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.

Field trials in Europe with Miscanthus over the past 25 years have demonstrated that interspecies hybrids such as M. 9 giganteus (M 9 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 9 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 Correspondence: John Clifton-

BackgroundPanax 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.MethodsRNA-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.ResultsAssemblies 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.ConclusionThis 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.

Crops during their early growth stages are vulnerable to a wide range of environmental stressors; thus, earlier seed invigoration and seedling establishment are essential in crop production. As an alternative to synthetic chemical treatments, plasma technology could be one of the emerging technologies to enhance seed germination and seedling vigor by managing environmental stressors. Recent studies have shown its beneficial effects in various stress conditions, suggesting that plasma treatment can be used for early crop stress management. This paper reviewed the effects of different types of plasma treatments on plant responses in terms of the seed surface environment (seed scarification and pathogen inactivation) and physiological processes (an enhanced antioxidant system and activated defense response) during the early growth stages of plants. As a result, plasma treatment can enhance seed invigoration and seedling establishment by alleviating the adverse effects of environmental stressors such as drought, salinity, and pathogen infection. More information on plasma applications and their mechanisms against a broad range of stressors is required to establish a better plasma technology for early crop stress management.

Lack of understanding the effects of single- and multiple-weed interference on soybean yield has led to inadequate weed management in Primorsky Krai, resulting in much lower average yield than neighboring regions. A 2 yr field experiment was conducted in a soybean field located in Bogatyrka (43.82°N, 131.6°E), Primorsky Krai, Russia, in 2013 and 2014 to investigate the effects of single and multiple interference caused by naturally established weeds on soybean yield and to model these effects. Aboveground dry weight was negatively affected the most by weed interference, followed by number of pods and seeds. Soybean yield under single-weed interference was best demonstrated by a rectangular hyperbolic model, showing that common ragweed and barnyardgrass were the most competitive weed species, followed by annual sowthistle, American sloughgrass, and common lambsquarters. In the case of multiple-weed interference, soybean yield loss was accurately described by a multivariate rectangular hyperbolic model, with total density equivalent as the independent variable. Parameter estimates indicated that weed-free soybean yields were similar in 2013 and 2014, i.e., estimated as 1.72 t and 1.75 t ha−1, respectively, and competitiveness of each weed species was not significantly different between the two years. Economic thresholds for single-weed interference were 0.74, 0.66, 1.15, 1.23, and 1.45 plants m−2for common ragweed, barnyardgrass, annual sowthistle, American sloughgrass, and common lambsquarters, respectively. The economic threshold for multiple-weed interference was 0.70 density equivalent m−2. These results, including the model, thus can be applied to a decision support system for weed management in soybean cultivation under single and multiple-weed interference in Primorsky Krai and its neighboring regions of Russia.