The N-Terminal Region of the Readthrough Domain Is Closely Related to Aphid Vector Specificity of Soybean dwarf virus

ABSTRACT It has been speculated that the N-terminal half of the readthrough domain (RTD) encoded by open reading frame 5 of Soybean dwarf virus (SbDV) is related to the vector specificity. To further investigate this hypothesis, transmissibility via aphids was tested on 17 SbDV isolates and comparisons of the deduced amino acid sequences of the coat protein (CP) and other proteins encoded by the RTD were made between these isolates. Isolates were distinguished into four strains: YS, causing yellowing in soybean and transmittable by Aulacorthum solani; DS, causing dwarfing and transmittable by A. solani; YP, causing yellowing and transmittable by Acyrthosiphon pisum; and DP, causing dwarfing and transmittable by A. pisum. Phylogenetic analysis showed that the trees for the CP and the C-terminal half of the RTD sequences contained clusters of isolates of the same symptom type, whereas the tree for the N-terminal half of the RTD contained clusters of isolates of the same aphid vector type. These results agreed with our previous data of the complete nucleotide sequences of four SbDV isolates, and strongly indicated a close relationship between the N-terminal half of the RTD amino acid sequences and aphid transmission specificity of SbDV.     

Emission Control of SO2 by Dry Coal-Cleaning and Bio-Briquette Technology

In China, the large amount of sulfur dioxide and dust discharged from the combustion of low-grade raw coal causes severe air pollution and acid rain. Therefore, the need to control the emission of such pollutants is urgent. It is well known that wet coal-cleaning technology is used to prepare clean coal from low-grade raw coal containing large amounts of sulfur and ash. However, this technology is not used in areas where water is scarce or severely polluted, because of the high cost of treating the wastewater. In an attempt to overcome this limitation, we studied an integrated technology, which combines dry coal-cleaning and bio-briquetting technologies, to prepare clean coal from low-grade raw coal. In the dry coal-cleaning method, refined coal was separated from ash and other minerals containing inorganic sulfur as pyrite by means of the differences in their electrostatic character. Most of the sulfur left in the refined coal was organic sulfur. The residual ash was fixed in combustion ashes of bio-briquettes made from coal, biomass, and slaked lime (Ca/S mole ratio =2) under pressure. By combining these two technologies, we were able to decrease the emission of sulfur dioxide and ash by 70≈90% compared to the combustion of raw coal.     

Self-EcoTILLING to identify single-nucleotide mutations in multigene family

TILLING (Targeting Induced Local Lesions IN Genomes) is a low-cost, high-throughput reverse genetic technique that employs a mismatch-specific endonuclease CEL-1 to discover induced point mutations in the genes of interest. The use of the TILLING technique to survey natural variation in genes is called EcoTILLING. Here, we report a modified EcoTILLING method for the discovery of mutations in multigene family, which we coin “Self-EcoTILLING” by using an allotetraploid Monochoria vaginalis ALS multigene family as an example. The mutations could be detected by TILLING of PCR products resulting from the primers specific to both Als1 and Als3 without involving the experimental step of mixture of reference and query DNA. Either of the two co-amplified loci could serve as reference DNA to the other. We demonstrate with this example that Self-EcoTILLING is a fast, reliable and economical technique of detecting single-nucleotide mutations in polyploid plants containing multigene family.     

Evaluation of the juice brix of wild sugarcanes (Saccharum spontaneum) indigenous to Japan

Modern sugarcane cultivars are derived from the interspecific crossing between Saccharum officinarum and wild sugarcane, Saccharum spontaneum. The introgression of valuable characteristics from wild sugarcane is recognized as extremely important, but this process typically requires long-term effort over multiple generations of backcrosses owing to the low sugar content of the initial interspecific hybrids. In this study, we aimed to identify Japanese wild sugarcanes with high juice brix in order to promote effective interspecific crossing of sugarcane. Sixty-four accessions from the Nansei Islands and 70 accessions from the Honshu were evaluated for juice brix. Wild sugarcanes with high juice brix were demonstrated to exist among wild sugarcanes indigenous to the Honshu. A significant difference was observed between the median juice brix values of wild sugarcanes of the Nansei Islands and those of the Honshu. The relationship between juice brix and stem traits was then examined in 20 wild sugarcanes, 10 each from the Nansei Islands and the Honshu. The reproducibility of juice brix value in both experiments was confirmed. In contrast to juice brix, stem traits, such as length, diameter, and volume, were typically smaller in wild sugarcanes from the Honshu. Moreover, a negative correlation was observed between the index of stem volume and juice brix. In this study, we identified outstanding wild sugarcanes with high juice brix. Using germplasms from the identified wild sugarcanes in interspecific crossing could contribute to the increases in both yield and sugar content.     

