Yong-Jin Park

Reverse transcriptase domain sequences from Mungbean (Vigna radiata) LTR retrotransposons: Sequence characterization and phylogenetic analysis

The conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy groups of long terminal repeat (LTR) retrotransposons were amplified from mungbean (Vigna radiata) genome using degenerate primers, cloned and sequenced. Among these 34% and 65% of respective clones of copia and gypsy RT sequences possessed stop codons or frame-shifts or both. The RT sequences corresponding to both the groups exhibit significant levels of heterogeneity. Presence of mungbean copia and gypsy RT sequences in other papilionoid legumes of the same (Phaseoleae) and different lineages (Loteae, Trifoleae, Cicereae) indicates existence of these elements prior to the radiation of papilionoid legumes and also supports the recent interpretations of close relationship between Phaseoleae and Loteae tribes of Papilionoideae subfamily. On the other hand significant homologies of some mungbean copia as well as gypsy RT sequences with those of unrelated plant species suggest their origin from different plant lineages and also that heterogeneous population of related elements were already existed throughout (even before the divergence of monocot and dicot) the evolution of these genera from their common ancestor.

Development of simple sequence repeat (SSR) markers to study diversity in the herbaceous peony (Paeonia lactiflora)

The herbaceous peony (Paeonia lactiflora Pall.) is a well-known herbaceous flowering plant that yields high medicinal and economic value in Korea and China. In this study, 14 novel polymorphic microsatellite markers were developed and characterized through the construction of a simple sequence repeat (SSR)-enriched library from genomic deoxyribonucleic acid (DNA) of P. lactiflora. In total, 103 alleles across 85 P. lactiflora accessions were detected, with an average of 7.4 alleles per locus. The values of the major allele frequency, genetic diversity, and polymorphism information content (PIC) ranged from 0.39 to 0.88 (mean = 0.61), 0.21 to 0.71 (mean = 0.50), and 0.19 to 0.67 (mean = 0.43), respectively. The mean genetic distance among the P. lactiflora accessions was 0.5559, indicating wide variation. These new SSR markers will be useful tools for assessing genetic diversity, understanding population structure, identifying genotypes, and breeding of P. lactiflora.

Comparison of Vegetation and Habitat Condition of Dendranthema boreale and Dendranthema indicum in Korea

This study compared the differences between the Dendranthema boreale and Dendranthema indicum in their habitat, soil adaptability, species composition and community structure in Korea. More D. boreale distributed than D. indicum to in the place where high elevation and on the surface of low degree slope. Both D. boreale and D. indicum growed well in south-east direction of the slope. The soil pH of D. boreale and D. indicum was 6.1 and 7.1, respectively. Ca, Mg, Na and organic matter content of the soil of D. boreale habitat was significantly lower than that of the D. indicum habitat. There were 102 and 88 taxa, in D. boreale and D. indicum habitat, respectively. Both species generally distributed along with herbs than along with trees. The important species found in D. boreale habitat were Artemisia princeps (57.1%) and Humulus japonicus (33.3%), and the D. indicum habitat were Miscanthus sinensis (42.9%) and Lonicera japonica (38.1%). The D. boreale group was classified into Artemisia princeps, Crepidiastrum denticulatum, Miscanthus sinensis, Humulus japonicus, Pueraria lobata, Lespedeza bicolor, Lonicera japonica and Rubus crataegifolius community. The D. indicum group was classified into Artemisia capillaris, Peucedanum japonicum, Boehmeria pannosa, Pinus thunbergii, Lonicera japonica, Quercus acutissima and Robinia pseudoacacia community. There is a large difference bewteen D. boreale and D. indicum in their habitat, soil adaptability, species composition and community structure.

