Hwang-Bae Sohn

Network analysis of the metabolome and transcriptome reveals novel regulation of potato pigmentation

Highlight An integrated approach of metabolomics and transcriptomics was applied to understand regulatory networks associated with biosynthesis of anthocyanins that are differentially regulated in light-red- and dark-purple-colored potato cultivars.

Complete Chloroplast Genome Sequences and Comparative Analysis of Chenopodium quinoa and C. album

The Chenopodium genus comprises ~150 species, including Chenopodium quinoa and Chenopodium album, two important crops with high nutritional value. To elucidate the phylogenetic relationship between the two species, the complete chloroplast (cp) genomes of these species were obtained by next generation sequencing. We performed comparative analysis of the sequences and, using InDel markers, inferred phylogeny and genetic diversity of the Chenopodium genus. The cp genome is 152,099 bp (C. quinoa) and 152,167 bp (C. album) long. In total, 119 genes (78 protein-coding, 37 tRNA, and 4 rRNA) were identified. We found 14 (C. quinoa) and 15 (C. album) tandem repeats (TRs); 14 TRs were present in both species and C. album and C. quinoa each had one species-specific TR. The trnI-GAU intron sequences contained one (C. quinoa) or two (C. album) copies of TRs (66 bp); the InDel marker was designed based on the copy number variation in TRs. Using the InDel markers, we detected this variation in the TR copy number in four species, Chenopodium hybridum, Chenopodium pumilio, Chenopodium ficifolium, and Chenopodium koraiense, but not in Chenopodium glaucum. A comparison of coding and non-coding regions between C. quinoa and C. album revealed divergent sites. Nucleotide diversity >0.025 was found in 17 regions—14 were located in the large single copy region (LSC), one in the inverted repeats, and two in the small single copy region (SSC). A phylogenetic analysis based on 59 protein-coding genes from 25 taxa resolved Chenopodioideae monophyletic and sister to Betoideae. The complete plastid genome sequences and molecular markers based on divergence hotspot regions in the two Chenopodium taxa will help to resolve the phylogenetic relationships of Chenopodium.

Expressing the sweet potato orange gene in transgenic potato improves drought tolerance and marketable tuber production

Potato (Solanum tuberosum L.) is generally considered to be sensitive to drought stress. Even short periods of water shortage can result in reduced tuber production and quality. We previously reported that transgenic potato plants expressing the sweet potato orange gene (IbOr) under the control of the stress-inducible SWPA2 promoter (referred to as SOR plants) showed increased tolerance to methyl viologen-mediated oxidative stress and high salinity, along with increased carotenoid contents. In this study, in an effort to improve the productivity and environmental stress tolerance of potato, we subjected transgenic potato plants expressing IbOr to water-deficient conditions in the greenhouse. The SOR plants exhibited increased tolerance to drought stress under greenhouse conditions. IbOr expression was associated with slightly negative phenotypes, including reduced tuber production. Controlling IbOr expression imparted the same degree of drought tolerance while ameliorating these negative phenotypic effects, leading to levels of tuber production similar to or better than those of wild-type plants under drought stress conditions. In particular, under drought stress, drought tolerance and the production of marketable tubers (over 80g) were improved in transgenic plants compared with non-transgenic plants. These results suggest that expressing the IbOr transgene can lead to significant gains in drought tolerance and tuber production in potato, thereby improving these agronomically important traits.

Barcode System for Genetic Identification of Soybean [Glycine max (L.) Merrill] Cultivars Using InDel Markers Specific to Dense Variation Blocks

For genetic identification of soybean [Glycine max (L.) Merrill] cultivars, insertions/deletions (InDel) markers have been preferred currently because they are easy to use, co-dominant and relatively abundant. Despite their biological importance, the investigation of InDels with proven quality and reproducibility has been limited. In this study, we described soybean barcode system approach based on InDel makers, each of which is specific to a dense variation block (dVB) with non-random recombination due to many variations. Firstly, 2,274 VBs were mined by analyzing whole genome data in six soybean cultivars (Backun, Sinpaldal 2, Shingi, Daepoong, Hwangkeum, and Williams 82) for transferability to dVB-specific InDel markers. Secondly, 73,327 putative InDels in the dVB regions were identified for the development of soybean barcode system. Among them, 202 dVB-specific InDels from all soybean cultivars were selected by gel electrophoresis, which were converted as 2D barcode types according to comparing amplicon polymorphisms in the five cultivars to the reference cultivar. Finally, the polymorphism of the markers were assessed in 147 soybean cultivars, and the soybean barcode system that allows a clear distinction among soybean cultivars is also detailed. In addition, the changing of the dVBs in a chromosomal level can be quickly identified due to investigation of the reshuffling pattern of the soybean cultivars with 27 maker sets. Especially, a backcross-inbred offspring, “Singang” and a recurrent parent, “Sowon” were identified by using the 27 InDel markers. These results indicate that the soybean barcode system enables not only the minimal use of molecular markers but also comparing the data from different sources due to no need of exploiting allele binning in new varieties.