Isolation of exfoliative toxin from Staphylococcus intermedius and its local toxicity in dogs

A rounding effect was demonstrated in cultured cells inoculated with the culture filtrates (CFs) of 60 strains of Staphylococcus intermedius derived from dogs affected with pyoderma. Exfoliative toxin (ET)-like toxin (ETLT) was isolated from the CF of S. intermedius strain D-52, which exhibited strong rounding activity and then was purified by gel filtration on a Sephadex G-75 column, and by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The ETLT caused exfoliation in 1-day-old chickens, suckling Syrian hamsters, and dogs, but not in suckling mice. The ETLT was serologically different from exfoliative toxin A (ETA), exfoliative toxin B (ETB), exfoliative toxin C (ETC), S. hyicus exfoliative toxin A (SHETA), and SHETB, as shown by Western blot analysis. The molecular weight of the ETLT was estimated at 30 kDa by SDS-PAGE. In the present study, we propose the ETLT was a novel type of ET, S. intermedius exfoliative toxin (SIET).     

Cloning of the gene coding for Staphylococcus intermedius exfoliative toxin and its expression in Escherichia coli

An exfoliative toxin (SIET)-producing strain (D-52) of Staphylococcus intermedius derived from canine pyoderma did not possess large plasmids. Therefore, the gene coding for SIET was considered to be located on the chromosomal DNA. The SIET gene was cloned from the chromosomal DNA of S. intermedius and was expressed in Escherichia coli. The nucleotide sequence of the SIET gene consists of a coding region of 990 bp specifying a polypeptide of 330 amino acid residues, which included a putative 42-residue signal sequence.     

Comparison of ratoon yield under high-level cutting in two varieties of forage sugarcane,KRFo93-1, and Shimanoushie

High-level cutting without stubble shaving has been recommended in the cultivation of forage sugarcane, KRFo93-1. However, it is unclear whether this management practice is appropriate for the more recently developed variety Shimanoushie. Therefore, the aim of this study was to compare the dry matter yield of both varieties to high-level cutting. The study included five ratoon crops (RC1–RC5). In KRFo93-1, dry matter yield was higher in HC plots (high-level cutting without stubble shaving plots) than in Control plots (stubble shaving after high-level cutting plots), and the differences were significant for the first three ratoon crops. A similar trend was observed in Shimanoushie; however, the dry matter yield of HC plots was slightly lower than Control plots in RC4 and RC5 owing to a lower stem number. Although the sum of dry matter yield of five ratoon crops was significantly higher in HC plots of both varieties, the influence of high-level cutting was more effective in KRFo93-1 than in Shimanoushie.     

Sat-BSA: an NGS-based method using local de novo assembly of long reads for rapid identification of genomic structural variations associated with agronomic traits

Advances in next generation sequencing (NGS)-based methodologies have accelerated the identifications of simple genetic variants such as point mutations and small insertions/deletions (InDels). Structural variants (SVs) including large InDels and rearrangements provide vital sources of genetic diversity for plant breeding. However, their analysis remains a challenge due to their complex nature. Consequently, novel NGS-based approaches are needed to rapidly and accurately identify SVs. Here, we present an NGS-based bulked-segregant analysis (BSA) technique called Sat-BSA (SVs associated with traits) for identifying SVs controlling traits of interest in crops. Sat-BSA targets allele frequencies at all SNP positions to first identify candidate genomic regions associated with a trait, which is then reconstructed by long reads-based local de novo assembly. Finally, the association between SVs, RNA-seq-based gene expression patterns and trait is evaluated for multiple cultivars to narrow down the candidate genes. We applied Sat-BSA to segregating F₂ progeny obtained from crosses between turnip cultivars with different tuber colors and successfully isolated two genes harboring SVs that are responsible for tuber phenotypes. The current study demonstrates the utility of Sat-BSA for the identification of SVs associated with traits of interest in species with large and heterozygous genomes.