start-ver=1.4 cd-journal=joma no-vol=29 cd-vols= no-issue=1 article-no= start-page=dsac001 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2022 dt-pub=20220112 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Chromosome-scale assembly of barley cv. 'Haruna Nijo' as a resource for barley genetics en-subtitle= kn-subtitle= en-abstract= kn-abstract=Cultivated barley (Hordeum vulgare ssp. vulgare) is used for food, animal feed, and alcoholic beverages and is widely grown in temperate regions. Both barley and its wild progenitor (H. vulgare ssp. spontaneum) have large 5.1-Gb genomes. High-quality chromosome-scale assemblies for several representative barley genotypes, both wild and domesticated, have been constructed recently to populate the nascent barley pan-genome infrastructure. Here, we release a chromosome-scale assembly of the Japanese elite malting barley cultivar 'Haruna Nijo' using a similar methodology as in the barley pan-genome project. The 4.28-Gb assembly had a scaffold N50 size of 18.9 Mb. The assembly showed high collinearity with the barley reference genome 'Morex' cultivar, with some inversions. The pseudomolecule assembly was characterized using transcript evidence of gene projection derived from the reference genome and de novo gene annotation achieved using published full-length cDNA sequences and RNA-Seq data for 'Haruna Nijo'. We found good concordance between our whole-genome assembly and the publicly available BAC clone sequence of 'Haruna Nijo'. Interesting phenotypes have since been identified in Haruna Nijo; its genome sequence assembly will facilitate the identification of the underlying genes. en-copyright= kn-copyright= en-aut-name=SakkourAreej en-aut-sei=Sakkour en-aut-mei=Areej kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=MascherMartin en-aut-sei=Mascher en-aut-mei=Martin kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=HimmelbachAxel en-aut-sei=Himmelbach en-aut-mei=Axel kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=HabererGeorg en-aut-sei=Haberer en-aut-mei=Georg kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=LuxThomas en-aut-sei=Lux en-aut-mei=Thomas kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=SpannaglManuel en-aut-sei=Spannagl en-aut-mei=Manuel kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=SteinNils en-aut-sei=Stein en-aut-mei=Nils kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=KawamotoShoko en-aut-sei=Kawamoto en-aut-mei=Shoko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 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=9 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) kn-affil= affil-num=3 en-affil=Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) kn-affil= affil-num=4 en-affil=Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health kn-affil= affil-num=5 en-affil=Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health kn-affil= affil-num=6 en-affil=Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health kn-affil= affil-num=7 en-affil=Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) kn-affil= affil-num=8 en-affil=Department of Informatics, National Institute of Genetics kn-affil= affil-num=9 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=Hordeum vulgare kn-keyword=Hordeum vulgare en-keyword=full-length cDNA kn-keyword=full-length cDNA en-keyword=RNA-Seq kn-keyword=RNA-Seq en-keyword=genome sequencing kn-keyword=genome sequencing en-keyword=pseudomolecules kn-keyword=pseudomolecules END start-ver=1.4 cd-journal=joma no-vol=101 cd-vols= no-issue= article-no= start-page=103297 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2021 dt-pub=20210930 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Germplasm evaluation for crop improvement: Analysis of grain quality and cadmium accumulation in barley en-subtitle= kn-subtitle= en-abstract=Evaluating genetic variation in barley (Hordeum vulgare) germplasm, combined with genome-wide genotyping, is vital for identifying genes controlling important grain-quality traits. For example, in addition... kn-abstract=Evaluating genetic variation in barley (Hordeum vulgare) germplasm, combined with genome-wide genotyping, is vital for identifying genes controlling important grain-quality traits. For example, in addition to traditional grain quality properties such as starch and protein contents, grain safety parameters such as heavy metal content, are important in the use of barley for human food and animal feed. A number of genes affecting grain quality have been identified by map-based cloning strategies and functionally analyzed by genetic transformation experiments. Moreover, germplasm evaluation yielded information that enabled the introgression of a key gene controlling grain cadmium accumulation into an elite barley cultivar, reducing the content of this heavy metal in grain. Genotyping of molecular markers and resequencing of germplasm accessions may provide information about how grain quality?related loci evolved and how the current allelic diversity was established. In this review, we describe germplasm resources for barley grain quality?related traits and the methods used to analyze the functions of genes controlling these traits, illustrating cadmium accumulation as an example. We also discuss future directions for the efficient identification of grain quality?related genes. en-copyright= kn-copyright= en-aut-name=SatoKazuhiro en-aut-sei=Sato en-aut-mei=Kazuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=TakedaKazuyoshi en-aut-sei=Takeda en-aut-mei=Kazuyoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=MaJian Feng en-aut-sei=Ma en-aut-mei=Jian Feng kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=3 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=Barley kn-keyword=Barley en-keyword=Core collection kn-keyword=Core collection en-keyword= Genome analysis kn-keyword= Genome analysis en-keyword=Genome-wide association study kn-keyword=Genome-wide association study END start-ver=1.4 cd-journal=joma no-vol= cd-vols= no-issue= article-no= start-page=1 end-page=10 dt-received= dt-revised= dt-accepted= dt-pub-year=2021 dt-pub=20210829 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Regulation of germination by targeted mutagenesis of grain dormancy genes in barley en-subtitle= kn-subtitle= en-abstract= kn-abstract=High humidity during harvest season often causes pre-harvest sprouting in barley (Hordeum vulgare). Prolonged grain dormancy prevents pre-harvest sprouting; however, extended dormancy can interfere with malt production and uniform germination upon sowing. In this study, we used Cas9-induced targeted mutagenesis to create single and double mutants in QTL FOR SEED DORMANCY 1 (Qsd1) and Qsd2 in the same genetic background. We performed germination assays in independent qsd1 and qsd2 single mutants, as well as in two double mutants, which revealed a strong repression of germination in the mutants. These results demonstrated that normal early grain germination requires both Qsd1 and Qsd2 function. However, germination of qsd1 was promoted by treatment with 3% hydrogen peroxide, supporting the notion that the mutants exhibit delayed germination. Likewise, exposure to cold temperatures largely alleviated the block of germination in the single and double mutants. Notably, qsd1 mutants partially suppress the long dormancy phenotype of qsd2, while qsd2 mutant grains failed to germinate in the light, but not in the dark. Consistent with the delay in germination, abscisic acid accumulated in all mutants relative to the wild type, but abscisic acid levels cannot maintain long-term dormancy and only delay germination. Elucidation of mutant allele interactions, such as those shown in this study, are important for fine-tuning traits that will lead to the design of grain dormancy through combinations of mutant alleles. Thus, these mutants will provide the necessary germplasm to study grain dormancy and germination in barley. en-copyright= kn-copyright= en-aut-name=HisanoHiroshi en-aut-sei=Hisano en-aut-mei=Hiroshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=HoffieRobert E. en-aut-sei=Hoffie en-aut-mei=Robert E. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=AbeFumitaka en-aut-sei=Abe en-aut-mei=Fumitaka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=MunemoriHiromi en-aut-sei=Munemori en-aut-mei=Hiromi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=MatsuuraTakakazu en-aut-sei=Matsuura en-aut-mei=Takakazu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=EndoMasaki en-aut-sei=Endo en-aut-mei=Masaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=MikamiMasafumi en-aut-sei=Mikami en-aut-mei=Masafumi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=NakamuraShingo en-aut-sei=Nakamura en-aut-mei=Shingo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=KumlehnJochen en-aut-sei=Kumlehn en-aut-mei=Jochen kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 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=10 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben kn-affil= affil-num=3 en-affil=Institute of Crop Science, NARO kn-affil= affil-num=4 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=5 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=6 en-affil=Institute of Agrobiological Sciences, NARO kn-affil= affil-num=7 en-affil=Institute of Agrobiological Sciences, NARO kn-affil= affil-num=8 en-affil=Institute of Crop Science, NARO kn-affil= affil-num=9 en-affil=Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben kn-affil= affil-num=10 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=Hordeum vulgare kn-keyword=Hordeum vulgare en-keyword=seed dormancy kn-keyword=seed dormancy en-keyword=targeted genome modification kn-keyword=targeted genome modification en-keyword=CRISPR kn-keyword=CRISPR en-keyword=Cas9 nuclease kn-keyword=Cas9 nuclease en-keyword=pre-harvest sprouting kn-keyword=pre-harvest sprouting END start-ver=1.4 cd-journal=joma no-vol=28 cd-vols= no-issue=3 article-no= start-page=dsab008 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2021 dt-pub=2021712 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Chromosome-scale genome assembly of the transformation-amenable common wheat cultivar ‘Fielder’ en-subtitle= kn-subtitle= en-abstract= kn-abstract=We have established a high-quality, chromosome-level genome assembly for the hexaploid common wheat cultivar ‘Fielder’, an American, soft, white, pastry-type wheat released in 1974 and known for its amenability to Agrobacterium tumefaciens-mediated transformation and genome editing. Accurate, long-read sequences were obtained using PacBio circular consensus sequencing with the HiFi approach. Sequence reads from 16 SMRT cells assembled using the hifiasm assembler produced assemblies with N50 greater than 20?Mb. We used the Omni-C chromosome conformation capture technique to order contigs into chromosome-level assemblies, resulting in 21 pseudomolecules with a cumulative size of 14.7 and 0.3?Gb of unanchored contigs. Mapping of published short reads from a transgenic wheat plant with an edited seed-dormancy gene, TaQsd1, identified four positions of transgene insertion into wheat chromosomes. Detection of guide RNA sequences in pseudomolecules provided candidates for off-target mutation induction. These results demonstrate the efficiency of chromosome-scale assembly using PacBio HiFi reads and their application in wheat genome-editing studies. en-copyright= kn-copyright= en-aut-name=SatoKazuhiro en-aut-sei=Sato en-aut-mei=Kazuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=AbeFumitaka en-aut-sei=Abe en-aut-mei=Fumitaka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=MascherMartin en-aut-sei=Mascher en-aut-mei=Martin kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=HabererGeorg en-aut-sei=Haberer en-aut-mei=Georg kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=GundlachHeidrun en-aut-sei=Gundlach en-aut-mei=Heidrun kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=SpannaglManuel en-aut-sei=Spannagl en-aut-mei=Manuel kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=ShirasawaKenta en-aut-sei=Shirasawa en-aut-mei=Kenta kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=IsobeSachiko en-aut-sei=Isobe en-aut-mei=Sachiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Institute of Crop Science, NARO kn-affil= affil-num=3 en-affil=Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben kn-affil= affil-num=4 en-affil=Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health kn-affil= affil-num=5 en-affil=Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health kn-affil= affil-num=6 en-affil=Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health kn-affil= affil-num=7 en-affil=Kazusa DNA Research Institute kn-affil= affil-num=8 en-affil=Kazusa DNA Research Institute kn-affil= en-keyword=Triticum aestivum kn-keyword=Triticum aestivum en-keyword=circular consensus sequencing kn-keyword=circular consensus sequencing en-keyword=genome assembly kn-keyword=genome assembly en-keyword= pseudomolecules kn-keyword= pseudomolecules en-keyword=genome editing kn-keyword=genome editing END start-ver=1.4 cd-journal=joma no-vol= cd-vols= no-issue= article-no= start-page=jkab244 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2021 dt-pub=2021713 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Chromosome-scale assembly of wild barley accession “OUH602” en-subtitle= kn-subtitle= en-abstract= kn-abstract=Barley (Hordeum vulgare) was domesticated from its wild ancestral form ca. 10,000?years ago in the Fertile Crescent and is widely cultivated throughout the world, except for in tropical areas. The genome size of both cultivated barley and its conspecific wild ancestor is approximately 5?Gb. High-quality chromosome-level assemblies of 19 cultivated and one wild barley genotype were recently established by pan-genome analysis. Here, we release another equivalent short-read assembly of the wild barley accession “OUH602.” A series of genetic and genomic resources were developed for this genotype in prior studies. Our assembly contains more than 4.4?Gb of sequence, with a scaffold N50 value of over 10?Mb. The haplotype shows high collinearity with the most recently updated barley reference genome, “Morex” V3, with some inversions. Gene projections based on “Morex” gene models revealed 46,807 protein-coding sequences and 43,375 protein-coding genes. Alignments to publicly available sequences of bacterial artificial chromosome (BAC) clones of “OUH602” confirm the high accuracy of the assembly. Since more loci of interest have been identified in “OUH602,” the release of this assembly, with detailed genomic information, should accelerate gene identification and the utilization of this key wild barley accession. en-copyright= kn-copyright= en-aut-name=SatoKazuhiro en-aut-sei=Sato en-aut-mei=Kazuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=MascherMartin en-aut-sei=Mascher en-aut-mei=Martin kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=HimmelbachAxel en-aut-sei=Himmelbach en-aut-mei=Axel kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=HabererGeorg en-aut-sei=Haberer en-aut-mei=Georg kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=SpannaglManuel en-aut-sei=Spannagl en-aut-mei=Manuel kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=SteinNils en-aut-sei=Stein en-aut-mei=Nils kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben kn-affil= affil-num=3 en-affil=Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben kn-affil= affil-num=4 en-affil=Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health kn-affil= affil-num=5 en-affil=Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health kn-affil= affil-num=6 en-affil=Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben kn-affil= en-keyword=genome assembly kn-keyword=genome assembly en-keyword= Hordeum vulgare ssp. spontaneum kn-keyword= Hordeum vulgare ssp. spontaneum en-keyword=OUH602 kn-keyword=OUH602 en-keyword= pseudomolecules kn-keyword= pseudomolecules en-keyword=wild barley kn-keyword=wild barley END start-ver=1.4 cd-journal=joma no-vol= cd-vols= no-issue= article-no= start-page= end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2021 dt-pub=2021818 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=RNA-Seq-based DNA marker analysis of the genetics and molecular evolution of Triticeae species en-subtitle= kn-subtitle= en-abstract= kn-abstract=The release of high-quality chromosome-level genome sequences of members of the Triticeae tribe has greatly facilitated genetic and genomic analyses of important crops such as wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to the large diploid genome size of Triticeae plants (ca. 5 Gbp), transcript analysis is an important method for identifying genetic and genomic differences among Triticeae species. In this review, we summarize our results of RNA-Seq analyses of diploid wheat accessions belonging to the genera Aegilops and Triticum. We also describe studies of the molecular relationships among these accessions and provide insight into the evolution of common hexaploid wheat. DNA markers based on polymorphisms within species can be used to map loci of interest. Even though the genome sequence of diploid Aegilops tauschii, the D-genome donor of common wheat, has been released, the diploid barley genome continues to provide