Novel genomic and EST-derived SSR markers in Japanese chestnuts

A total of 366 novel simple sequence repeat (SSR) markers were developed in Japanese chestnut (Castanea crenata), comprising 220 genomic SSRs derived from enriched genomic libraries and 146 expressed sequence tag (EST)–SSRs obtained from large-scale EST sequencing analysis. Thirty accessions, comprising Japanese, Chinese (C. mollissima), European (Castanea sativa), and American chestnuts (Castanea dentata), were used for evaluation of SSR polymorphism and transferability across species. The EST–SSRs showed less polymorphism than the genomic SSRs and were more transferable. The mean observed heterozygosity (H_O) and the mean expected heterozygosity (H_E) of genomic SSRs in the Japanese chestnuts were 0.63 and 0.68, respectively; those of EST-SSRs were each 0.47. Although about 80% of the genomic SSRs were amplified in all 4 species, more than 95% of the EST–SSRs were transferable across all 4 species. The many novel SSRs developed in this study will be applicable for the construction of genetic linkage maps, QTL analysis of phenotypic traits, high-throughput genotyping of marker-assisted selection, and association genetics.     

Evaluation of the Affinity of Some Toxic Elements to Schwertmannite in Natural Streams Contaminated with Acid Mine Drainage

In order to evaluate fixation potential of schwertmannite for fluvial transport of various toxic elements, we examined bottom precipitates and stream waters collected from the rivers contaminated with acid mine drainage (AMD), which arose from the abandoned Nishinomaki mine (Shimonita, Gunma, Japan). Mineralogical and morphological observations revealed that schwertmannite was the main mineral of the precipitates. The affinity of various toxic ions to schwertmannite was evaluated on the basis of (1) apparent solid?Cliquid partition coefficients (K _d??s) between precipitates and stream waters, (2) coprecipitation behaviors during schwertmannite formation in a laboratory test, and (3) consideration on coprecipitation processes using partial charge model (PCM). As a result, oxyanions of V, As, Mo and Sb, K _d??s of which were relatively large (>10⁴ (ml g^?1)), were considered to be immobilized by schwertmannite precipitates. A laboratory test also demonstrated that these ions except Mo coprecipitated with schwertmannite. In addition, partial charges and average electronegativities predicted on the basis of PCM suggested that the oxyanions of V, As, Mo, and Sb could create stable inner sphere complexes with schwertmannite embryos, which results in their high affinity to schwertmannite. On the other hand, cationic ions of Mn, Cu, Zn, Sr, Cs, and U, K _d??s of which were relatively small (<10⁴ (ml g^?1)), were thought to have a tendency to flow downstream without uptake by schwertmannite precipitates. All these results suggested that schwertmannite has high fixation potential for fluvial transport of various toxic oxyanions in AMD-contaminated rivers.     

In vitro and in vivo consequences of VLA-2 expression on rhabdomyosarcoma cells

Cloned integrin alpha 2 subunit complementary DNA was expressed on human rhabdomyosarcoma (RD) cells to give a functional VLA-2 (alpha 2 beta 1) adhesion receptor. The VLA-2-positive RDA2 cells not only showed increased adhesion to collagen and laminin in vitro, but also formed substantially more metastatic tumor colonies in nude mice after either intravenous or subcutaneous injection. These results show that a specific adhesion receptor (VLA-2) can markedly enhance both experimental and spontaneous metastasis. In contrast to the metastasis results, there was no difference in either the in vitro growth rate or apparent in vivo tumorigenicity of RD and RDA2 cells.     

Improved method for in situ biolistic transformation to analyze barley–powdery mildew interactions

Although the use of stable transformants is indispensable to elucidate mechanisms underlying molecular plant–pathogen interactions, this approach remains difficult to apply to crops. Alternatively, biolistic transformation has often been used as a transient expression method in various plants. In this study, we developed a method for in situ biolistic transformation without separating leaves from barley seedlings by using a hand-held particle bombardment system because unwounded leaves are preferable for analyzing interactions between barley and Blumeria graminis f. sp. hordei which requires healthy living cells. As a result, we found that the infection rate in intact leaves was higher than in separated leaves and that the transformation efficiencies in leaves were higher when plants were grown in vermiculite rather than in culture soil. Furthermore, we determined the appropriate inoculation time after bombardment to analyze the incompatible interaction and successfully monitored the gradual occurrence of cell death over time. Our system was suitable for relatively long-term follow-up analysis of the fate of each single cell during plant–pathogen interactions.     

