Joon-Woo Ahn

Transcriptome profiling in response to different types of ionizing radiation and identification of multiple radio marker genes in rice.

Ionizing radiation (IR) affects gene expression from plant genomes. To monitor the genome-wide transcriptional changes induced by three types of IR, we used the rice Affymetrix GeneChip microarray to identify genes that are up- or down-regulated by gamma rays (GAs), cosmic rays (CRs) and ion beams (IBs). The overall expression patterns in rice seedlings generated from seeds exposed to GAs and IBs were similar but differed for CRs exposure. Expression profiles of genes involved in metabolic pathways and cellular response were identified using MapMan analysis. This result revealed that IRs induced gene expression related to sucrose-starch metabolisms; sugar and starch accumulation was significantly increased in response to three types of IR in rice. In addition, we compared the genes commonly up- or down-regulated by exposure to three types of IR and identified 53 candidate radio marker genes (RMGs) that were differentially regulated by radiation exposure but not by other stresses. Among these genes, we selected six RMGs commonly applicable to different types of IR by specific coexpression networks using the algorithm for the reconstruction of accurate cellular networks (aracne) and confirmed the expression of these genes by reverse transcription-polymerase chain reaction (RT-PCR) analysis. Our results provided insight into the mechanisms of the responses to different types of IR and identified multiple marker genes to predict sensitivity to three types of IR.

Selection and molecular characterization of a high tocopherol accumulation rice mutant line induced by gamma irradiation

Tocopherols are micronutrients with antioxidant properties. They are synthesized by photosynthetic bacteria and plants, and play important roles in animal and human nutrition. In this study, we isolated a new rice mutant line with elevated tocopherol content (MRXII) from an in vitro mutagenized population induced by gamma irradiation. The mutant exhibited greater seed longevity than the control, indicating a crucial role for tocopherols in maintaining viability during quiescence, and displayed faster seedling growth during the early growth stage. To study the molecular mechanism underlying vitamin E biosynthesis, we examined the expression patterns of seven rice genes encoding vitamin E biosynthetic enzymes. Accumulation levels of the OsVTE2 transcript and OsVTE2 protein in the MRXII mutant were significantly higher than in the control. Sequence analysis revealed that the MRXII mutant harbored a point mutation in the OsVTE2 promoter region, which resulted in the generation of MYB transcription factor—binding cis-element. These results help identify the promoter regions that regulate OsVTE2 transcription, and offer insights into the regulation of tocopherol content.

Improvement of soybean through radiation-induced mutation breeding techniques in Korea

Mutation breeding techniques have been used to induce new genetic variations and improve agronomic traits in soybean. In Korea, the Korea Atomic Energy Research Institute (KAERI) has unique radiation facilities to induce plant mutations and has been conducting soybean mutation breeding programmes since the mid-1960s. Until now, the KAERI has developed five soybean mutant cultivars exhibiting early maturity, high yield and seed-coat colour change. In this paper, we review these five mutant cultivars in terms of how to successfully induce unique agronomic characteristics through mutation breeding programmes. A number of induced mutants exhibiting null lipoxygenase enzymes, altered protein patterns or Kunitz trypsin inhibitor activity could serve as genetic resources for the genetic analysis of target genes, and one mutant population has been developed for a reverse genetic study.

Identification of gamma ray irradiation-induced mutations in membrane transport genes in a rice population by TILLING

A high-salt environment represents environmental stress for most plants. Those that can grow and thrive in such an environment must have membrane transport systems that can respond effectively. Plant roots absorb Na+ from the soil, and the plant must maintain Na+ homeostasis to survive salt stress. A major mechanism by which salt-tolerant plants adapt to salt stress is through modulation of ion transport genes. We have subjected a population of rice plants to mutagenesis, and identified lines with both single-nucleotide polymorphisms (SNPs) in membrane transport genes and altered responses to salt stress. Primers labeled with FAM or HEX fluorescent dyes were designed for nine target genes encoding membrane transport proteins that are believed to regulate salt stress tolerance. A TILLING (Targeting Induced Local Lesions IN Genome) assay was performed on 2,961 M2 rice mutant lines using electrophoresis. After the TILLING assay, a total of 41 mutant lines containing SNPs in the target genes were identified and screened. The average number of mutations per gene was 1/492 kb in lines having SNPs, and the percentage of mutation sites per total sequence was 0.67. Among the 41 lines, nine had altered sequences in the exon region of the genes. Of these nine lines, seven were tolerant to salt stress after exposure to 170 mM NaCl for three weeks, while the other two lines were not more salt-tolerant than the control lines. Furthermore, five mutant lines containing SNPs in the coding region of OsAKT1, OsHKT6, OsNSCC2, OsHAK11 and OsSOS1 showed changed expression levels for each gene. We conclude that variation in membrane transport genes, such as expression levels and protein structures, may affect the rice plants tolerance to salt stress. These mutations represent traits that may be selected for large rice mutant populations, permitting efficient acquisition of salt-tolerant lines.

Evaluation of Nutritive Value and Identification of Fungi in Silage from New Kenaf (Hibiscus cannabinus) Cultivars

The effects of harvesting stage of new Kenaf cultivars on the nutritive values, amino acid contents and fungal abundance were investigated. The late and mid-late maturing cultivars offered more DM than did early-maturing cultivars. The DM was highest at 100 DAS in all Kenaf silage. For all cultivars, the crude protein content (7.4–18.4%) of silage was reduced if harvesting was delayed. The neutral detergent fiber (NDF) and acid detergent fiber (ADF) contents were not significantly different among the cultivars; however NDF and ADF contents increased significantly upon late harvesting. All silages had pH values under 4.0, ensuring stable storage. The optimum harvesting time for silage production, as evidenced by yield, fermentation characteristics and nutritive value, was 100 DAS. The concentrations of amino acid in the silage were lower than that in the hay. Silage produced by all Kenaf cultivars exhibited low yeast biodiversity; only one species (Pichia fermentans) was detected when the harvesting date was optimal.

Evaluation of genetic diversity in Korean soybean landraces by protein banding patterns using high-throughput screening

The agronomic performance and storage protein patterns of 722 soybean landraces collected from eight geographically different Korean locations were investigated. The days to 50% flowering, days to maturity, and 100-seed weight ranged from 68.9 to 71.9 (d), 140.1 to 146.6 (d), and 22.4 to 26.8 (g), respectively. High-throughput protein profiling electrophoresis was performed, and the banding patterns were analyzed. Among the 722 soybean landraces, lipoxygenase bands were found to be absent in 21 lines. Nei’s gene diversity (h) ranged from 0 to 0.2642, with an average value of 0.1565. The mean coefficient of gene differentiation (Gst) was 0.0944, and the estimated gene flow (Nm) in the population was 4.7971. In a correlation matrix between the agronomic traits and protein banding patterns, the acidic banding pattern was significantly associated with all the other factors. The phenotypic and genotypic differences of the collection areas were evaluated, and the excellent soybean lines with high-value proteins, including 11S globulins, or without antinutritional factors such as lipoxygenase and trypsin inhibitor were selected.