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.     

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.

     

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.     

Effects of introgressions from <Emphasis Type="Italic">Festuca pratensis</Emphasis> on winter hardiness of <Emphasis Type="Italic">Lolium perenne</Emphasis>

Previous studies reported that some genotypes with introgressed Festuca chromosome segment(s) in Lolium genome showed enhanced winter hardiness compared to Lolium. The aim of this study was to search comprehensively for the Festuca pratensis chromosome regions affecting winter hardiness-related traits when introgressed into the Lolium perenne genome. Association between F. pratensis introgression and winter hardiness-related traits (fall and winter hardiness indexes, early-spring dry matter yield, and freezing tolerance) were screened in the diploid introgression populations (n = 203) that had some F. pratensis chromosome segments introgressed. Eighty-four intron markers corresponding to unique rice genes randomly distributed across the genome were used for genotyping. Winter hardiness of almost all plants in the introgression populations was lower than that of the F. pratensis and triploid hybrid parents, but the average was higher than that of L. perenne. A significant positive effect of F. pratensis introgression on early-spring dry matter yield was detected on chromosome 7. This quantitative trait locus (QTL) was confirmed by linkage analysis using a backcross population with F. pratensis introgression in the target region of chromosome 7. However, the contribution of the newly identified QTL was rather small (6.7–9.6%), suggesting that superior winter hardiness of F. pratensis compared to L. perenne is conferred by multiple small-effect QTLs. We also detected a previously unreported negative effect of Festuca introgression on winter hardiness. Newly obtained QTL information in this study would contribute to the design of Festuca/Lolium hybrid breeding.     

Preliminary Study on Geographical Distribution and Evolutionary Relationships Between Cultivated and Wild Adzuki Bean (Vigna angularis var. angularis and var. nipponensis) by AFLP Analysis

A set of representative 146 adzuki (Vigna angularis var. angularis, and var. nipponensis)germplasm from 6 Asian countries traditionally for adzuki bean production, together with an out group stand-ard rice bean (Vigna umbellata), were analyzed by AFLP methodology using 12 informative primer pairs.313 unambiguous polymorphic bands were created. According to the dendrogram by cluster analysis based onAFLP banding, 143 of the accessions were distinct and revealed enough genetic diversity for identification andclassification of accessions within Vigna angularis. A neighbor joining tree was generated using newly devel-oped Innan's nucleotide diversity estimate from the AFLP data. From analysis, 7 distinct evolutionary groups,named as "Chinese cultivated", "Japanese cultivated", "Japanese complex-Korean cultivated", "Chinesewild", "China Taiwan wild", "Nepal-Bhutan cultivated" and "Hymalayan wild", were detected. Nucleotidediversity with geographical distribution of each group is discussed, regarding the evolutionary relationships be-tween wild and cultivated adzuki beans. The preliminary results indicated that cultivated adzuki bean should bedomesticated from at least 4 progenitors in at least 3 geographical origins.     

Characterization of a new Apple dimple fruit viroid variant that causes yellow dimple fruit formation in ‘Fuji’ apple trees

A 303-nucleotide viroid was isolated from an apple tree (Malus × domestica, ‘Fuji’) cultivated in Japan. The viroid had 84.9% overall nucleotide sequence homology to Apple dimple fruit viroid (ADFVd), a member of Pospiviroidae, reported from Italy. This viroid differed from the Italian variant by 47 mutations (38 substitutions, six deletions and three insertions), and most of these mutations occurred on either side of the central conserved region. The leaves and branches of the infected trees did not have any disease symptoms, but the fruits were dimpled and yellow. The infected scions were top-grafted onto a healthy ‘Fuji’ apple tree, which tested positive for this viroid in a northern hybridization analysis, and yellow dimple fruits were produced in the second growing season. We propose that this viroid is a new variant of ADFVd and causes yellow dimple fruit formation in ‘Fuji’ apple trees.