Hong-Keun Choi

Anatomical patterns of aerenchyma in aquatic and wetland plants

A well-developed aerenchyma is a major characteristic of aquatic plants. However, because such tissues are also found in wetland and terrestrial plants, it is not always possible to use their presence or absence to distinguish aquatic species. Whereas patterns of aerenchyma in roots have been studied in detail, those of the shoots have not. We collected and tested 110 species of various aquatic and wetland plants, including ferns (5), basal angiosperms (5), monocots (65), and eudicots (35). Three common and two rare types of aerenchyma were observed in their roots (three schizogeny and two lysigeny), plus five types of schizogeny in their shoots. We re-confirmed that, although a well-developed aerenchyma is more common in most organs of aquatic plants than in wetland plants, this presence cannot be used as strict evidence for the aquatic quality of vascular plants. Here, aerenchyma patterns were stable at the genus level, and the consistency of pattern was stronger in the roots than in the shoots. Furthermore, significant trends were verified in several higher taxa, and those consistencies of patterns partially coincided with their phylogeny.

A phylogenetic analysis ofPanax (Araliaceae): Integrating cpDNA restriction site and nuclear rDNA ITS sequence data

A phylogenetic analysis ofPanax was performed using restriction site variations of eight PCR-amplified chloroplast regions. Twenty populations were examined, representing 13 of the 14 species ofPanax. Aralia cordata was used as the outgroup. The 11 restriction endonucleases produced a total of 105 restriction sites and length variations from the large single-copy region of cpDNA. Forty restriction variations are polymorphic. The cpDNA tree is largely congruent with the nuclear ribosomal ITS phylogeny. Similar to the ITS tree, the cpDNA dataset suggests the following relationships: (1)P. trifolius from eastern North America is sister to the clade consisting of all otherPanax species; (2)P. ginseng andP. japonicus from eastern Asia form a clade withP. quinquefolius from eastern North America; (3) the HimalayanP. pseudoginseng is most closely related toP. stipuleanatus of southwestern China; and (4) the medicinally importantP. notoginseng forms a clade with the closely relatedP. bipinnatifidus, P. ginseng, P. japonicus, P. major, P. quinquefolius, P. sinensis, P. wangianus, andP. zingiberensis. Two biogeographic disjunctions are detectable withinPanax. One is the connection of the eastern North AmericanP. trifolius with the rest ofPanax species. The other is the more recent disjunction between the North AmericanP. quinquefolius and the eastern AsianP. ginseng andP. japonicus. The active orogenies caused by the collision of the Indian Plate with Asia may have facilitated the diversification ofPanax taxa in Asia in the late Tertiary.

Taxonomy and distribution of Zostera (Zosteraceae) in eastern Asia, with special reference to Korea

Abstract The genus Zostera is a marine angiosperm in the family Zosteraceae, and five species have been reported in Korea. However, their morphological characteristics and distribution remain unclear. This study is intended to clarify the taxonomic characteristics and distribution of Zostera species in Korea. The results confirm that four species, Zostera japonica , Zostera marina , Zostera asiatica , and Zostera caulescens are distributed along the seacoast of South Korea, and these species are distinguished by the shape of leaf apex, number of leaf vein, number of fibrous strands between the midvein and its first side vein. Populations of Zostera caespitosa , which had previously reported from Korea, were not found. However, this species is easily distinguished from other Korean Zostera species by having an obcordate apex of leaf and rhizomes with extremely shortened internodes.

Systematic Rearrangement of Korean Scirpus L. s.l. (Cyperaceae) as Inferred from Nuclear ITS and Chloroplast rbcL Sequences

The genus Scirpus L. s.l. (Cyperaceae) has been accepted as a polyphyletic taxon by most plant taxonomists. This genus was separated into different genera by several different authors: Scirpus s. str., Trichophorum Pers., Bolboschoenus (Asch.) Palla, Schoenoplectus (Rchb.) Palla, and Schoenoplectiella Lye. The heterogeneity of Korean Scirpus s.l. has not yet been studied. We examined 17 taxa of Korean Scirpus s.l. by morphological characters and phylogenetic analyses based on nuclear ITS and chloroplast rbcL sequences. Phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian method provided sufficient resolution. The phylogeny revealed the polyphyly of Korean Scirpus s.l. with five distinct clades. These clades correspond to Bolboschoenus, Schoenoplectus s.str., and Schoenoplectiella, Scirpus s.str., and Trichophorum, respectively. These five genera were delimited in terms of the morphology of tuber, bract, and inflorescence. By virtue of our findings, we suggest that the 17 taxa of Korean Scirpus s.l. should be placed into five genera as follows: Bolboschoenus (two species), Schoenoplectus (three species), Schoenoplectiella (six species), Scirpus s.str. (five species), and Trichophorum (one species).

