the provision of perennial lignocellulosic biomass across much of Europe as part of a lower carbon economy. However, even with favourable policies in some European countries, uptake has been slow. M × g, as a sterile clone, can only be propagated vegetatively, which leads to high establishment costs and low multiplication rates. Consequently, a decade ago, a strategic decision to develop rapidly multiplied seeded hybrids was taken. To make progress on this goal, we have (1) harnessed the genetic diversity in Miscanthus by crossing and progeny testing thousands of parental combinations to select several candidate seed‐based hybrids adapted to European environments, (2) established field scale seed production methods with annual multiplication factors >1500×, (3) developed the agronomy for establishing large stands from seed sown plug plants to reduce establishment times by a year compared to M × g, (4) trialled a range of harvest techniques to improve compositional quality and logistics on a large scale, (5) performed spatial analyses of yield potential and land availability to identify regional opportunities across Europe and doubled the area within the bio‐climatic envelope, (6) considered on‐farm economic, practical and environmental benefits that can be attractive to growers. The technical barriers to adoption have now been overcome sufficiently such that Miscanthus is ready to use as a low‐carbon feedstock in the European bio‐economy.

ZEBRA-NECROSIS, a thylakoid-bound protein, is critical for the photoprotection of developing chloroplasts during early leaf development

The zebra-necrosis (zn) mutant of rice (Oryza sativa) produces transversely green/yellow-striped leaves. The mutant phenotype is formed by unequal impairment of chloroplast biogenesis before emergence from the leaf sheath under alternate light/dark or high/low temperatures (restrictive), but not under constant light and temperature (permissive) conditions. Map-based cloning revealed that ZN encodes a thylakoid-bound protein of unknown function. Virus-induced gene silencing of a ZN homolog in Nicotiana benthamiana causes leaf variegation with sporadic green/yellow sectors, indicating that ZN is essential for chloroplast biogenesis during early leaf development. Necrotic lesions often occur in the yellow sectors as a result of an excessive accumulation of reactive oxygen species (ROS). The phenotypic severity (leaf variegation and necrosis) and ROS levels are positively correlated with an increase in light intensity under restrictive conditions. In the mutant leaves, chlorophyll (Chl) metabolism, ROS scavenging activities, maximum quantum yield of photosystem II (PSII), and structures and functions of the photosynthetic complexes are normal in the Chl-containing cells, suggesting that ROS are mainly generated from the defective plastids of the Chl-free cells. The PSII activity of normal chloroplasts is hypersensitive to photoinhibition because the recovery rates of PSII are much slower. In the PSII repair, the degradation of damaged D1 is not impaired, suggesting a reduced activity of new D1 synthesis, possibly because of higher levels of ROS generated from the Chl-free cells by excess light. Together, we propose that ZN is required for protecting developing chloroplasts, especially during the assembly of thylakoid protein complexes, from incidental light after darkness.

Miscanthus as a potential bioenergy crop in East Asia

Miscanthus is a perennial rhizomatous grass with C4 photosynthesis and native to East Asia. This grass has been considered as a weed in East Asia, and never been considered as a bioenergy crop until the end of the 20th century. Meanwhile, it has been studied as a potential bioenergy crop in Europe since the 1980s. Soaring energy consumption and heavy dependency of its energy production on imported petroleum have led to initiate finding alternative energy in East Asia. Miscanthus has high water and nutrient-use efficiency, and cold tolerance, high biomass yield potential up to 40 t DM ha−1 with long sustainable productivity up to more than 15 years after the first establishment, and high carbon sequestration capacity. In this regard, Miscanthus is one of the most ideal bioenergy crops in East Asia; potential areas where sufficient size of land is available include Mongolia, the far eastern part of Russia such as Primorski-Krai, Amur Oblast, and Khabarovsk-Krai, and northern parts of China such as Jilin, Heilongjiang, and Neimenggu. Although low temperature and rainfall may be limiting factors, it is expected that Miscanthus can be cultivated for commercial biomass production in this region, particularly Primorski-Krai. To facilitate Miscanthus biomass production and its commercial use for biofuel production in East Asia, it is necessary to introduce a new Miscanthus variety with cold and drought tolerance, and to develop a Miscanthus plantation technology and production management system.

Transcriptome profiling and comparative analysis of Panax ginseng adventitious roots

Background Panax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essential. Methods RNA-seq analysis of adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS), was performed using the Illumina HiSeq platform. After transcripts were assembled, expression profiling was performed. Results Assemblies were generated from ∼85 million and ∼77 million high-quality reads from CP and CS cultivars, respectively. A total of 35,527 and 27,716 transcripts were obtained from the CP and CS assemblies, respectively. Annotation of the transcriptomes showed that approximately 90% of the transcripts had significant matches in public databases. We identified several candidate genes involved in ginsenoside biosynthesis. In addition, a large number of transcripts (17%) with different gene ontology designations were uniquely detected in adventitious roots compared to normal ginseng roots. Conclusion This study will provide a comprehensive insight into the transcriptome of ginseng adventitious roots, and a way for successful transcriptome analysis and profiling of resource plants with less genomic information. The transcriptome profiling data generated in this study are available in our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use.

