A eukaryotic marine microalga was isolated from Jungmun Saekdal Beach, Jeju Island, Korea and an integrated approach, including molecular phylogeny and morphology, was used to determine its taxonomical status. Molecular phylogenetic evidence inferred from the small subunit (SSU) 18S rRNA sequence and internal transcribed spacer (ITS) secondary structure analysis clearly showed that the isolate belonged to the recently described species, Jaagichlorella roystonensis. Distinctive morphological keys of the species were also observed by light microscopy and scanning/ transmission electron microscopy (S/TEM). In this study, a Korean marine J. roystonensis species was described for the first time and was subsequently added to the national culture collections in Korea.

A eukaryotic microalga was isolated from seawater in Janghang Harbor, Korea and its morphological, molecular, and physiological characteristics were investigated. Due to its simple morphology, no distinctive characters were found by morphological observation, such as light microscope or scanning/transmission electron microscopy (S/ TEM). However, molecular phylogenetic evidence inferred from the concatenated small subunit (SSU) 18S rRNA and internal transcribed spacer (ITS) sequence data indicated that the isolate belonged to the newly described Micractinium singularis. Furthermore, it was clustered with Antarctic Micractinium strains and it also showed a psychrotolerant property, surviving at temperatures as low as 5°C. However, its optimal growth temperatures range from 15°C to 25°C, indicating that this microalga is a mesophile. Additionally, gas chromatography-mass spectrometry (GC/MS) analysis showed that the isolate was rich in nutritionally important omega-3 polyunsaturated fatty acid, and high-performance liquid chromatography analysis (HPLC) revealed that the high-value antioxidant lutein was biosynthesized as an accessory pigment by this microalga, with glucose as the major monosaccharide. Therefore, in this study, a Korean marine M. singularis species was discovered, characterized, and described. It was subsequently added to the national culture collections.

The Arabidopsis gene AVP1 encodes a vacuolar H+-translocating inorganic pyrophosphatase (EC3.6.1.1) that functions as an electronic proton pump in the vacuolar membrane and affects growth development and stress responses in plants. This study was conducted to evaluate the molecular properties of the A. thaliana vacuolar H+-pyrophosphatase (AVP1) gene in rice. Incorporation and expression of the transgene was confirmed by PCR and quantitative real-time PCR, respectively. Expression of the AVP1 gene in transgenic rice plants (TRP1 and TRP2) resulted in significantly enhanced tolerance to 100 mM NaCl under greenhouse conditions when compared to control wild-type (WT) rice plants. Augmented AVP1 expression in the transgenic rice plants also affected total biomass and improved ion homeostasis through increased accumulation of Na+ ions in whole tissues when compared to control WT rice plants under high salinity conditions. The Fv/Fm values of transgenic rice plants were higher than those of WT rice plants, even though the values decreased over time in both WT and transgenic (TRP1 to TRP8) rice plants. Furthermore, rice grain yield and biomass of the transgenic rice plants were at least 15% higher based on the culm and root weights and panicle and spikelet numbers when compared to those of the WT rice plants during the farming season in Korea. Thus, these results suggest that ectopic AVP1 expression conferred tolerance and stress resistance to genetically modified transgenic crop plants by improving cellular ion homeostasis against salt conditions, which enhanced the rice yield and biomass under natural conditions in paddy fields.

In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for screening target loci with agricultural traits. We propose the variation block method, a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing short-read DNA sequences of the cultivar to a reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in the cultivar set are used to split the genomes, and the resulting sequence regions are named as variation blocks. Finally, the genomes are compared using the variation blocks. The variation block method identified recurring recombination blocks accurately and successfully represented block-level diversities in the publicly available genomes of 31 soybeans and 23 rice accessions. The practicality of this approach was demonstrated by the identification of a putative locus determining soybean hilum color. We suggest that the variation block method is an efficient genomics method for recombination block-level comparison of crop genomes. We expect that this method holds the prospect of developing crop genomics by bringing genomics technology to the field of crop breeding.

