Chunlan Lian

An improved technique for isolating codominant compound microsatellite markers

An approach for developing codominant polymorphic markers (compound microsatellite (SSR) markers), with substantial time and cost savings, is introduced in this paper. In this technique, fragments flanked by a compound SSR sequence at one end were amplified from the constructed DNA library using compound SSR primer (AC)6(AG)5 or (TC)6(AC)5 and an adaptor primer for the suppression-PCR. A locus-specific primer was designed from the sequence flanking the compound SSR. The primer pairs of the locus-specific and compound SSR primers were used as a compound SSR marker. Because only one locus-specific primer was needed for design of each marker and only a common compound SSR primer was needed as the fluorescence-labeled primer for analyzing all the compound SSR markers, this approach substantially reduced the cost of developing codominant markers and analyzing their polymorphism. We have demonstrated this technique for Dendropanax trifidus and easily developed 11 codominant markers with high polymorphism for D. trifidus. Use of the technique for successful isolation of codominant compound SSR markers for several other plant species is currently in progress.

Outcrossing and paternity analysis of Pinus densiflora (Japanese red pine) by microsatellite polymorphism.

This study employed microsatellite loci to analyse outcrossing rate and pollen dispersal in Japanese red pine (Pinus densiflora) in an isolated stand. The average offspring outcrossing rate for 29 cones was 0.955. Significant differences in outcrossing rates between offspring groups on individual branches that extended in different directions at different heights were not detected. Male parents of 874 offspring collected from the maternal tree were assessed by exclusion using polymorphisms at three microsatellite loci. Paternity analysis indicated that at least 31% of the offspring were fertilized by pollen from trees outside the stand. The average distance of pollen migration within the study stand was 68 m, with a maximum value of 325 m. There was excess mating with nearby P. densiflora trees, of which only a few were predominant pollen donors. In addition, a weakly directional bias in P. densiflora pollination was also detected in the study stand, suggesting that female strobili on a branch of the maternal tree were more easily fertilized by pollen from trees in that direction.

Cadmium accumulation and distribution in populations of Phytolacca americana L. and the role of transpiration.

The concentrations of heavy metals in Phytolacca americana L. and corresponding soil samples from three contaminated sites and an uncontaminated site were studied. Hydroponic experiments were also conducted to investigate the Cd uptake ability and mechanism of P. americana. The field results showed that the average Cd concentration was 42 mg kg(-1) in P. americana leaves, with the highest concentration of 402 mg kg(-1) found at Datianwan. A significant relationship was observed between the concentrations of Cd in leaves and those of corresponding soils on a logarithmic scale. Under laboratory hydroponic conditions, the maximum Cd concentration in aerial tissues of P. americana was 637 mg kg(-1), under treatment with 100 microM Cd. The population from the uncontaminated site (Zijinshan) also had a remarkable ability to accumulate Cd in shoots to concentrations well in excess of 100 microM in the hydroponic experiment, similar to the population from contaminated site, suggesting that Cd accumulation is a constitutive trait of P. americana. In the presence of 100 microM Cd, the addition of polyethylene glycol decreased leaf transpiration, the shoot Cd concentration, and the shoot/root Cd concentration ratio. There was a significantly positive relationship between the shoot Cd concentration and the leaf transpiration of P. americana. A similar significant positive correlation was also obtained between the shoot/root Cd concentration and leaf transpiration. Moreover, pretreatment with 5 microM abscisic acid or 5 microM HgCl(2) significantly decreased the Cd concentration in P. americana shoots. These results suggest that transpiration has an important role in Cd accumulation in shoots of P. americana.

