Identification of the tetrad-sterility-causing Solanum stoloniferum Schltdl. & Bouché cytoplasm in interspecific hybrids with S. tuberosum L.

Tetrad sterility, in which only clumps of four premature pollen grains are released from anthers, has been observed in some modern potato cultivars. It is a form of cytoplasmic male sterility caused by the cytoplasm derived from the Mexican tetraploid species Solanum stoloniferum Schltdl. & Bouché., an important source of resistance to Potato virus Y in potato breeding. However, since S. stoloniferum is highly polymorphic, the source of tetrad-sterility-causing cytoplasm is unknown among diverse S. stoloniferum accessions. In this study, we directly crossed 24 S. stoloniferum accessions with pollen from 4x?S. tuberosum and obtained 39 hybrids from 12 accessions. Nineteen hybrids from six accessions showed tetrad sterility, with either D/γ- or W/γ-type cytoplasm, and were triploid, tetraploid, or hexaploid. The W/γ-type cytoplasm was not necessarily associated with tetrad sterility. Sequence comparisons of 17 mitochondrial genes and their intergenic regions revealed a length polymorphism in the intergenic region between rpl5 and rps10, in which an amplified band of 859 bp was associated with tetrad sterility. This specific cytoplasm causing tetrad sterility is named TSC_sto. The 859-bp band will be a useful diagnostic marker for identifying TSC_sto in potato breeding.

     

AFLP analysis of diploid species in the genus Vigna subgenus Ceratotropis

A representative set of germplasm of genusVigna subgenus Ceratotropis specieswas used to analyze genetic diversity using amplified fragment lengthpolymorphism (AFLP) methodology. The germplasm was selected based onmorphological diversity and geographic origin and includes 18 out of the 21species in the subgenus Ceratotropis. Genetic diversitywithin and between taxa was measured using information generated by AFLP bandpolymorphism from which Jaccard's similarity coefficient and nucleotidediversity were estimated. The data were also used to generate phenograms tovisualize relationships among analyzed accessions. All species in sectionsCeratotropis and Aconitifoliae arewell separated. However, most of the species in sectionAngulares show a high level of similarity suggesting a lowlevel of genetic differentiation. In section Angulares onespecies, V. trinervia, is welldifferentiated from the other species and represents a separate evolutionarybranch between section Ceratotropis and other species insection Angulares. The relationships between the newlydescribed species V. aridicola,V. exilis, V.nepalensis and V.tenuicaulis and other species in the subgenusCeratotropis are described for the first time based on AFLPdata.     

Genetic diversity of wild soybean (<Emphasis Type="Italic">Glycine soja</Emphasis> Sieb. et Zucc.) and Japanese cultivated soybeans [<Emphasis Type="Italic">G. max</Emphasis> (L.) Merr.] based on microsatellite (SSR) analysis and the selection of a core collection

Wild soybeans, Glycine soja, are a source of genetic variation to improve soybeans. To improve the efficiency evaluation of conserved germplasm a core or mini-core collection approach that maximizes allelic diversity in a proportion of the whole collection has frequently been advocated. The genetic diversity of a wild soybean collection (1,305 accessions) plus Japanese cultivated soybeans (53 accessions) were analyzed at 20 SSR marker loci. Higher levels of allelic diversity were found in wild soybeans (28 alleles per locus) than Japanese cultivated soybean (five alleles per locus). The genetic distance between wild soybeans from different regions reflected their proximity. Accessions from Russia consisted of a diverse array of alleles resulting in accessions being spread further apart in a PCA plot than accessions from other regions. Accessions of wild soybean from Korea included many rare alleles and thus had a high representation in the core collection. The two core collections developed here, traditional and mini, consisted of 192 accessions with 97% of the allelic diversity (14% of the whole collection) and 53 accessions with 62.4% of the allelic diversity (5% of the whole collection), respectively.     

De novo assembly of the complete organelle genome sequences of azuki bean (Vigna angularis) using next-generation sequencers

Since chloroplasts and mitochondria are maternally inherited and have unique features in evolution, DNA sequences of those organelle genomes have been broadly used in phylogenetic studies. Thanks to recent progress in next-generation sequencer (NGS) technology, whole-genome sequencing can be easily performed. Here, using NGS data generated by Roche GS Titanium and Illumina Hiseq 2000, we performed a hybrid assembly of organelle genome sequences of Vigna angularis (azuki bean). Both the mitochondrial genome (mtDNA) and the chloroplast genome (cpDNA) of V. angularis have very similar size and gene content to those of V. radiata (mungbean). However, in structure, mtDNA sequences have undergone many recombination events after divergence from the common ancestor of V. angularis and V. radiata, whereas cpDNAs are almost identical between the two. The stability of cpDNAs and the variability of mtDNAs was further confirmed by comparative analysis of Vigna organelles with model plants Lotus japonicus and Arabidopsis thaliana.     

Mercury Speciation in the Water of Minamata Bay, Japan

The speciation of mercury (Hg) in Minamata Bay (Japan) was studied over a 2-year period (2006?C2008). Concentrations of dissolved total Hg, dissolved methylmercury (MeHg), particulate total Hg, and suspended solids were 0.43?±?0.14 ng/l (mean?±?standard deviation), 0.10?±?0.06 ng/l, 3.04?±?2.96 ng/l, and 5.94?±?2.10 mg/l, respectively. Correlations between concentrations of particulate total Hg and suspended solids at four depths (surface: 0 m; mid-depth: ?6 m, ?10 m; and bottom +1 m layer) were only significant in the bottom +1 m layer. The mean dissolved MeHg concentration and the ratio of dissolved MeHg to dissolved total Hg were considerably higher in summer compared to other seasons. The data suggest that bottom sediment was not the sole source of MeHg, and that MeHg may be produced in the water column by the conversion of divalent Hg eluted from resuspended bottom sediment. The correlation between seawater characteristics such as salinity, temperature, dissolved oxygen (DO), and dissolved MeHg concentration indicates that Hg methylation could be influenced by the heterotrophic activity of microorganisms in the seawater. In particular, inverse correlations were observed between DO, salinity, and MeHg concentration. However, dissolved MeHg concentrations did not correlate with seawater characteristics such as pH or chlorophyll-a.     

DaizuBase,an integrated soybean genome database including BAC-based physical maps

Soybean [Glycine max (L) Merrill] is one of the most important leguminous crops and ranks fourth after to rice, wheat and maize in terms of world crop production. Soybean contains abundant protein and oil, which makes it a major source of nutritious food, livestock feed and industrial products. In Japan, soybean is also an important source of traditional staples such as tofu, natto, miso and soy sauce. The soybean genome was determined in 2010. With its enormous size, physical mapping and genome sequencing are the most effective approaches towards understanding the structure and function of the soybean genome. We constructed bacterial artificial chromosome (BAC) libraries from the Japanese soybean cultivar, Enrei. The end-sequences of approximately 100,000 BAC clones were analyzed and used for construction of a BAC-based physical map of the genome. BLAST analysis between Enrei BAC-end sequences and the Williams82 genome was carried out to increase the saturation of the map. This physical map will be used to characterize the genome structure of Japanese soybean cultivars, to develop methods for the isolation of agronomically important genes and to facilitate comparative soybean genome research. The current status of physical mapping of the soybean genome and construction of database are presented.