Conservation genetics of endangeredBrasenia schreberi based on RAPD and AFLP markers

Brasenia schreberi J.F. Gmelin is a declared endangered species found in the lakes and ponds of South Korea. For planning its conservation strategy, we examined the genetic diversity within and among six populations, using randomly amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP). Polymorphisms were more frequently detected per loci with AFLP (69.3%) than RAPD (36.8%). High genetic diversity was recognized within populations: polymorphic loci (PPL) values ranged from 36.3% in the CJM population to 74.5% in the GGT population, with a mean value of 47.8% based on AFLP markers. Great genetic differentiation (θB) was detected among the six populations (0.670 on RAPD and 0.196 on AFLP), and we calculated a low rate of gene flow (Nem), i.e., 0.116 on RAPD and 0.977 on AFLP. Furthermore, a Mantel test revealed that no correlation existed between genetic distances and geographical distances among the six local populations, based on RAPD or AFLP markers. These results are attributed to a number of factors, including an insufficient length of time for genetic diversity to be reduced following a natural decline in population size and isolation, adaptation of the genetic system to small population conditions, and a restricted gene flow rate. Based on both its genetic diversity and population structure, we suggest that a strategy for conserving and restoringB. schreberi must focus on maintaining historical processes, such as high levels of outbreeding, while monitoring increased gene flow among populations. This is because a reduction in genetic diversity as a result of genetic drift is undesirable.

A phenetic analysis of Typha in Korea and far east Russia.

We used principal components analysis (PCA) and UPGMA cluster analysis to determine taxonomically definable limits and to estimate the phenetic relationships among four Typhaspecies from Korea and far east Russia using 25 quantitative characters. A scatter plot of the first two principal components resolved four clusters among the 77 specimens of Typha examined from Korea and far east Russia. The clusters corresponded to the four currently recognized species. Typha latifolia was readily distinguished from other species by having wide leaves and female inflorescences. Typha angustifolia was distinguished from T. orientalis and T. laxmanni by the long male inflorescences and large gap between male and female inflorescences. Typha laxmanniwas distinguished from T. orientalis by a higher ratio of male and female inflorescence lengths than others. UPGMA analysis also showed that individuals of Typha species from Korea and far east Russia form discrete clusters corresponding to four species.

Genome-wide Identification and Analysis of Genes Associated with Lysigenous Aerenchyma Formation in Rice Roots

Plants develop lysigenous aerenchyma to improve their survival in soils that are low in oxygen, such as in paddy fields. To investigate the genes involved in this formation in rice, we sampled the lysigenous aerenchyma formed part (LAFP) and lysigenous aerenchyma unformed part (LAUP) from seminal roots and conducted transcriptome analysis with a whole-genome microarray platform, i.e., Agilent 4X44K arrays. In all, 268 genes were highly upregulated in LAFP and 259 genes in LAUP, showing fold-changes of at least 1.5 (log2) and p-values <0.01. The MapMan toolkit was used for functional characterization of differentially expressed genes. As expected, genes associated with ethylene signaling and the redox response, heat shock proteins, and secondary metabolite metabolism (e.g., flavonoids and phenylpropanoids) were prominent in LAFP. By contrast, genes related to auxins, peroxidase, glucosidase, and proteins active in pathogen responses were expressed more highly in LAUP. Previous research has shown that genes detected in LAFP, such as our candidates, are important for conferring tolerance to multiple abiotic stresses while genes expressed in LAUP are necessary for root development and soil stress (i.e., drought and nutrient deficiencies) tolerance. This genome-wide examination of the formation of lysigenous aerenchyma in rice roots presents potential candidate genes involved in the molecular mechanism that supports this production.

Genetic diversity and population structure of diploid and polyploid species of Isoëtes in East Asia based on amplified fragment length polymorphism markers.

Isoëtes L. is critically endangered in areas of East Asia, including Taiwan, Japan, and South Korea. The genetic diversity and the population structure of six Isoëtes species from East Asia were evaluated by using amplified fragment length polymorphism (AFLP). Three AFLP‐selective primer combinations generated a total 923 amplification products, of which 919 (99.6%) were polymorphic. The levels of genetic diversity of two diploid species (I. taiwanensis [percentage of polymorphic loci \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} \newcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\encodingdefault{OT2} \normalfont \selectfont} \DeclareTextFontCommand{\textcyr}{\cyr} \pagestyle{empty} \DeclareMathSizes{10}{9}{7}{6} \begin{document} \landscape

Taxonomic Study of Korean Scirpus L. s.l. (Cyperaceae) II: Pattern of Phenotypic Evolution Inferred from Molecular Phylogeny

( \mathrm{PPL}\,) =33.1\% {\mbox{--}} 38.3\%