Variations in cryptic assemblages in coral-rubble interstices at a reef slope in Ishigaki Island,Japan

The interstices of coral rubble provide a good refuge for cryptic small crustaceans and molluscs, which are important prey items for reef fishes. In this study, we focused on the assemblage composition of cryptic mobile species along the depth gradient at an outer reef slope. Traps with coral rubble (22 × 18 × 6 cm) were set at three sites at different depths, and mobile animals that colonized the traps were sorted. In total, 117 species of larger animals (mainly Decapoda and Gastropoda) were recorded: 71 species at the 3 m point, 53 species at the 11 m point, and 37 species at the 22 m point. On average, 260.3 individuals were captured in the traps at 3 m, while 95.3 and 57.8 individuals were captured at 11 and 22 m, respectively. MDS ordination showed that assemblage composition differed among the three sites. The most abundant species at the 3 m was the galathean crab Galathea mauritiana, followed by the gastropod Diala albugo. At 11 and 22 m, the galathean crab Sadayoshia edwardsii was most abundant. Thus, at the reef slope, the benthic assemblage was most diverse at the shallow site, and specific communities occurred at the three sites.     

Optimization model for cropping-plan placement in paddy fields considering agricultural profit and nitrogen load management in Japan

An optimization model for cropping-plan placement on field plots is presented for supporting decision-making on agricultural management by a farming organization. The mixed 0?C1 programming technique is employed to select the next planting crop at each field plot in a holistic manner. Reduction of total nitrogen discharged from field plots to the downstream end of the drainage canals is expressed as an objective function of the model to balance an achievement of economic goal and environmental conservation. Some Japanese governmental policies on regulating rice cropping areas and on promoting production of particular upland field crops can be formulated in the model. A computational example of cropping-plan placement on field plots managed under integrated policies is given by operating the optimization model with various weights associated with the objectives. The procured trade-off curve and corresponding patterns of cropping-plan could be useful in the decision-making by the farming organization.     

Direct genotyping of single pollen grains of a self-compatible mutant of Japanese pear (Pyrus pyrifolia) revealed inheritance of a duplicated chromosomal segment containing a second S-haplotype

Radiation mutant 415-1, which is the first known diploid pollen-part self-compatible mutant of pears (Pyrus spp.), has a decreased ability to produce pollen. To determine whether the self-compatibility trait is associated with this defect, we directly analyzed the genotypes of individual pollen grains by using polymerase chain reaction amplification of DNA from single pollen grains. We isolated single pollen grains from 415-1 and succeeded in genotyping the S-RNase gene and three simple sequence repeat (SSR) markers in linkage group 17. Out of 173 individual pollen grains, 28 (16 %) were S-heteroallelic. These pollen grains had two alleles each of the S-RNase gene and of two linked SSR loci, all on a duplicated chromosomal segment, but only one allele of a non-duplicated locus farther away on the same chromosome. The segregation ratio of each marker in the pollen from 415-1 was approximately the same as that observed in outcross progeny. This suggests that the decrease in frequency of pollen with the duplicated S-haplotype occurred during meiosis or pollen formation, but that the probability of fertilization by S-heteroallelic pollen is equal to that of single-allelic pollen. However, the partial sterility in 415-1 can also be attributed to one or more unidentified lethal mutations unlinked to the duplicated segment encompassing the S-haplotype. Single-pollen genotyping can be used in a variety of applications in genetic research because in cases where all pollen genotypes are proportionately represented in the progeny, segregation ratios can be obtained without producing the next generation.     

Identification of QTLs controlling harvest time and fruit skin color in Japanese pear (Pyrus pyrifolia Nakai)

Using an F₁ population from a cross between Japanese pear (Pyrus pyrifolia Nakai) cultivars ‘Akiakari’ and ‘Taihaku’, we performed quantitative trait locus (QTL) analysis of seven fruit traits (harvest time, fruit skin color, flesh firmness, fruit weight, acid content, total soluble solids content, and preharvest fruit drop). The constructed simple sequence repeat-based genetic linkage map of ‘Akiakari’ consisted of 208 loci and spanned 799 cM; that of ‘Taihaku’ consisted of 275 loci and spanned 1039 cM. Out of significant QTLs, two QTLs for harvest time, one for fruit skin color, and one for flesh firmness were stably detected in two successive years. The QTLs for harvest time were located at the bottom of linkage group (LG) Tai3 (nearest marker: BGA35) and at the top of LG Tai15 (nearest markers: PPACS2 and MEST050), in good accordance with results of genome-wide association study. The PPACS2 gene, a member of the ACC synthase gene family, may control harvest time, preharvest fruit drop, and fruit storage potential. One major QTL associated with fruit skin color was identified at the top of LG 8. QTLs identified in this study would be useful for marker-assisted selection in Japanese pear breeding programs.