Genotypic variation of cadmium accumulation and distribution in rice

An effective way to reduce the risk of cadmium (Cd) entering the food chain is to use low Cd-accumulation rice cultivars, particularly in Asia. The fundamental requirement for breeding low grain Cd-accumulation cultivars is to know the genotypic variation in Cd accumulation and the physiological processes and genetic basis governing the Cd accumulation in rice grain. In this experiment, genotypic variation in Cd accumulation and distribution among rice organs was studied using thirty-five rice varieties. They were grown with irrigation water containing 2 ppm Cd throughout rice growing season under field condition in 2007. At harvest, plants were sampled and analyzed for Cd concentration and accumulation in each rice organ. Significant variation of Cd concentration and accumulation in rice organs were found among thirty-five rice cultivars, revealing more than 8-fold varietal differences in grain Cd concentration and shoot Cd accumulation. Cd concentration and accumulation in grain were significantly different among cultivar groups, showing the highest in indica and the lowest in temperate japonica. Tongil-type and tropical japonica rice showed a Cd concentration intermediate to that of temperate japonica and indica rice. The higher Cd accumulation in grain of indica rice was attributable to the greater ability of Cd uptake. The greater ability of root-shoot translocation in tropical japonica and shoot-grain redistribution in tongil-type resulted in the significantly higher grain Cd concentration in these cultivar groups than in temperate japonica. For over 35 cultivars tested, grain Cd concentration revealed a significant positive correlation with root Cd concentration and shoot Cd concentration and accumulation while no significant correlation with root-shoot translocation factor and shoot-grain redistribution ratio. However, correlation analyses within each cultivar group showed that grain Cd concentration was significantly correlated with root-shoot translocation factor in indica, with root Cd concentration in tongil-type, with shoot Cd concentration and accumulation in tropical japonica, and with shoot Cd accumulation and shoot-grain redistribution ratio in temperate japonica. These results indicate that genotypic variation in grain Cd accumulation, in general, is controlled by all the three physiological processes but the major physiological process governing its genotypic variation within cultivar group is different depending on cultivar groups.

Modelling rice competition with Echinochloa crus-galli and Eleocharis kuroguwai in transplanted rice cultivation.

Field experiments were conducted to investigate rice — Echinochloa crus-galli and rice — Eleocharis kuroguwai competition under transplanted rice cultivation in four major rice production areas; Suwon, Daejeon, Iksan, and Naju in Korea. Rice yield data were used to predict rice yield as a function of plant densities of E. crus-galli and E. kuroguwai using a rectangular hyperbola and to determine economic threshold (ET) levels of the weeds. Both weed species significantly reduced number of tillers at early rice growth stage, resulting in significant reduction in number of spikes, and the other yield components such as number of grains, maturity and 1,000-grain weight at later growth stage. The weed competitivity represented by parameter ranged from 0.0145 to 0.0346 for E. crus-galli and from 0.0037 to 0.0187 for E. kuroguwai, indicating that the competition effect of E. crus-galli on rice yield was slightly greater than that of E. kuroguwai. The ET values of E. crus-galli were between 0.298 and 1.078 plants m−2, while those of E. kuroguwai were between 0.848 and 5.298 plants m−2, depending on weed competitivity and herbicide price. Therefore, our results can be used to support decision-making on herbicide application for E. crus-galli and E. kuroguwai management in transplanted rice cultivation.

Sequencing of transcriptomes from two Miscanthus species reveals functional specificity in rhizomes, and clarifies evolutionary relationships.