key information about the physical structures of diploid wheat genomes. We describe how a series of RNA-Seq analyses of wheat relatives has helped uncover the structural and evolutionary features of genomic and genetic systems in wild and cultivated Triticeae species. en-copyright= kn-copyright= en-aut-name=SatoKazuhiro en-aut-sei=Sato en-aut-mei=Kazuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=YoshidaKentaro en-aut-sei=Yoshida en-aut-mei=Kentaro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=TakumiShigeo en-aut-sei=Takumi en-aut-mei=Shigeo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Graduate School of Agricultural Science, Kobe University kn-affil= affil-num=3 en-affil=Graduate School of Agricultural Science, Kobe University kn-affil= en-keyword=Aegilops kn-keyword=Aegilops en-keyword=DNA marker kn-keyword=DNA marker en-keyword=Hordeum kn-keyword=Hordeum en-keyword=RNA-Seq kn-keyword=RNA-Seq en-keyword=Triticeae kn-keyword=Triticeae en-keyword=Triticum kn-keyword=Triticum END start-ver=1.4 cd-journal=joma no-vol=27 cd-vols= no-issue=4 article-no= start-page=dsaa023 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2020 dt-pub=20200926 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=History and future perspectives of barley genomics en-subtitle= kn-subtitle= en-abstract= kn-abstract=Barley (Hordeum vulgare), one of the most widely cultivated cereal crops, possesses a large genome of 5.1Gbp. Through various international collaborations, the genome has recently been sequenced and assembled at the chromosome-scale by exploiting available genetic and genomic resources. Many wild and cultivated barley accessions have been collected and preserved around the world. These accessions are crucial to obtain diverse natural and induced barley variants. The barley bioresource project aims to investigate the diversity of this crop based on purified seed and DNA samples of a large number of collected accessions. The long-term goal of this project is to analyse the genome sequences of major barley accessions worldwide. In view of technical limitations, a strategy has been employed to establish the exome structure of a selected number of accessions and to perform high-quality chromosome-scale assembly of the genomes of several major representative accessions. For the future project, an efficient annotation pipeline is essential for establishing the function of genomes and genes as well as for using this information for sequence-based digital barley breeding. In this article, the author reviews the existing barley resources along with their applications and discuss possible future directions of research in barley genomics. en-copyright= kn-copyright= en-aut-name=SatoKazuhiro en-aut-sei=Sato en-aut-mei=Kazuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=Hordeum vulgare kn-keyword=Hordeum vulgare en-keyword=genome sequencing kn-keyword=genome sequencing en-keyword=genetic resources kn-keyword=genetic resources END start-ver=1.4 cd-journal=joma no-vol=1 cd-vols= no-issue=2 article-no= start-page=100053 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2020 dt-pub=20200613 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Protocol for Genome Editing to Produce Multiple Mutants in Wheat en-subtitle= kn-subtitle= en-abstract= kn-abstract=Here, we describe a protocol for producing multiple recessive mutants via genome editing in hexaploid wheat (Triticum aestivum) cv. Fielder. Using Agrobacterium-delivered CRISPR/Cas9 and three sub-genome-specific primer sets, all possible combinations of single, double, and triple transgene-free mutants can be generated. The technique for acceleration of generation advancement with embryo culture reduces time for mutant production. The mutants produced by this protocol can be used for the analysis of gene function and crop improvement. For complete details on the use and execution of this protocol, please refer to Abe et?al. (2019). en-copyright= kn-copyright= en-aut-name=AbeFumitaka en-aut-sei=Abe en-aut-mei=Fumitaka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=IshidaYuji en-aut-sei=Ishida en-aut-mei=Yuji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=HisanoHiroshi en-aut-sei=Hisano en-aut-mei=Hiroshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=EndoMasaki en-aut-sei=Endo en-aut-mei=Masaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=KomariToshihiko en-aut-sei=Komari en-aut-mei=Toshihiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=TokiSeiichi en-aut-sei=Toki en-aut-mei=Seiichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 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=7 ORCID= affil-num=1 en-affil=Division of Basic Research, Institute of Crop Science, NARO kn-affil= affil-num=2 en-affil=Plant Innovation Center, Japan Tobacco Inc. kn-affil= affil-num=3 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=4 en-affil=Division of Applied Genetics, Institute of Agrobiological Sciences, NARO kn-affil= affil-num=5 en-affil=Plant Innovation Center, Japan Tobacco Inc. kn-affil= affil-num=6 en-affil=Division of Applied Genetics, Institute of Agrobiological Sciences, NARO kn-affil= affil-num=7 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= END 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=28 cd-vols= no-issue=5 article-no= start-page=1362 end-page=1369 dt-received= dt-revised= dt-accepted= dt-pub-year=2019 dt-pub=20190730 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Genome-Edited Triple-Recessive Mutation AltersSeed Dormancy in Wheat en-subtitle= kn-subtitle= en-abstract= kn-abstract=1Common wheat has three sets of sub-genomes, making mutations difficult to observe, especially for traits controlled by recessive genes. Here, we produced hexaploid wheat lines with loss of function of homeoalleles of Qsd1, which controls seed dormancy in barley, by Agrobacterium-mediated CRISPR/Cas9. Of the eight transformed wheat events produced, three independent events carrying multiple mutations in wheat Qsd1 homeoalleles were obtained. Notably, one line had mutations in every homeoallele. We crossed this plant with wild-type cultivar Fielder to generate a transgene-free triple-recessive mutant, as revealed by Mendelian segregation. The mutant showed a significantly longer seed dormancy period than wild-type, which may result in reduced pre-harvest sprouting of grains on spikes. PCR, southern blotting, and whole-genome shotgun sequencing revealed that this segregant lacked transgenes in its genomic sequence. This technique serves as a model for trait improvement in wheat, particularly for genetically recessive traits, based on locus information from diploid barley. en-copyright= kn-copyright= en-aut-name=AbeFumitaka en-aut-sei=Abe en-aut-mei=Fumitaka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=HaqueEmdadul en-aut-sei=Haque en-aut-mei=Emdadul kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=HisanoHiroshi en-aut-sei=Hisano en-aut-mei=Hiroshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=TanakaTsuyoshi en-aut-sei=Tanaka en-aut-mei=Tsuyoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=KamiyaYoko en-aut-sei=Kamiya en-aut-mei=Yoko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=MikamiMasafumi en-aut-sei=Mikami en-aut-mei=Masafumi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=KawauraKanako en-aut-sei=Kawaura en-aut-mei=Kanako kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=EndoMasaki en-aut-sei=Endo en-aut-mei=Masaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=OnishiKazumitsu en-aut-sei=Onishi en-aut-mei=Kazumitsu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=HayashiTakeshi en-aut-sei=Hayashi en-aut-mei=Takeshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 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=11 ORCID= affil-num=1 en-affil=Division of Wheat and Barley Research, Institute of Crop Science, NARO kn-affil= affil-num=2 en-affil=Division of Wheat and Barley Research, Institute of Crop Science, NARO kn-affil= affil-num=3 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=4 en-affil=Division of Basic Research, Institute of Crop Science, NARO kn-affil= affil-num=5 en-affil=Kihara Institute for Biological Research, Yokohama City University kn-affil= affil-num=6 en-affil=Graduate School of Nanobioscience, Yokohama City University kn-affil= affil-num=7 en-affil=Kihara Institute for Biological Research, Yokohama City University kn-affil= affil-num=8 en-affil=Division of Applied Genetics, Institute of Agrobiological Sciences, NARO kn-affil= affil-num=9 en-affil=Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine kn-affil= affil-num=10 en-affil=Division of Basic Research, Institute of Crop