Ho Bang Kim

Simple sequence repeat marker development from Codonopsis lanceolata and genetic relation analysis

In this study, we developed 15 novel polymorphic simple sequence repeat (SSR) markers by SSR-enriched genomic library construction from Codonopsis lanceolata. We obtained a total of 226 non-redundant contig sequences from the assembly process and designed primer sets. These markers were applied to 53 accessions representing the cultivated C. lanceolata in South Korea. Fifteen markers were sufficiently polymorphic, and were used to analyze the genetic relationships between the cultivated C. lanceolata. One hundred three alleles of the 15 SSR markers ranged from 3 to 19 alleles at each locus, with an average of 6.87. By cluster analysis, we detected clear genetic differences in most of the accessions, with genetic distance varying from 0.73 to 0.93. Phylogenic analysis indicated that the accessions that were collected from the same area were distributed evenly in the phylogenetic tree. These results indicate that there is no correlative genetic relationship between geographic areas. These markers will be useful in differentiating C. lanceolata genetic resources and in selecting suitable lines for a systemic breeding program.

Current status and prospects of citrus genomics

Citrus is an economically important fruit tree with the largest amount of fruit production in the world. It provides important nutrition such as vitamin C and other health-promoting compounds including its unique flavonoids for human health. However, it is classified into the most difficult crops to develop new cultivars through conventional breeding approaches due to its long juvenility and some unique reproductive biological features such as gamete sterility, nucellar embryony, and high level of heterozygosity. Due to global warming and changes in consumer trends, establishing a systematic and efficient breeding programs is highly required for sustainable production of high quality fruits and diversification of cultivars. Recently, reference genome sequences of sweet orange and clementine mandarin have been released. Based on the reference whole-genome sequences, comparative genomics, reference-guided resequencing, and genotyping-by-sequencing for various citrus cultivars and crosses could be performed for the advance of functional genomics and development of traits-related molecular markers. In addition, a full understanding of gene function and gene co-expression networks can be provided through combined analysis of various transcriptome data. Analytic information on whole-genome and transcriptome will provide massive data on polymorphic molecular markers such as SNP, INDEL, and SSR, suggesting that it is possible to construct integrated maps and high-density genetic maps as well as physical maps. In the near future, integrated maps will be useful for map-based precise cloning of genes that are specific to citrus with major agronomic traits to facilitate rapid and efficient marker-assisted selection.

Development and Characterization of Microsatellite Primers for Zanthoxylum schinifolium (Rutaceae)

Premise of the study: Polymorphic microsatellite markers of Zanthoxylum schinifolium (Rutaceae), a promising medicinal plant with effective antibacterial, anticancer, and anti-inflammatory compounds, were developed and evaluated for further genetic studies based on genetic variation among individuals or populations. Methods and Results: Following the selective hybridization method, microsatellite-enrichment libraries were constructed. Using these libraries, we obtained 15 polymorphic and three monomorphic microsatellite markers for Z. schinifolium. The number of alleles observed in each of the 15 polymorphic loci ranged from two to eight, and the observed and expected heterozygosities ranged from 0.070 to 0.677 and from 0.093 to 0.688, respectively. Eleven of these developed markers were successfully amplified for Z. piperitum, a related species. Conclusions: These microsatellite markers can be valuable tools for further genetic studies of Z. schinifolium, such as genetic resource conservation for maintaining breeding material and individual identification for breeding program improvement and variety management.

Current status and prospects of molecular marker development for systematic breeding program in citrus

세계적인 과수작물로서의 경제적 중요성에도 불구하고, 감귤 생산은 주로 자연교잡 실생이나 눈 돌연변이로부터의 선발 또는 단순 품종 도입 등을 통해 이루어지고 있는 실정이다. 긴 유년기, 다배성, 자가불화합성과 같은 감귤 고유의 식물학적 특성, 주요 형질들(병저항성, 수량성, 품질 등)의 QTL에 의한 조절 등은 전통...

Development of novel simple sequence repeat markers from ramie (Boehmeria nivea L. Gaudich) and analysis of genetic diversity in its genetic resources

Boehmeria nivea (ramie), a subshrub of the Urticaceae family and an important fiber crop, has been grown in Asian countries, including Korea, for many centuries. Traditionally, in some regions of Korea, ramie leaves are also used as a major ingredient in ‘Songpyeon’ rice cakes. Despite its economic importance, the molecular genetics of ramie have not yet been studied in detail. Researchers from Yeong-Gwang Agricultural Technology Center collected genetic resources of ramie from a variety of local sites in Korea. Nuclear internal transcribed spacer sequences amplified from 90 genetic resources showed no variation in size or sequence between them or B. nivea reference samples, indicating that all the genetic resources could be taxonomically classified as B. nivea. To systematically and efficiently manage these genetic resources, we developed simple sequence repeat (SSR) markers for ramie using the magnetic bead hybridization selection method. Finally, we selected 17 SSR markers that showed possible polymorphism among the genetic resources and analyzed the genetic diversity of ramie collection. These 17 markers detected a total of 140 alleles, ranging from 3 to 17 alleles per accession. The average genetic diversity value was 0.61, ranging from 0.37 to 0.84. Average polymorphism information content was 0.56, ranging from 0.34 to 0.82. Genetic cluster analysis based on SSR data revealed that the genetic collection of ramie plants could be classified into four distinct clusters. A purity test on several of the genetic resources using polymorphic SSR markers revealed that some resources were impure. These newly developed SSR markers might be useful for diverse genetic analysis including the management of genetic collections, establishment of core collections, and cultivar identification.

Physiological importance and possible applications of β-substituted alanine synthase in plants

Cysteine, as well as its precursors and derivatives, plays important roles in plant development and stress responses. In plants, a diverse range of reactions affecting cysteine content are catalyzed by the β-substituted alanine synthase (BSAS) enzyme family. Individual BSAS family members use similar reaction mechanisms involving pyridoxal phosphate cofactors and show catalytic preferences for biosynthesis, degradation, or modification of the cysteine amino acid. In Arabidopsis thaliana (Arabidopsis) of the Brassicaceae family, four distinct biochemical activities are characterized at the gene level, namely, O-acetylserine sulfhydrylase, β-cyanoalanine synthase, l-cysteine desulfhydrase, and S-sulfocysteine synthase activities. Reverse genetic approaches in Arabidopsis were used to elucidate the physiological roles of metabolites of cysteine metabolism (O-acetylserine, sulfide, cysteine, cyanide, and S-sulfocysteine) during the processes of root hair development, pollen tube germination, heavy metal tolerance, defense responses, stomatal closure, and autophagy. Key catalytic residues determining reaction specificities in different BSAS enzymes are being identified, along with the roles of macromolecular complexes involving BSAS. The biochemical properties of BSAS active sites are being investigated in various organisms, including plants, for possible application to the development of new biological materials and drugs. Systematic and comparative genomic studies of BSAS enzymes in Brassica plants, close relatives of Arabidopsis, requiring high cysteine production for optimum growth and disease resistance, will be useful for the future study of the diversification of BSAS and the biotechnological improvement of these important crop plants.