start-ver=1.4 cd-journal=joma no-vol=577 cd-vols= no-issue= article-no= start-page=577 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2019 dt-pub=20190510 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Development of Genome-Wide SNP Markers for Barley via Reference- Based RNA-Seq Analysis en-subtitle= kn-subtitle= en-abstract= kn-abstract= 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. en-copyright= kn-copyright= en-aut-name=TanakaTsuyoshi en-aut-sei=Tanaka en-aut-mei=Tsuyoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=IshikawaGoro en-aut-sei=Ishikawa en-aut-mei=Goro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=Ogiso-TanakaEri en-aut-sei=Ogiso-Tanaka en-aut-mei=Eri kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=YanagisawaTakashi en-aut-sei=Yanagisawa en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=SatoKazuhiro en-aut-sei=Sato en-aut-mei=Kazuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= affil-num=1 en-affil=Breeding Informatics Research Unit, Division of Basic Research, Institute of Crop Science, National Agriculture and Food Research Organization (NARO), kn-affil= affil-num=2 en-affil=Breeding Strategies Research Unit, Division of Basic Research, Institute of Crop Science, National Agriculture and Food Research Organization (NARO) kn-affil= affil-num=3 en-affil=Soybean and Field Crop Applied Genomics Research Unit, Division of Field Crop Research, Institute of Crop Science, National Agriculture and Food Research Organization (NARO) kn-affil= affil-num=4 en-affil=Wheat and Barley Breeding Unit, Division of Wheat and Barley Research, Institute of Crop Science, National Agriculture and Food Research Organization (NARO) kn-affil= affil-num=5 en-affil=Group of Genome Diversity, Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=Japanese barley breeding kn-keyword=Japanese barley breeding en-keyword=RNA-Seq kn-keyword=RNA-Seq en-keyword=amplicon sequencing kn-keyword=amplicon sequencing en-keyword= barley; genotyping kn-keyword= barley; genotyping en-keyword=barley kn-keyword=barley en-keyword=genotyping kn-keyword=genotyping END start-ver=1.4 cd-journal=joma no-vol=7 cd-vols= no-issue= article-no= start-page=144 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2016 dt-pub=20160211 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Extraintestinal Infections Caused by Non-toxigenic Vibrio cholerae non-O1/non-O139 en-subtitle= kn-subtitle= en-abstract= kn-abstract= 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. en-copyright= kn-copyright= en-aut-name=ChowdhuryGoutam en-aut-sei=Chowdhury en-aut-mei=Goutam kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=JoshiSangeeta en-aut-sei=Joshi en-aut-mei=Sangeeta kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=BhattacharyaSanjay en-aut-sei=Bhattacharya en-aut-mei=Sanjay kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=SekarUma en-aut-sei=Sekar en-aut-mei=Uma kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=BirajdarBalaji en-aut-sei=Birajdar en-aut-mei=Balaji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=BhattacharyyaArpita en-aut-sei=Bhattacharyya en-aut-mei=Arpita kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=ShinodaSumio en-aut-sei=Shinoda en-aut-mei=Sumio kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=RamamurthyThandavarayan en-aut-sei=Ramamurthy en-aut-mei=Thandavarayan kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= affil-num=1 en-affil=Department of Bacteriology, National Institute of Cholera and Enteric Diseases kn-affil= affil-num=2 en-affil=Manipal Hospital kn-affil= affil-num=3 en-affil=Tata Medical Center kn-affil= affil-num=4 en-affil=Sri Ramachandra Medical Centre kn-affil= affil-num=5 en-affil=Metropolis Healthcare Ltd-Global Hospital kn-affil= affil-num=6 en-affil=Metropolis Healthcare Ltd-Global Hospital kn-affil= affil-num=7 en-affil=Collaborative Research Centre of Okayama University for Infectious Diseases in India, National Institute of Cholera and Enteric Diseases kn-affil= affil-num=8 en-affil=Translational Health Science and Technology Institute, NCR Biotech Science Cluster kn-affil= END