Science, NARO kn-affil= affil-num=11 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=CRISPR/Cas9 kn-keyword=CRISPR/Cas9 en-keyword=Qsd1 kn-keyword=Qsd1 en-keyword=multiple mutation kn-keyword=multiple mutation en-keyword=seed dormancy kn-keyword=seed dormancy en-keyword=wheat kn-keyword=wheat END start-ver=1.4 cd-journal=joma no-vol=36 cd-vols= no-issue=4 article-no= start-page=611 end-page=620 dt-received= dt-revised= dt-accepted= dt-pub-year=2017 dt-pub=201704 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Selection of transformation-efficient barley genotypes based on TFA (transformation amenability) haplotype and higher resolution mapping of the TFA loci en-subtitle= kn-subtitle= en-abstract= kn-abstract=Key message: The genetic substitution of transformation amenability alleles from ‘Golden Promise’ can facilitate the development of transformation-efficient lines from recalcitrant barley cultivars. Abstract: Barley (Hordeum vulgare) cv. ‘Golden Promise’ is one of the most useful and well-studied cultivars for genetic manipulation. In a previous report, we identified several transformation amenability (TFA) loci responsible for Agrobacterium-mediated transformation using the F2 generation of immature embryos, derived from ‘Haruna Nijo’ × ‘Golden Promise,’ as explants. In this report, we describe higher density mapping of these TFA regions with additional SNP markers using the same transgenic plants. To demonstrate the robustness of transformability alleles at the TFA loci, we genotyped 202 doubled haploid progeny from the cross ‘Golden Promise’ × ‘Full Pint.’ Based on SNP genotype, we selected lines having ‘Golden Promise’ alleles at TFA loci and used them for transformation. Of the successfully transformed lines, DH120366 came the closest to achieving a level of transformation efficiency comparable to ‘Golden Promise.’ The results validate that the genetic substitution of TFA alleles from ‘Golden Promise’ can facilitate the development of transformation-efficient lines from recalcitrant barley cultivars. en-copyright= kn-copyright= en-aut-name=HisanoHiroshi en-aut-sei=Hisano en-aut-mei=Hiroshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=MeintsBrigid en-aut-sei=Meints en-aut-mei=Brigid kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=MoscouMatthew J. en-aut-sei=Moscou en-aut-mei=Matthew J. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=CistueLuis en-aut-sei=Cistue en-aut-mei=Luis kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=Ech?varriBego?a en-aut-sei=Ech?varri en-aut-mei=Bego?a kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 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=6 ORCID= en-aut-name=HayesPatrick M. en-aut-sei=Hayes en-aut-mei=Patrick M. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Department Crop and Soil Sciences, Washington State University kn-affil= affil-num=3 en-affil=The Sainsbury Laboratory kn-affil= affil-num=4 en-affil=Department Genetica y Produccion Vegetal kn-affil= affil-num=5 en-affil= kn-affil= affil-num=6 en-affil= Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=7 en-affil=Department Crop and Soil Science, Oregon State University kn-affil= en-keyword=Agrobacterium tumefaciens kn-keyword=Agrobacterium tumefaciens en-keyword=Doubled haploid kn-keyword=Doubled haploid en-keyword=Hordeum vulgare (barley) kn-keyword=Hordeum vulgare (barley) en-keyword=Single nucleotide polymorphism kn-keyword=Single nucleotide polymorphism en-keyword=Transformation kn-keyword=Transformation END start-ver=1.4 cd-journal=joma no-vol=12 cd-vols= no-issue= article-no= start-page= end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2011 dt-pub=20110519 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=454 sequencing of pooled BAC clones on chromosome 3H of barley en-subtitle= kn-subtitle= en-abstract= kn-abstract=Background: Genome sequencing of barley has been delayed due to its large genome size (ca. 5,000Mbp). Among the fast sequencing systems, 454 liquid phase pyrosequencing provides the longest reads and is the most promising method for BAC clones. Here we report the results of pooled sequencing of BAC clones selected with ESTs genetically mapped to chromosome 3H. Results: We sequenced pooled barley BAC clones using a 454 parallel genome sequencer. A PCR screening system based on primer sets derived from genetically mapped ESTs on chromosome 3H was used for clone selection in a BAC library developed from cultivar "Haruna Nijo". The DNA samples of 10 or 20 BAC clones were pooled and used for shotgun library development. The homology between contig sequences generated in each pooled library and mapped EST sequences was studied. The number of contigs assigned on chromosome 3H was 372. Their lengths ranged from 1,230 bp to 58,322 bp with an average 14,891 bp. Of these contigs, 240 showed homology and colinearity with the genome sequence of rice chromosome 1. A contig annotation browser supplemented with query search by unique sequence or genetic map position was developed. The identified contigs can be annotated with barley cDNAs and reference sequences on the browser. Homology analysis of these contigs with rice genes indicated that 1,239 rice genes can be assigned to barley contigs by the simple comparison of sequence lengths in both species. Of these genes, 492 are assigned to rice chromosome 1. Conclusions: We demonstrate the efficiency of sequencing gene rich regions from barley chromosome 3H, with special reference to syntenic relationships with rice chromosome 1. en-copyright= kn-copyright= en-aut-name=SatoKazuhiro en-aut-sei=Sato en-aut-mei=Kazuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=MotoiYuka en-aut-sei=Motoi en-aut-mei=Yuka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=YamajiNami en-aut-sei=Yamaji en-aut-mei=Nami kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=YoshidaHideya en-aut-sei=Yoshida en-aut-mei=Hideya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= affil-num=1 en-affil= kn-affil=Okayama Univ, Inst Plant Sci & Resources affil-num=2 en-affil= kn-affil=Okayama Univ, Inst Plant Sci & Resources affil-num=3 en-affil= kn-affil=Okayama Univ, Inst Plant Sci & Resources affil-num=4 en-affil= kn-affil=Okayama Univ, Inst Plant Sci & Resources END start-ver=1.4 cd-journal=joma no-vol=38 cd-vols= no-issue= article-no= start-page=D26 end-page=D32 dt-received= dt-revised= dt-accepted= dt-pub-year=2010 dt-pub=201001 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=NBRP databases: databases of biological resources in Japan en-subtitle= kn-subtitle= en-abstract= kn-abstract=The National BioResource Project (NBRP) is a Japanese project that aims to establish a system for collecting, preserving and providing bioresources for use as experimental materials for life science research. It is promoted by 27 core resource facilities, each concerned with a particular group of organisms, and by one information center. The NBRP database is a product of this project. Thirty databases and an integrated database-retrieval system (BioResource World: BRW) have been created and made available through the NBRP home page (http://www.nbrp.jp). The 30 independent databases have individual features which directly reflect the data maintained by each resource facility. The BRW is designed for users who need to search across several resources without moving from one database to another. BRW provides access to a collection of 4.5-million records on bioresources including wild species, inbred lines, mutants, genetically engineered lines, DNA clones and so on. BRW supports summary browsing, keyword searching, and searching by DNA sequences or gene ontology. The results of searches provide links to online requests for distribution of research materials. A circulation system allows users to submit details of papers published on research conducted using NBRP resources. en-copyright= kn-copyright= en-aut-name=YamazakiYukiko en-aut-sei=Yamazaki en-aut-mei=Yukiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=AkashiRyo en-aut-sei=Akashi en-aut-mei=Ryo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=BannoYutaka en-aut-sei=Banno en-aut-mei=Yutaka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=EndoTakashi en-aut-sei=Endo en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=EzuraHiroshi en-aut-sei=Ezura en-aut-mei=Hiroshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=Fukami-KobayashiKaoru en-aut-sei=Fukami-Kobayashi en-aut-mei=Kaoru kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=InabaKazuo en-aut-sei=Inaba en-aut-mei=Kazuo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=IsaTadashi en-aut-sei=Isa en-aut-mei=Tadashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=KameiKatsuhiko