BackgroundMiscanthus is a promising biomass crop for temperate regions. Despite the increasing interest in this plant, limited sequence information has constrained research into its biology, physiology, and breeding. The whole genome transcriptomes of M. sinensis and M. sacchariflorus presented in this study may provide good resources to understand functional compositions of two important Miscanthus genomes and their evolutionary relationships.ResultsFor M. sinensis, a total of 457,891 and 512,950 expressed sequence tags (ESTs) were produced from leaf and rhizome tissues, respectively, which were assembled into 12,166 contigs and 89,648 singletons for leaf, and 13,170 contigs and 112,138 singletons for rhizome. For M. sacchariflorus, a total of 288,806 and 267,952 ESTs from leaf and rhizome tissues, respectively, were assembled into 8,732 contigs and 66,881 singletons for leaf, and 8,104 contigs and 63,212 singletons for rhizome. Based on the distributions of synonymous nucleotide substitution (Ks), sorghum and Miscanthus diverged about 6.2 million years ago (MYA), Saccharum and Miscanthus diverged 4.6 MYA, and M. sinensis and M. sacchariflorus diverged 1.5 MYA. The pairwise alignment of predicted protein sequences from sorghum-Miscanthus and two Miscanthus species found a total of 43,770 and 35,818 nsSNPs, respectively. The impacts of striking mutations found by nsSNPs were much lower between sorghum and Miscanthus than those between the two Miscanthus species, perhaps as a consequence of the much higher level of gene duplication in Miscanthus and resulting ability to buffer essential functions against disturbance.ConclusionsThe ESTs generated in the present study represent a significant addition to Miscanthus functional genomics resources, permitting us to discover some candidate genes associated with enhanced biomass production. Ks distributions based on orthologous ESTs may serve as a guideline for future research into the evolution of Miscanthus species as well as its close relatives sorghum and Saccharum.

Phenotypic Characterization of Transgenic Miscanthus sinensis Plants Overexpressing Arabidopsis Phytochrome B

Phytochromes are dimeric pigment proteins with reversible photochromism between red and far-red light-absorbing forms. They are photoreceptors that regulate various aspects of plant growth and development and have been used for biotechnological applications to improve agricultural performance of crops. Miscanthus species have been suggested as one of the most promising energy crops. In this paper, Arabidopsis phytochrome B (PHYB) gene was introduced into Miscanthus sinensis using Agrobacterium-mediated transformation method that we developed recently, with the herbicide resistance gene (BAR) as a selection marker. After putative transgenic plants were selected using the herbicide resistance assay, genomic integration of the transgene was confirmed by genomic PCR and Southern blot analysis, and transgene expression was validated by Northern blot analysis. Compared to nontransformed control plants, transgenic plants overexpressing PHYB showed phenotypes with increased phytochrome B function, which includes increased chlorophyll content, decreased plant height, and delayed flowering. Therefore, these results suggest that Arabidopsis phytochrome B is functional in M. sinensis and provide a method to develop Miscanthus varieties with enhanced agricultural performance using phytochromes.

Improvement of ginsenoside production by Panax ginseng adventitious roots induced by γ-irradiation

In order to evaluate effects of γ-rays on adventitious root formation and ginsenoside production, embryogenic calli induced from cotyledon explants of Panax ginseng C.A. Meyer were treated with γ-rays of 0, 10, 30, 50, 70, and 100 Gy. The highest frequency of adventitious root formation of 75 % occurred at γ-irradiation of 30 Gy, which is considered adequate dosage for selecting mutant cell lines. Five mutated adventitious roots (MAR)3-lines out of the propagation of 142 adventitious root lines treated with 30 Gy were selected based a 100-fold increase in proliferation rate compared to control adventitious roots (CAR) and content of the seven major ginsenosides (Rb1, Rb2, Rc, Rd, Re, Rf, and Rg1) was determined. In the CAR and four of the MAR3-lines (except for MAR3-109), the Rb/Rg ratio was greater than 1.0, thereby indicating altered ginsenoside composition in these root lines. The HPLC analysis of the MAR3-13 and MAR3-26 lines confirmed different ginsenoside profiles, including the three unidentified ginsenoside candidates, Gm1, Gm2, and Gm3. The ginsenosides of the MAR3-13 and MAR3-26 lines showed high hydroxyl and superoxide radical scavenging activities.

Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed

Barnyardgrass (Echinochloa crus-galli) is a pernicious weed in agricultural fields worldwide. The molecular mechanisms underlying its success in the absence of human intervention are presently unknown. Here we report a draft genome sequence of the hexaploid species E. crus-galli, i.e., a 1.27 Gb assembly representing 90.7% of the predicted genome size. An extremely large repertoire of genes encoding cytochrome P450 monooxygenases and glutathione S-transferases associated with detoxification are found. Two gene clusters involved in the biosynthesis of an allelochemical 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) and a phytoalexin momilactone A are found in the E. crus-galli genome, respectively. The allelochemical DIMBOA gene cluster is activated in response to co-cultivation with rice, while the phytoalexin momilactone A gene cluster specifically to infection by pathogenic Pyricularia oryzae. Our results provide a new understanding of the molecular mechanisms underlying the extreme adaptation of the weed.Barnyardgrass is a problematic agricultural weed. Here, via genomic analysis, Guo et al. identify genes potentially underlying its success, including a gene cluster activated in response to co-cultivation with rice that leads to synthesis of the allelochemical DIMBOA.