Community Structure and Habitat Environment of Genus Liriope Group in Korea

This text was analyzed and investigated the vegetation and floristic composition by cluster analysis and classification of phytosociological method, to evaluate the species composition, habitat environment and community structure of Liriope platyphylla and Liriope spicata group in Korea. The southeast slope gradient of the habitat of L. platyphylla and L. spicata was 6.7 to 8.4%, and the habitat altitude of L. platyphylla (41.0 m), L. spicata (114.9 m) was different. Habitat distribution of L. spicata was broader than L. platyphylla. Appearing plants of L. platyphylla and L. spicata group was 58 taxa, 99 taxa, respectively, and Coverage of tree layer was 87.5%, 92.5% respectively. In genus Liriope group, the highest appearing frequency of plant grow in the moist valley as Quercus serrata. Thus, plants of genus Liriope growth was better in moist shade. The vegetation of L. platyphylla group was classified into Quercus serrata community, Castanopsis sieboldii community, Pinus densiflora community and Pinus thunbergii community, and the Liriope spicata group was classified into Quercus serrata community, Quercus alien community, Quercus acutissima community, Prunus verecunda community, Robinia pseudoacacia community, Pinus densiflora community and Pinus thunbergii community. In genus Liriope group, Quercus serrata and Pinus densiflora communities was the closest the similarities.

A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice (Oryza sativa) at the Germination Stage

Salt toxicity is the major factor limiting crop productivity in saline soils. In this paper, 295 accessions including a heuristic core set (137 accessions) and 158 bred varieties were re-sequenced and ~1.65 million SNPs/indels were used to perform a genome-wide association study (GWAS) of salt-tolerance-related phenotypes in rice during the germination stage. A total of 12 associated peaks distributed on seven chromosomes using a compressed mixed linear model were detected. Determined by linkage disequilibrium (LD) blocks analysis, we finally obtained a total of 79 candidate genes. By detecting the highly associated variations located inside the genic region that overlapped with the results of LD block analysis, we characterized 17 genes that may contribute to salt tolerance during the seed germination stage. At the same time, we conducted a haplotype analysis of the genes with functional variations together with phenotypic correlation and orthologous sequence analyses. Among these genes, OsMADS31, which is a MADS-box family transcription factor, had a down-regulated expression under the salt condition and it was predicted to be involved in the salt tolerance at the rice germination stage. Our study revealed some novel candidate genes and their substantial natural variations in the rice genome at the germination stage. The GWAS in rice at the germination stage would provide important resources for molecular breeding and functional analysis of the salt tolerance during rice germination.

Assessment of Genetic Diversity and Population Structure of the Sub Core Set in Sesame (Sesamum indicum) using SSR Markers

Sesame is queen of oil seed crops and widely cultivated in Asia and Africa. The aim of this study was to develop a mini sub core set representing the diverse germplasm of sesame and to assess the genetic diversity, population structure and phylogenetic relationship of the resulted sub core set to be used in whole genome resequencing platform. One hundred twelve accessions out of 277 accessions were selected by the PowerCore program. A total of 155 alleles were captured from the 158 alleles detected in the primary core population, and rare alleles and specific alleles were also maintained in the sub core set accessions representing almost 100% of the primary core population. Among the sub core set accessions, four sub populations were observed with some admixture accessions. Although the genetic diversity of Pop-1 which includes most accessions from Korea is relatively lower than that of other three sub populations, it can maintain maximum number of accessions in the sub core set with the same percentage as in the primary core set probably because of the specific features of these accessions. Based on this framework of genetically defined populations, the effective use and conservation management of Sesamum indicum for crop improvement might be possible.

Rice Germplasm in Korea and Association Mapping

Rice is a traditional staple food crop in Korea and many other countries. Although the center of rice origin is still unclear, it is believed to be introduced from China to the Korean Peninsula in the early Bronze Age via one of two possible routes—across the West Sea or along the northeastern seashore from China according to Hammer (2005) and Vavilov (1935). Rice germplasm has evolved through several millennia of cultivation and selection by our farming ancestors. An important consequence of the domestication of both plants and animals is a reduction of genetic variability (Hancock, 2004). Maintaining biodiversity is an important worldwide problem and different countries have various policies intended to preserve biodiversity. Because conservation of biodiversity and ecosystems is closely linked to the quality of human life, the preservation and improvement of ecosystems are problematic for agriculture.