en-aut-sei=Kamei en-aut-mei=Katsuhiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=KasaiFumie en-aut-sei=Kasai en-aut-mei=Fumie kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=KobayashiMasatomo en-aut-sei=Kobayashi en-aut-mei=Masatomo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= en-aut-name=KurataNori en-aut-sei=Kurata en-aut-mei=Nori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=12 ORCID= en-aut-name=KusabaMakoto en-aut-sei=Kusaba en-aut-mei=Makoto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=13 ORCID= en-aut-name=MatuzawaTetsuro en-aut-sei=Matuzawa en-aut-mei=Tetsuro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=14 ORCID= en-aut-name=MitaniShohei en-aut-sei=Mitani en-aut-mei=Shohei kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=15 ORCID= en-aut-name=NakamuraTaro en-aut-sei=Nakamura en-aut-mei=Taro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=16 ORCID= en-aut-name=NakamuraYukio en-aut-sei=Nakamura en-aut-mei=Yukio kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=17 ORCID= en-aut-name=NakatsujiNorio en-aut-sei=Nakatsuji en-aut-mei=Norio kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=18 ORCID= en-aut-name=NaruseKiyoshi en-aut-sei=Naruse en-aut-mei=Kiyoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=19 ORCID= en-aut-name=NikiHironori en-aut-sei=Niki en-aut-mei=Hironori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=20 ORCID= en-aut-name=NitasakaEiji en-aut-sei=Nitasaka en-aut-mei=Eiji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=21 ORCID= en-aut-name=ObataYuichi en-aut-sei=Obata en-aut-mei=Yuichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=22 ORCID= en-aut-name=OkamotoHitoshi en-aut-sei=Okamoto en-aut-mei=Hitoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=23 ORCID= en-aut-name=OkumaMoriya en-aut-sei=Okuma en-aut-mei=Moriya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=24 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=25 ORCID= en-aut-name=SerikawaTadao en-aut-sei=Serikawa en-aut-mei=Tadao kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=26 ORCID= en-aut-name=ShiroishiToshihiko en-aut-sei=Shiroishi en-aut-mei=Toshihiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=27 ORCID= en-aut-name=SugawaraHideaki en-aut-sei=Sugawara en-aut-mei=Hideaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=28 ORCID= en-aut-name=UrushibaraHideko en-aut-sei=Urushibara en-aut-mei=Hideko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=29 ORCID= en-aut-name=YamamotoMasatoshi en-aut-sei=Yamamoto en-aut-mei=Masatoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=30 ORCID= en-aut-name=YaoitaYoshio en-aut-sei=Yaoita en-aut-mei=Yoshio kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=31 ORCID= en-aut-name=YoshikiAtsushi en-aut-sei=Yoshiki en-aut-mei=Atsushi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=32 ORCID= en-aut-name=KoharaYuji en-aut-sei=Kohara en-aut-mei=Yuji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=33 ORCID= affil-num=1 en-affil= kn-affil=Natl Inst Genet affil-num=2 en-affil= kn-affil=Miyazaki Univ affil-num=3 en-affil= kn-affil=Kyushu Univ affil-num=4 en-affil= kn-affil=Kyoto Univ affil-num=5 en-affil= kn-affil=Univ Tsukuba affil-num=6 en-affil= kn-affil=RIKEN, BioResource Ctr affil-num=7 en-affil= kn-affil=Univ Tsukuba affil-num=8 en-affil= kn-affil= affil-num=9 en-affil= kn-affil=Chiba Univ affil-num=10 en-affil= kn-affil=Natl Inst Environm Studies affil-num=11 en-affil= kn-affil=RIKEN, BioResource Ctr affil-num=12 en-affil= kn-affil=Natl Inst Genet affil-num=13 en-affil= kn-affil=Hiroshima Univ affil-num=14 en-affil= kn-affil=Kyoto Univ affil-num=15 en-affil= kn-affil=Tokyo Womens Med Univ affil-num=16 en-affil= kn-affil=RIKEN, BioResource Ctr affil-num=17 en-affil= kn-affil= affil-num=18 en-affil= kn-affil=Kyoto Univ affil-num=19 en-affil= kn-affil= affil-num=20 en-affil= kn-affil=Natl Inst Genet affil-num=21 en-affil= kn-affil=Kyushu Univ affil-num=22 en-affil= kn-affil=RIKEN, BioResource Ctr affil-num=23 en-affil= kn-affil=RIKEN, Brain Sci Inst affil-num=24 en-affil= kn-affil=RIKEN, BioResource Ctr affil-num=25 en-affil= kn-affil=Okayama Univ affil-num=26 en-affil= kn-affil=Kyoto Univ affil-num=27 en-affil= kn-affil=Natl Inst Genet affil-num=28 en-affil= kn-affil=Natl Inst Genet affil-num=29 en-affil= kn-affil=Univ Tsukuba affil-num=30 en-affil= kn-affil=Kyoto Inst Technol affil-num=31 en-affil= kn-affil=Hiroshima Univ affil-num=32 en-affil= kn-affil=RIKEN, BioResource Ctr affil-num=33 en-affil= kn-affil=Natl Inst Genet END start-ver=1.4 cd-journal=joma no-vol=10 cd-vols= no-issue= article-no= start-page= end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2009 dt-pub=20091204 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Development and implementation of high-throughput SNP genotyping in barley en-subtitle= kn-subtitle= en-abstract= kn-abstract=Background: High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource. Results: Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM. Conclusion: The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material. en-copyright= kn-copyright= en-aut-name=CloseTimothy J. en-aut-sei=Close en-aut-mei=Timothy J. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=BhatPrasanna R. en-aut-sei=Bhat en-aut-mei=Prasanna R. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=LonardiStefano en-aut-sei=Lonardi en-aut-mei=Stefano kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=WuYonghui en-aut-sei=Wu en-aut-mei=Yonghui kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=RostoksNils en-aut-sei=Rostoks en-aut-mei=Nils kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=RamsayLuke en-aut-sei=Ramsay en-aut-mei=Luke kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=DrukaArnis en-aut-sei=Druka en-aut-mei=Arnis kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=SteinNils en-aut-sei=Stein en-aut-mei=Nils kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=SvenssonJan T. en-aut-sei=Svensson en-aut-mei=Jan T. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=WanamakerSteve en-aut-sei=Wanamaker en-aut-mei=Steve kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=BozdagSerdar en-aut-sei=Bozdag en-aut-mei=Serdar kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= en-aut-name=RooseMikeal L. en-aut-sei=Roose en-aut-mei=Mikeal L. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=12 ORCID= en-aut-name=MoscouMatthew J. en-aut-sei=Moscou en-aut-mei=Matthew J. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=13 ORCID= en-aut-name=ChaoShiaoman en-aut-sei=Chao en-aut-mei=Shiaoman kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=14 ORCID= en-aut-name=VarshneyRajeev K. en-aut-sei=Varshney en-aut-mei=Rajeev K. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=15 ORCID= en-aut-name=SzuecsPeter en-aut-sei=Szuecs en-aut-mei=Peter kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=16 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=17 ORCID= en-aut-name=HayesPatrick M. en-aut-sei=Hayes en-aut-mei=Patrick M. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=18 ORCID= en-aut-name=MatthewsDavid E. en-aut-sei=Matthews en-aut-mei=David E. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=19 ORCID= en-aut-name=KleinhofsAndris en-aut-sei=Kleinhofs en-aut-mei=Andris kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=20 ORCID= en-aut-name=MuehlbauerGary J. en-aut-sei=Muehlbauer en-aut-mei=Gary J. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=21 ORCID= en-aut-name=DeYoungJoseph en-aut-sei=DeYoung en-aut-mei=Joseph kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=22 ORCID= en-aut-name=MarshallDavid F. en-aut-sei=Marshall en-aut-mei=David F. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=23 ORCID= en-aut-name=MadishettyKavitha en-aut-sei=Madishetty en-aut-mei=Kavitha kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=24 ORCID= en-aut-name=FentonRaymond D. en-aut-sei=Fenton en-aut-mei=Raymond D. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=25 ORCID= en-aut-name=CondaminePascal en-aut-sei=Condamine en-aut-mei=Pascal kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=26 ORCID= en-aut-name=GranerAndreas en-aut-sei=Graner en-aut-mei=Andreas kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=27 ORCID= en-aut-name=WaughRobbie en-aut-sei=Waugh en-aut-mei=Robbie kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=28 ORCID= affil-num=1 en-affil= kn-affil=Univ Calif Riverside, Dept Bot & Plant Sci affil-num=2 en-affil= kn-affil=Univ Calif Riverside, Dept Bot & Plant Sci affil-num=3 en-affil= kn-affil=Univ Calif Riverside, Dept Comp Sci affil-num=4 en-affil= kn-affil=Univ Calif Riverside, Dept Comp Sci affil-num=5 en-affil= kn-affil=Scottish Crop Res Inst affil-num=6 en-affil= kn-affil=Scottish Crop Res Inst affil-num=7 en-affil= kn-affil=Scottish Crop Res Inst affil-num=8 en-affil= kn-affil=Leibniz Inst Plant Genet & Crop Plant Res IPK affil-num=9 en-affil= kn-affil=Univ Calif Riverside, Dept Bot & Plant Sci affil-num=10 en-affil= kn-affil=Univ Calif Riverside, Dept Bot & Plant Sci affil-num=11 en-affil= kn-affil=Univ Calif Riverside, Dept Comp Sci affil-num=12 en-affil= kn-affil=Univ Calif Riverside, Dept Bot & Plant Sci affil-num=13 en-affil= kn-affil=Univ Calif Riverside, Dept Bot & Plant Sci affil-num=14 en-affil= kn-affil=USDA ARS, Biosci Res Lab affil-num=15 en-affil= kn-affil=Leibniz Inst Plant Genet & Crop Plant Res IPK affil-num=16 en-affil= kn-affil=Oregon State Univ, Dept Crop & Soil Sci affil-num=17 en-affil= kn-affil=Okayama Univ, Bioresources Res Inst affil-num=18 en-affil= kn-affil=Oregon State Univ, Dept Crop & Soil Sci affil-num=19 en-affil= kn-affil=Cornell Univ, USDA ARS affil-num=20 en-affil= kn-affil=Washington State Univ, Dept Crop & Soil Sci affil-num=21 en-affil= kn-affil=Univ Minnesota, Dept Agron & Plant Genet affil-num=22 en-affil= kn-affil=Univ Calif Los Angeles, So Calif Genotyping Consortium affil-num=23 en-affil= kn-affil=Scottish Crop Res Inst affil-num=24 en-affil= kn-affil=Univ Calif Riverside, Dept Bot & Plant Sci affil-num=25 en-affil= kn-affil=Univ Calif Riverside, Dept Bot & Plant Sci affil-num=26 en-affil= kn-affil=Univ Calif Riverside, Dept Bot & Plant Sci affil-num=27 en-affil= kn-affil=Leibniz Inst Plant Genet & Crop Plant Res IPK affil-num=28 en-affil= kn-affil=Scottish Crop Res Inst END start-ver=1.4 cd-journal=joma no-vol=61 cd-vols= no-issue=1 article-no= start-page=35 end-page=42 dt-received= dt-revised= dt-accepted= dt-pub-year=2011 dt-pub=201103 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Expression and functional analysis of the barley Nud gene using transgenic rice en-subtitle= kn-subtitle= en-abstract= kn-abstract=Most cereal crops have hulless grains (naked caryopses) with a free-threshing trait, whereas the majority of barley cultivars show hulled (covered) caryopses. The naked caryopsis in barley is genetically controlled by a single locus, nod. The Nud gene (the covered caryopsis allele) encodes an ethylene response factor (ERF) family transcription factor that regulates a lipid biosynthetic pathway. For functional analysis of the barley Nud gene, we produced transgenic rice expressing Nod in the developing caryopses. All transgenic lines had caryopses that were easily dehulled at maturity, indicating that the naked caryopsis phenotype remained in spite of expression of the Nod transgene. Histochemical and lipid analyses of the transgenic rice caryopses did not show increased lipid accumulation on the surface of developing caryopses, suggesting that the Nud-mediated lipid pathway may not function in rice caryopses. The predicted rice ortholog of Nod, Os06ERF was expressed specifically in the developing caryopses. However, expression of Os06ERF ceased at an earlier developmental stage than that of the native Nod gene in barley caryopses, which was also the case for expression of the Nod transgene. This raises the alternative hypothesis that the timing of Nod expression may be critical for activating the pathway for hull-caryopsis adhesion. en-copyright= kn-copyright= en-aut-name=KakedaKatsuyuki en-aut-sei=Kakeda en-aut-mei=Katsuyuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=IshiharaNorimitsu en-aut-sei=Ishihara en-aut-mei=Norimitsu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=IzumiYohei en-aut-sei=Izumi en-aut-mei=Yohei kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 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=4 ORCID= en-aut-name=TaketaShin en-aut-sei=Taketa en-aut-mei=Shin kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= affil-num=1 en-affil=Mie Univ, Grad Sch Bioresources kn-affil= affil-num=2 en-affil=Mie Univ, Grad Sch Bioresources kn-affil= affil-num=3 en-affil=Okayama Univ, Inst Plant Sci & Resources kn-affil= affil-num=4 en-affil=Okayama Univ, Inst Plant Sci & Resources kn-affil= affil-num=5 en-affil=Okayama Univ, Inst Plant Sci & Resources kn-affil= en-keyword=Nud gene kn-keyword=Nud gene en-keyword=transformation kn-keyword=transformation en-keyword=covered/naked caryopsis kn-keyword=covered/naked caryopsis en-keyword=lipid biosynthesis kn-keyword=lipid biosynthesis en-keyword=ERF/AP2 kn-keyword=ERF/AP2 en-keyword=grass kn-keyword=grass END start-ver=1.4 cd-journal=joma no-vol=60 cd-vols= no-issue=5 article-no= start-page=461 end-page=468 dt-received= dt-revised= dt-accepted= dt-pub-year=2010 dt-pub=201012 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=NBRP, National Bioresource Project of Japan and plant bioresource management en-subtitle= kn-subtitle= en-abstract= kn-abstract=The National BioResource Project has been organized and established to promote research activities using valuable bioresources. A total of twenty-eight bioresources for ten animals, nine plants and nine microorganisms/cell lines developed or collected in Japan were selected for the project. Resources are categorized into several different groups in the project; genetic resources, germplasm, genome resources and their information. Choices of how many resources must be preserved and maintained and in which categories are dependent on the status of the research community of each organism. These resources, if utilized systematically and intelligently, are powerful means for leading new scientific discoveries. Some examples can be seen in this paper. This paper reviews plant bioresources with the main focus on rice resource activities within the project. en-copyright= kn-copyright= en-aut-name=KurataNori en-aut-sei=Kurata en-aut-mei=Nori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=SatohHikaru en-aut-sei=Satoh en-aut-mei=Hikaru kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=KitanoHidemi en-aut-sei=Kitano en-aut-mei=Hidemi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=NagatoYasuo en-aut-sei=Nagato en-aut-mei=Yasuo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=EndoTakashi en-aut-sei=Endo en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 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=6 ORCID= en-aut-name=AkashiRyo en-aut-sei=Akashi en-aut-mei=Ryo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=EzuraHiroshi en-aut-sei=Ezura en-aut-mei=Hiroshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=KusabaMakoto en-aut-sei=Kusaba en-aut-mei=Makoto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=KobayashiMasatomo en-aut-sei=Kobayashi en-aut-mei=Masatomo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=NitasakaEiji en-aut-sei=Nitasaka en-aut-mei=Eiji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= en-aut-name=KasaiFumie en-aut-sei=Kasai en-aut-mei=Fumie kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=12 ORCID= en-aut-name=YamazakiYukiko en-aut-sei=Yamazaki en-aut-mei=Yukiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=13 ORCID= en-aut-name=YoshimuraAtsushi en-aut-sei=Yoshimura en-aut-mei=Atsushi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=14 ORCID= affil-num=1 en-affil= kn-affil=Res Org Informat & Syst, Genet Strains Res Ctr, Natl Inst Genet affil-num=2 en-affil= kn-affil=Kyushu Univ, Fac Agr, Inst Genet Resources affil-num=3 en-affil= kn-affil=Nagoya Univ, Biosci & Biotechnol Ctr affil-num=4 en-affil= kn-affil=Univ Tokyo, Grad Sch Agr & Life Sci affil-num=5 en-affil= kn-affil=Kyoto Univ, Genet Lab, Grad Sch Agr affil-num=6 en-affil= kn-affil=Okayama Univ, Inst Plant Sci & Resources, Barley & Wild Plant Resource Ctr affil-num=7 en-affil= kn-affil=Miyazaki Univ, Frontier Sci Res Ctr affil-num=8 en-affil= kn-affil=Univ Tsukuba, Grad Sch Life & Environm Sci, Ctr Gene Res affil-num=9 en-affil= kn-affil=Hiroshima Univ, Grad Sch Sci affil-num=10 en-affil= kn-affil=RIKEN BioResource Ctr affil-num=11 en-affil= kn-affil=Kyushu Univ, Grad Sch Sci affil-num=12 en-affil= kn-affil=Natl Inst Environm Studies, Div Environm Biol affil-num=13 en-affil= kn-affil=Res Org Informat & Syst, Ctr Genet Resources Informat, Natl Inst Genet affil-num=14 en-affil= kn-affil=Kyushu Univ, Fac Agr, Plant Breeding Lab en-keyword=NBRP kn-keyword=NBRP en-keyword=plant bioresources kn-keyword=plant bioresources en-keyword=germplasm kn-keyword=germplasm en-keyword=line/strain/accession kn-keyword=line/strain/accession en-keyword=rice kn-keyword=rice END start-ver=1.4 cd-journal=joma no-vol=59 cd-vols= no-issue=4 article-no= start-page=383 end-page=390 dt-received= dt-revised= dt-accepted= dt-pub-year=2009 