We investigated Arctic plants to determine if they have a specific mechanism enabling them to adapt to extreme environments because they are subject to such conditions throughout their life cycles. Among the cell defense systems of the Arctic mouse-ear chickweed Cerastium arcticum, we identified a stress-responsive dehydrin gene CaDHN that belongs to the SK5 subclass and contains conserved regions with 1 S-segment at the N-terminus and 5 K-segments from the N-terminus to the C-terminus. To investigate the molecular properties of CaDHN, yeast were transformed with CaDHN. CaDHN-expressing transgenic yeast (TG) cells recovered more rapidly from challenge with exogenous stimuli, including oxidants (hydrogen peroxide, menadione, and tert-butyl hydroperoxide), high salinity, freezing and thawing, and metal (Zn2+), than wild-type (WT) cells. TG cells were sensitive to copper, cobalt, and sodium dodecyl sulfate. In addition, the cell survival of TG cells was higher than that of WT cells when cells at the mid-log and stationary stages were exposed to increased ethanol concentrations. There was a significant difference in cultures that have an ethanol content >16%. During glucose-based batch fermentation at generally used (30℃) and low (18℃) temperatures, TG cells produced a higher alcohol concentration through improved cell survival. Specifically, the final alcohol concentrations were 13.3% and 13.2% in TG cells during fermentation at 30℃ and 18℃, respectively, whereas they were 10.2% and 9.4%, respectively, in WT cells under the same fermentation conditions. An in vitro assay revealed that purified CaDHN acted as a reactive oxygen species (ROS)-scavenger by neutralizing H2O2 and a chaperone by preventing high temperature-mediated catalase inactivation. Taken together, our results show that CaDHN expression in transgenic yeast confers tolerance to various abiotic stresses by improving redox homeostasis and enhances fermentation capacity, especially at low temperatures (18℃).

Although much effort has been made to find agronomically important loci in the soybean plant, extensive linkage disequilibrium and genome duplication have limited efficient genome-wide linkage analyses that can identify important regulatory genes. In this respect, recombination block-based analysis of cultivated plant genomes is a potential critical step for molecular breeding and target locus screening. We propose a new three-step method of detecting recombination blocks and comparative genomics of bred cultivars. It utilizes typical reshuffling features of their genomes, which have been generated by the recombination processes of breeding ancestral genomes. To begin with, mutations were detected by comparing genomes to a reference genome. Next, sequence blocks were examined for likenesses and difference with respect to the reference genome. The boundaries between the blocks were taken as recombination sites. All recombination sites found in the cultivar set were used to split the genomes, and the resulting sequence fragments were named as core recombination blocks (CRBs). Finally, the genomes were compared at the CRB level, instead of at the sequence level. In the genomes of the five Korean soybean cultivars used, the CRB-based comparative genomics method produced long and distinct CRBs that are as large as 22.9 Mb. We also demonstrated efficiency in detecting functionally useful target loci by using indel markers, each of which represents a CRB. We further showed that the CRB method is generally applicable to both monocot and dicot crops, by analyzing publicly available genomes of 31 soybeans and 23 rice accessions.

Chilling stress affects growth and yield of warm-climate crops such as soybean (Glycine max L.) that is susceptible to low temperature (10-18℃). A comparative proteomic approach was employed to explore the mechanisms underlying soybean response to chilling stress. Soybean seedlings were germinated for 3-4 days and exposed to low temperature (10℃) for 3 days, and the proteins were extracted from seedling leaves. Protein separation by SDS-PAGE followed by liquid chromatography electro-spray ionization tandem mass spectrometry (LC-ESI MS/MS) was effective approach to identify proteins, based on the number of peptides reliably identified. A total of 77 proteins out of 704 proteins were identified in the presence of chilling stress. Most proteins identified had functions related to cell signaling, metabolism, energy and transport, protein biosynthesis and degradation, cytoskeleton, and were involved in regulating reactions and defending against stress. It is therefore likely that the response of soybean plant’s proteome to chilling stress is complex, and that the identification proteins may play an important role in regulating adaptation activities following challenge to chilling stress to facilitate cellular homeostasis. Furthermore, our result suggest that new ways of engineering stress-tolerant plants responding climate change by providing outline for agriculturally important chilling stress.

Resequencing data is actively used for searching QTL or analyzing genetic diversity in the crops. However, the complexity of genome, caused by genome duplication, limits the utility of genome-wide association studies and linkage analyses to identify genes that regulate agronomically valuable traits. Here, we propose a comparative genomics approach based on core or common variation-based recombination blocks (CRB) using single nucleotide variation (SNV) density information. We found that the soybean genomes are assembled with long and distinct CRBs as large as 10Mb. CRB-based comparative genomics enabled us to accurately identify recombination blocks at the whole-chromosome level. We identified the Ih locus that determines the yellow hilum color in soybeans using CRB-based mapping with representative indel markers. These results suggest that the CRB-based comparison method is a promising platform for molecular breeding and map-based cloning.