Frontiers Research Foundation Acta Medica Okayama 1664-462X 577 2019 Development of Genome-Wide SNP Markers for Barley via Reference- Based RNA-Seq Analysis 577 EN Tsuyoshi Tanaka Breeding Informatics Research Unit, Division of Basic Research, Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Goro Ishikawa Breeding Strategies Research Unit, Division of Basic Research, Institute of Crop Science, National Agriculture and Food Research Organization (NARO) Eri Ogiso-Tanaka Soybean and Field Crop Applied Genomics Research Unit, Division of Field Crop Research, Institute of Crop Science, National Agriculture and Food Research Organization (NARO) Takashi Yanagisawa Wheat and Barley Breeding Unit, Division of Wheat and Barley Research, Institute of Crop Science, National Agriculture and Food Research Organization (NARO) Kazuhiro Sato Group of Genome Diversity, Institute of Plant Science and Resources, Okayama University Marker-assisted selection of crop plants requires DNA markers that can distinguish between the closely related strains often used in breeding. The availability of reference genome sequence facilitates the generation of markers, by elucidating the genomic positions of new markers as well as of their neighboring sequences. In 2017, a high quality genome sequence was released for the six-row barley (Hordeum vulgare) cultivar Morex. Here, we developed a de novo RNA-Seq-based genotyping procedure for barley strains used in Japanese breeding programs. Using RNA samples from the seedling shoot, seedling root, and immature flower spike, we mapped next-generation sequencing reads onto the transcribed regions, which correspond to ∼590 Mb of the whole ∼4.8-Gbp reference genome sequence. Using 150 samples from 108 strains, we detected 181,567 SNPs and 45,135 indels located in the 28,939 transcribed regions distributed throughout the Morex genome. We evaluated the quality of this polymorphism detection approach by analyzing 387 RNA-Seq-derived SNPs using amplicon sequencing. More than 85% of the RNA-Seq SNPs were validated using the highly redundant reads from the amplicon sequencing, although half of the indels and multiple-allele loci showed different polymorphisms between the platforms. These results demonstrated that our RNA-Seq-based de novo polymorphism detection system generates genome-wide markers, even in the closely related barley genotypes used in breeding programs. No potential conflict of interest relevant to this article was reported.

Frontiers Research Foundation Acta Medica Okayama 1664302X 7 2016 Extraintestinal Infections Caused by Non-toxigenic Vibrio cholerae non-O1/non-O139 144 EN Goutam Chowdhury Department of Bacteriology, National Institute of Cholera and Enteric Diseases Sangeeta Joshi Manipal Hospital Sanjay Bhattacharya Tata Medical Center Uma Sekar Sri Ramachandra Medical Centre Balaji Birajdar Metropolis Healthcare Ltd-Global Hospital Arpita Bhattacharyya Metropolis Healthcare Ltd-Global Hospital Sumio Shinoda Collaborative Research Centre of Okayama University for Infectious Diseases in India, National Institute of Cholera and Enteric Diseases Thandavarayan Ramamurthy Translational Health Science and Technology Institute, NCR Biotech Science Cluster Vibrio cholerae is an aerobic, sucrose fermentative Gram-negative bacterium that generally prevails in the environment. Pathogenic V. cholerae is well-known as causative agent of acute diarrhea. Apart from enteric infections, V. cholerae may also cause other diseases. However, their role in causing extraintestinal infections is not fully known as it needs proper identification and evaluation. Four cases of extraintestinal infections due to V. cholerae non-O1/non-O139 have been investigated. The isolates were screened for phenotypic and genetic characteristics with reference to their major virulence genes. Serologically distinct isolates harbored rtx, msh, and hly but lacked enteric toxin encoding genes that are generally present in toxigenic V. cholerae. Timely detection of this organism can prevent fatalities in hospital settings. The underlying virulence potential of V. cholerae needs appropriate testing and intervention. No potential conflict of interest relevant to this article was reported.