Genetic structure and reproduction dynamics of Salix reinii during primary succession on Mount Fuji, as revealed by nuclear and chloroplast microsatellite analysis

The early stage of volcanic desert succession is underway on the southeastern slope of Mount Fuji. We used markers of nuclear microsatellites (simple sequence repeats; SSR) and chloroplast microsatellites (cpSSR) to investigate the population genetic structure and reproduction dynamics of Salix reinii, one of the dominant pioneer shrubs in this area. The number of S. reinii genets in a patch and the area of the largest genet within the patch increased with patch area, suggesting that both clonal growth and seedling recruitment are involved in the reproduction dynamics of S. reinii. Five polymorphic cpSSR markers were developed for S. reinii by sequencing the noncoding regions between universal sequences in the chloroplast genome. Nineteen different cpSSR haplotypes were identified, indicating that S. reinii pioneer genets were created by the long‐distance dispersal of seeds originating from different mother genets around the study site, where all vegetation was destroyed during the last eruption. Furthermore, the clustered distributions of different haplotypes within each patch or plot suggested that newly colonized genets tended to be generated from seeds dispersed near the initially established mother genets. These results revealed that the establishment of the S. reinii population on the southeastern slope of Mount Fuji involved two sequential modes of seed dispersal: long‐distance dispersal followed by short‐distance dispersal.

MICROSATELLITE MARKERS REVEAL POPULATION GENETIC STRUCTURE OF THE TOXIC DINOFLAGELLATE ALEXANDRIUM TAMARENSE (DINOPHYCEAE) IN JAPANESE COASTAL WATERS1

This is the first report to explore the fine‐scale diversity, population genetic structure, and biogeography of a typical planktonic microbe in Japanese and Korean coastal waters and also to try to detect the impact of natural and human‐assisted dispersals on the genetic structure and gene flow in a toxic dinoflagellate species. Here we present the genetic analysis of Alexandrium tamarense (Lebour) Balech populations from 10 sites along the Japanese and Korean coasts. We used nine microsatellite loci, which varied widely in number of alleles and gene diversity across populations. The analysis revealed that Neis genetic distance correlated significantly with geographic distance in pair‐wise comparisons, and that there was genetic differentiation in about half of 45 pair‐wise populations. These results clearly indicate genetic isolation among populations according to geographic distance and restricted gene flow via natural dispersal through tidal currents among the populations. On the other hand, high P‐values in Fishers combined test were detected in five pair‐wise populations, suggesting similar genetic structure and a close genetic relationship between the populations. These findings suggest that the genetic structure of Japanese A. tamarense populations has been disturbed, possibly by human‐assisted dispersal, which has resulted in gene flow between geographically separated populations.

A Simple Method for Developing Microsatellite Markers using Amplified Fragments of Inter-simple Sequence Repeat (ISSR)

10 A primer IP1 designed from the sequenced region at one end of the microsatellite and for nested PCR another primer IP2 based on the sequence between IP1 and the microsatellite were prepared. These two primers were used to determine the other sequence flanking the microsatellite by a “walking” method. With this approach, we developed several microsatellite markers from Salix reinii, Pinus densiflora and Robinia pseudoacacia, respectively. The absence of enrichment processes and screening procedures makes it easier to develop microsatellite markers, and this approach provides an alternative for the development of microsatellite markers in any organism.

Mating system, pollen and propagule dispersal, and spatial genetic structure in a high-density population of the mangrove tree Kandelia candel.

Mangrove tree species form ecologically and economically important forests along the tropical and subtropical coastlines of the world. Although low intrapopulation genetic diversity and high interpopulation genetic differentiation have been detected in most mangrove tree species, no direct investigation of pollen and propagule dispersal through paternity and/or parentage analysis and spatial genetic structure within populations has been conducted. We surveyed the mating system, pollen and propagule dispersal, and spatial genetic structure in a natural population of Kandelia candel, one of the typical viviparous mangrove tree species, using nuclear and chloroplast microsatellite markers. High diversity and outcrossing rates were observed. Paternity and parentage analysis and modelling estimations revealed the presence of an extremely short‐distance component of pollen and propagule dispersal (pollen: 15.2 ± 14.9 m (SD) by paternity analysis and 34.4 m by modelling; propagule: 9.4 ± 13.8 m (SD) by parentage analysis, and 18.6 m by modelling). Genetic structure was significant at short distances, and a clumped distribution of chloroplast microsatellite genotypes was seen in K. candel adults. We conclude that the K. candel population was initiated by limited propagule founders from outside by long‐distance dispersal followed by limited propagule dispersal from the founders, resulting in a half‐sib family structure.