Inhibitory effects of extracts from Smilacina japonica on lipopolysaccharide induced nitric oxide and prostaglandin E 2 production in RAW264.7 macrophages

Smilacina japonica is a localized common rhizomatous flowering plant, This plant is often used in Korean traditional systems of medicine as a remedy for migrain, diplegia, physical impurity, blood circulation, abscess and contusion. Generally drugs that are used for arthritis have antinociceptive and anti-inflammatory properties. However, validity of the anti-inflammatory activity has not been scientifically investigated so far. Therefore, the aim of this study was to investigate the anti-inflammatory potential of S. japonica using the ethanolic extract and its sub- fractions. To evaluate the anti-inflammatory effects, we examined the inflammatory mediators such as nitric oxide (NO) and prostaglandin E2 (PGE2) on RAW 264.7 macrophages. Our results indicated that hexane fraction significantly inhibited the LPS induced NO and PGE2 production in the cells. The hexane fractions inhibitory activity for NO tests with IC50 values showed in 53.3 μg/ml and PGE2 tests with IC50 values showed at 32.5 μg/ml. Theseis result suggest a potential role of hexane fraction from S. japonica as source of anti-inflammatory agent.

Chromosome Reshuffling Patterns of Korean Soybean Cultivars using Genome-wide 202 InDel Markers

Knowledge of the chromosomal constitution of the ancestors of modern soybean will complement plant breeding efforts to improve agronomic and economic characteristics of soybean. Variation block (VB)-based comparison using genome-wide insertion/deletion (InDel) markers was used on a diverse panel of 147 soybean cultivars to assess the impact of chromosomal changes during modern breeding. There were identical variation patterns of the examined InDels consistently appearing in the genome parts arising from parental varieties, indicating that soybean chromosomes in descendants should be all determined by genetic reshuffling of VBs inherited from parental chromosomes. Structure analysis of the accessions through the 202 InDels separated the accessions into four subgroups. Gene introgression revealed by the structure analysis agreed with the fact that a limited number of landraces and elite varieties were introduced and used as donors for breeding soybean cultivars in pedigree analysis. Especially, VBs became more reshuffled over time as a result of the breeding process, which resulted in using breeding parents with new VB-types for improving the end-use value of soybean. Therefore, their clustering using the 202 VB-specific InDels is strongly influenced by the difference in breeding ancestors among the subgroups. This indicates that the 202 InDel markers are very useful for genetic study by analyzing the reshuffling patterns of the parental genomes in the descendant.

Agronomic characteristics and field resistance to bacterial soft rot of transgenic potato overexpressing the soybean calmodulin 4 gene (SCaM4)

We performed in vitro assay and field trials to assess levels of changes in intrinsic properties and resistance against soft rot of the potato cv. Dejima upon the introduction of a soybean calmodulin 4 gene (SCaM4). Field trials with four lines overexpressing SCaM4 gene were conducted over two seasons, and harvested tubers were evaluated in bioassay for resistance to Pectobacterium carotovorum ssp. carotovorum. The SCaM4 transgenic potato lines inoculated with CFU/ml of P. carotovorum ssp. carotovorum showed enhanced resistance compared to control. Among the SCaM4 transgenic lines, the transgenic line SCaM4-4 exhibited the highest tolerance to soft rot in vitro assays, so did in field trials. In the field trial, the soft rot resistance of SCaM4-4 line was more than 5 times higher compared to that of control cultivar, Dejima. The major agronomic characteristics of the SCaM4 transgenic lines were not different from those of the nontransgenic `Dejima`. The result demonstrated that the transformation of a calmodulin 4 gene was a successful strategy in development of potato cultivar enhanced to soft rot.