Development of microsatellite markers from an ectomycorrhizal fungus, Tricholoma matsutake, by an ISSR-suppression-PCR method

Abstract. An inter-simple sequence repeat (ISSR)-suppression-PCR technique established to develop microsatellite markers of plant species was applied to an ectomycorrhizal fungus, Tricholoma matsutake. Six polymorphic SSR markers were developed. All six polymorphic SSR markers were single-locused and co-dominant. Alleles produced by these six single-locused markers ranged from two to nine per locus and the expected heterozygosities were calculated as values from 0.098 to 0.803. The results indicated that the ISSR-suppression-PCR technique was effective and applicable to the development of microsatellite markers from ectomycorrhizal fungi. Furthermore, the six microsatellite loci did not amplify DNA from any other ectomycorrhizal species investigated, except for Tricholoma nauseosum (Swedish matsutake) and Tricholoma fulvocastaneum, suggesting that population genetics and reproduction of T. matsutake could be investigated by the SSR markers developed in the present study.

Patch establishment and development of a clonal plant, Polygonum cuspidatum, on Mount Fuji

Microsatellite analysis was used to investigate the patch establishment and development of Polygonum cuspidatum Sieb. et Zucc, a clonal herbaceous plant that dominates the primary succession on the southeast slope of Mount Fuji. Genotypes of P. cuspidatum in 155 patches at the study site differed from each other. This indicates that P. cuspidatum patches are initially established by seed dispersed on the bare scoria field, and not by clonal rhizome extension. Genetic differentiation was estimated using the FST values between subpopulations at the study site. There was almost no genetic differentiation between subpopulations, indicating the presence of massive gene flow. The pollen fathers of seeds and maternal genets of current‐year seedlings were inferred from the microsatellite allele composition by a simple exclusion method. The wide, random distribution of pollen fathers suggests that pollen dispersal occurs over a broad area. Maternal analysis showed a tendency for seed dispersal to be biased to the area nearby and down slope from the mother plants. Patch establishment under massive gene flow may result from such pollen and seed dispersal. To understand the process of patch development, aerial photographs taken from 1962 to 1999 were compared, and then genets in each of 36 patches were identified from the microsatellite genotypes of P. cuspidatum shoots. The comparison of aerial photographs showed that most of the patches enlarged each year and that some neighbouring patches combined during growth. Genet analysis demonstrated a high correlation between patch area and the area of the largest genet within it, and that new genets were recruited at the patch periphery. These findings indicate that both vegetative and sexual reproduction, i.e. rhizome extension and the establishment of new seedlings, contribute to the development of P. cuspidatum patches.

Genetic structure of pine sawyer Monochamus alternatus (Coleoptera: Cerambycidae) populations in Northeast Asia: consequences of the spread of pine wilt disease.

Abstract We studied the phylogeography and genetic diversity of the pine sawyer Monochamus alternatus (Hope) (Coleoptera: Cerambycidae) to understand its colonization dynamics, potential for further invasion, and potential species divergence. This species is the main vector of the pine wood nematode Bursaphelenchus xylophilus (Steiner and Buhrer), which is the causative agent of pine wilt disease in Japan. The genetic structure was studied using sequences of mitochondrial DNA and microsatellites. The phylogenetic analysis revealed two distinct lineages within M. alternatus. There is no clear boundary between haplotypic distributions of the two clades. Coalescence should have been extended by population subdivision. There might also be a fusion of the two distinct populations, and both are completely saturated. Analysis of the microsatellite genotypes of populations in Japan showed a complex genetic structure. Estimates of overall population differentiation (FST) were significantly different from zero. The populations are thought to be at demographical nonequilibrium or to show restricted gene flow among prefectures. Although neighboring populations often had similar genetic compositions, significant isolation by distance in the total population was not detected. It is suggested that population expansion may have occurred not only by natural dispersal on a small scale, but also by long-distance dispersal likely enhanced by the relocation, (by humans) of infested wood. Our data suggest that M. alternatus is a species capable of dispersing over a large area, and therefore, multiple invasions of M. alternatus from distant areas is a possibility.