dt-pub=200912 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Mapping of QTL for intermedium spike on barley chromosome 4H using EST-based markers en-subtitle= kn-subtitle= en-abstract= kn-abstract=The lateral spikelets of two-rowed barley are reduced in size and sterile, but in six-rowed barley all three spikelets are fully fertile. The trait is largely controlled by alleles at the vrs1 locus on chromosome arm 2HL, as modified by the allele present at the I locus on chromosome arm 4HS. Molecular markers were developed to saturate the 4HS region by exploiting expressed sequence-tags, either previously mapped in barley to this region, or present in the syntenic region of rice chromosome 3. Collinearity between rice and barley was strong in the 4.8 cM interval BJ468164-AV933435 and the 10 cM interval AV942364-BJ455560. A major QTL for lateral spikelet fertility (the I locus) explained 44% of phenotypic variance, and was located in the interval CB873567-BJ473916. The genotyping of near-isogenic lines for I placed the locus in a region between CB873567 and EBmac635, and therefore the most likely position of the I locus was proximal to CB873567 in a 5.3 cM interval between CB873567-BJ473916. en-copyright= kn-copyright= en-aut-name=ShahinniaFahimeh en-aut-sei=Shahinnia en-aut-mei=Fahimeh kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=Sayed-TabatabaeiBadraldin Ebrahim en-aut-sei=Sayed-Tabatabaei en-aut-mei=Badraldin Ebrahim kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 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=3 ORCID= en-aut-name=PourkheirandishMohammad en-aut-sei=Pourkheirandish en-aut-mei=Mohammad kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=KomatsudaTakao en-aut-sei=Komatsuda en-aut-mei=Takao kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= affil-num=1 en-affil= kn-affil=NIAS, Plant Genome Res Unit affil-num=2 en-affil= kn-affil=Isfahan Univ Technol, Dept Biotechnol affil-num=3 en-affil= kn-affil=Okayama Univ, Bioresources Res Inst affil-num=4 en-affil= kn-affil=NIAS, Plant Genome Res Unit affil-num=5 en-affil= kn-affil=NIAS, Plant Genome Res Unit en-keyword=lateral spikelet fertility kn-keyword=lateral spikelet fertility en-keyword=row-type kn-keyword=row-type en-keyword=mapping kn-keyword=mapping en-keyword=rice genome kn-keyword=rice genome en-keyword=synteny kn-keyword=synteny END start-ver=1.4 cd-journal=joma no-vol=59 cd-vols= no-issue=5 article-no= start-page=645 end-page=650 dt-received= dt-revised= dt-accepted= dt-pub-year=2009 dt-pub=200912 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Genetic analysis of seed dormancy QTL in barley en-subtitle= kn-subtitle= en-abstract= kn-abstract=Seed dormancy in wild barley enables drought escape by preventing germination during the hot summer in and environments. Dormancy in cultivated barley has different effects: it can delay the malting process and/or it can prevent pre-harvest sprouting. Thus, cloning dormancy genes in barley will contribute to understanding the domestication process and it will facilitate optimizing the trait for efficient agronomic and industrial uses. Rates of seed germination were used to evaluate dormancy on physiologically matured grain samples that were dried and stored frozen until use. With this phenotypic scoring procedure, many genetic factors controlling seed dormancy has been reported as quantitative trait loci (QTL). Of these QTL, one at the centrometic region of chromosome 5H (Qsd1) has been most frequently identified and shows the largest effect across mapping populations. We also identified this QTL using the EST map based on Haruna Nijo (H. vulgare ssp. vulgare) crossed with wild barley H602 (H. vulgare ssp. spontaneum). We have derived both doubled haploid and recombinant chromosome substitution lines (RCSLs) from this cross. At least four QTLs are segregating in this germplasm. RCSLs having only the Qsd1 segment of wild barley in a Haruna Nijo genetic background were identified and 910 BC(3)F(2) plants were scored for dormancy. In these lines, segregation for dormancy fit a mono-factorial ratio. These germplasm resources are appropriate for map based cloning of Qsd1. Strategies for cloning Qsd1 with these resources are discussed. en-copyright= kn-copyright= en-aut-name=SatoKazuhiro en-aut-sei=Sato en-aut-mei=Kazuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=MatsumotoTakashi en-aut-sei=Matsumoto en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=OoeNatsuko en-aut-sei=Ooe en-aut-mei=Natsuko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=TakedaKazuyoshi en-aut-sei=Takeda en-aut-mei=Kazuyoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= affil-num=1 en-affil= kn-affil=Okayama Univ, Bioresources Res Inst affil-num=2 en-affil= kn-affil=Natl Inst Agrobiol Sci affil-num=3 en-affil= kn-affil=Okayama Univ, Bioresources Res Inst affil-num=4 en-affil= kn-affil=Okayama Univ, Bioresources Res Inst en-keyword=seed dormancy kn-keyword=seed dormancy en-keyword=Hordeum vulgare kn-keyword=Hordeum vulgare en-keyword=QTL kn-keyword=QTL en-keyword=cloning kn-keyword=cloning en-keyword=genetic analysis kn-keyword=genetic analysis END start-ver=1.4 cd-journal=joma no-vol=59 cd-vols= no-issue=4 article-no= start-page=341 end-page=349 dt-received= dt-revised= dt-accepted= dt-pub-year=2009 dt-pub=200912 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Validation of rice blast resistance genes in barley using a QTL mapping population and near-isolines en-subtitle= kn-subtitle= en-abstract= kn-abstract=There are prior reports of Pyricularia grisea-the causal agent of blast of rice-causing disease in barley. In order to determine the specificity of this resistance in barley, we extended our previous mapping efforts to include blast isolates from barley and rice grown in Thailand and we assessed two resistance phenotypes: leaf blast (LB) and neck blast (NB). The largest-effect resistance QTL, on chromosome I H, was associated with NB and LB and is located in a region rich in resistance genes, including QTL conferring resistance to stripe rust (incited by Puccinia striiformis f. sp. hordei) and the mildew (Blumeria graminis f. sp. hordei) resistance gene Mla. The LB, NB and mildew resistance alleles trace to one parent (Baronesse) whereas the stripe rust resistance allele traces to the other parent (BCD47) of the mapping population. Baronesse is the susceptible recurrent parent of a set of near-isogenic lines (NILs) for three stripe rust resistance QTL, including one on 1H. Unigene (EST) derived single nucleotide polymorphism haplotypes of these NILs were aligned with the blast mapping population QTL using Mla as an anchor. Baronesse and all NILs without the 1H introgression were resistant to LB and NB. However, two NILs with the I H introgression were resistant to LB and NB. Both are resistant to stripe rust. Therefore, the QTL conferring resistance to stripe rust is separable by recombination from the blast resistance QTL. en-copyright= kn-copyright= en-aut-name=KongprakhonPhinyarat en-aut-sei=Kongprakhon en-aut-mei=Phinyarat kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=Cuesta-MarcosAlfonso en-aut-sei=Cuesta-Marcos en-aut-mei=Alfonso kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=HayesPatrick M. en-aut-sei=Hayes en-aut-mei=Patrick M. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=RichardsonKelley L. en-aut-sei=Richardson en-aut-mei=Kelley L. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=SirithunyaPattama en-aut-sei=Sirithunya en-aut-mei=Pattama kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 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=6 ORCID= en-aut-name=SteffensonBrian en-aut-sei=Steffenson en-aut-mei=Brian kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=ToojindaTheerayuth en-aut-sei=Toojinda en-aut-mei=Theerayuth kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= affil-num=1 en-affil= kn-affil=Kasetsart Univ Chalermphrakiat Sakon Nakhon Prov, Fac Nat Resources & Agro Ind affil-num=2 en-affil= kn-affil=Oregon State Univ, Dept Crop & Soil Sci affil-num=3 en-affil= kn-affil=Oregon State Univ, Dept Crop & Soil Sci affil-num=4 en-affil= kn-affil=ARS, USDA affil-num=5 en-affil= kn-affil=Rajamangala Univ Technol Lanna, Lampang Agr Res & Training Ctr affil-num=6 en-affil= kn-affil=Okayama Univ, Res Inst Bioresources affil-num=7 en-affil= kn-affil=Univ Minnesota, Dept Plant Pathol affil-num=8 en-affil= kn-affil=Kasetsart Univ, Rice Gene Discovery Unit, Natl Res Ctr Genet Engn & Biotechnol en-keyword=rice blast kn-keyword=rice blast en-keyword=barley kn-keyword=barley en-keyword=resistance gene kn-keyword=resistance gene en-keyword=QTL mapping kn-keyword=QTL mapping en-keyword=near-isolines kn-keyword=near-isolines END start-ver=1.4 cd-journal=joma no-vol=59 cd-vols= no-issue=1 article-no= start-page=21 end-page=26 dt-received= dt-revised= dt-accepted= dt-pub-year=2009 dt-pub=200903 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Mapping of the eibi1 gene responsible for the drought hypersensitive cuticle in wild barley (Hordeum spontaneum) en-subtitle= kn-subtitle= en-abstract= kn-abstract=Segregation analysis showed that eibi1, a drought hypersensitive Cuticle wild barley mutant, was monogenic and recessive, and mapped in two F, Populations, one made from a cross between the mutant and a Cultivated barley (cv. Morex), and the other between the mutant and another wild barley. A microsatellite marker screen showed that the gene was located oil barley chromosome 3H, and a set of markers already assigned to this chromosome, including both microsatellites and ESTs, was used to construct a genetic map. eibi1 co-segregated with barley EST AV918546, and was located to bin 6. The synteny between barley and rice ill this region is incomplete, with a large discrepancy in map distances, and the presence Of Multiple inversions. en-copyright= kn-copyright= en-aut-name=ChenGuoxiong en-aut-sei=Chen en-aut-mei=Guoxiong kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=KomatsuduTakao en-aut-sei=Komatsudu en-aut-mei=Takao kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=PourkheirandishMohammad en-aut-sei=Pourkheirandish en-aut-mei=Mohammad kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=SameriMohammad en-aut-sei=Sameri en-aut-mei=Mohammad 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= en-aut-name=KrugmanTamar en-aut-sei=Krugman en-aut-mei=Tamar kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=FahimaTzion en-aut-sei=Fahima en-aut-mei=Tzion kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=KorolAbraham B. en-aut-sei=Korol en-aut-mei=Abraham B. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=NevoEviatar en-aut-sei=Nevo en-aut-mei=Eviatar kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= affil-num=1 en-affil= kn-affil=Natl Inst Agrobiol Sci, Plant Genome Res Unit affil-num=2 en-affil= kn-affil=Natl Inst Agrobiol Sci, Plant Genome Res Unit affil-num=3 en-affil= kn-affil=Natl Inst Agrobiol Sci, Plant Genome Res Unit affil-num=4 en-affil= kn-affil=Natl Inst Agrobiol Sci, Plant Genome Res Unit affil-num=5 en-affil= kn-affil=Okayama Univ, Bioresources Res Inst affil-num=6 en-affil= kn-affil=Univ Haifa, Inst Evolut affil-num=7 en-affil= kn-affil=Univ Haifa, Inst Evolut affil-num=8 en-affil= kn-affil=Univ Haifa, Inst Evolut affil-num=9 en-affil= kn-affil=Univ Haifa, Inst Evolut en-keyword=wild barley kn-keyword=wild barley en-keyword=Hordeum spontaneum kn-keyword=Hordeum spontaneum en-keyword=eibi1 mutant kn-keyword=eibi1 mutant en-keyword=genetic mapping kn-keyword=genetic mapping en-keyword=rice kn-keyword=rice en-keyword=synteny kn-keyword=synteny END start-ver=1.4 cd-journal=joma no-vol=19 cd-vols= no-issue=6 article-no= start-page=487 end-page=497 dt-received= dt-revised= dt-accepted= dt-pub-year=2012 dt-pub=201212 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Discovery of High-Confidence Single Nucleotide Polymorphisms from Large-Scale De Novo Analysis of Leaf Transcripts of Aegilops tauschii, A Wild Wheat Progenitor en-subtitle= kn-subtitle= en-abstract= kn-abstract=Construction of high-resolution genetic maps is important for genetic and genomic research, as well as for molecular breeding. Single nucleotide polymorphisms (SNPs) are the,predominant class of genetic variation and can be used as molecular markers. Aegilops tauschii, the D-genome donor of common wheat, is considered a valuable genetic resource for wheat improvement. Our previous study implied that Ae. tauschii accessions can be genealogically divided into two major lineages. In this study, the transcriptome of two Ae. tauschii accessions from each lineage, lineage 1 (L1) and 2 (L2), was sequenced, yielding 9435 SNPs and 739 insertion/deletion polymorphisms (indels) after de novo assembly of the reads. Based on 36 contig sequences, 31 SNPs and six indels were validated on 20 diverse Ae. tauschii accessions. Because almost all of the SNP markers were polymorphic between L1 and L2, and the D-genome donor of common wheat is presumed to belong to L2, these markers are available for D-genome typing in crosses between common wheat varieties and L1-derived synthetic wheat. Due to the conserved synteny between wheat and barley chromosomes, the high-density expressed sequence tag barley map and the hypothetical gene order in barley can be applied to develop markers on target chromosomal regions in wheat. en-copyright= kn-copyright= en-aut-name=IehisaJulio Cesar Masaru en-aut-sei=Iehisa en-aut-mei=Julio Cesar Masaru kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=ShimizuAkifumi en-aut-sei=Shimizu en-aut-mei=Akifumi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 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=3 ORCID= en-aut-name=NasudaShuhei en-aut-sei=Nasuda en-aut-mei=Shuhei kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=TakumiShigeo en-aut-sei=Takumi en-aut-mei=Shigeo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= affil-num=1 en-affil= kn-affil=Kobe Univ, Grad Sch Agr Sci, Lab Plant Genet affil-num=2 en-affil= kn-affil=Univ Shiga Prefecture, Dept Biol Resources Management, Sch Environm Sci affil-num=3 en-affil= kn-affil=Okayama Univ, Inst Plant Sci & Resources affil-num=4 en-affil= kn-affil=Kyoto Univ, Grad Sch Agr, Lab Plant Genet affil-num=5 en-affil= kn-affil=Kobe Univ, Grad Sch Agr Sci, Lab Plant Genet en-keyword=Aegilops tauschii kn-keyword=Aegilops tauschii en-keyword=expression sequence tag kn-keyword=expression sequence tag en-keyword=next generation sequencing kn-keyword=next generation sequencing en-keyword=single nucleotide polymorphism kn-keyword=single nucleotide polymorphism en-keyword=wheat kn-keyword=wheat END start-ver=1.4 cd-journal=joma no-vol=16 cd-vols= no-issue=2 article-no= start-page=81 end-page=89 dt-received= dt-revised= dt-accepted= dt-pub-year=2009 dt-pub=200904 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Development of 5006 Full-Length CDNAs in Barley: A Tool for Accessing Cereal Genomics Resources en-subtitle= kn-subtitle= en-abstract= kn-abstract=A collection of 5006 full-length (FL) cDNA sequences was developed in barley. Fifteen mRNA samples from various organs and treatments were pooled to develop a cDNA library using the CAP trapper method. More than 60% of the clones were confirmed to have complete coding sequences, based on comparison with rice amino acid and UniProt sequences. Blastn homologies (E < 1E-5) to rice genes and Arabidopsis genes were 89 and 47%, respectively. Of the 5028 possible amino acid sequences derived from the 5006 FLcDNAs, 4032 (80.2%) were classified into 1678 GreenPhyl multigenic families. There were 555 cDNAs showing low homology to both rice and Arabidopsis. Gene ontology annotation by InterProScan indicated that many of these cDNAs (71%) have no known molecular functions and may be unique to barley. The cDNAs showed high homology to Barley 1 GeneChip oligo probes (81%) and the wheat gene index (84%). The high homology between FLcDNAs (27%) and mapped barley expressed sequence tag enabled assigning linkage map positions to 151-233 FLcDNAs on each of the seven barley chromosomes. These comprehensive barley FLcDNAs provide strong platform to connect preexisting genomic and genetic resources and accelerate gene identification and genome analysis in barley and related species. en-copyright= kn-copyright= en-aut-name=SatoKazuhiro en-aut-sei=Sato en-aut-mei=Kazuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=Shin-ITadasu en-aut-sei=Shin-I en-aut-mei=Tadasu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=SekiMotoaki en-aut-sei=Seki en-aut-mei=Motoaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=ShinozakiKazuo en-aut-sei=Shinozaki en-aut-mei=Kazuo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=YoshidaHideya en-aut-sei=Yoshida en-aut-mei=Hideya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=TakedaKazuyoshi en-aut-sei=Takeda en-aut-mei=Kazuyoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=YamazakiYukiko en-aut-sei=Yamazaki en-aut-mei=Yukiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=ConteMatthieu en-aut-sei=Conte en-aut-mei=Matthieu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=KoharaYuji en-aut-sei=Kohara en-aut-mei=Yuji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= affil-num=1 en-affil= kn-affil=Okayama Univ, Bioresources Res Inst affil-num=2 en-affil= kn-affil=Natl Inst Genet affil-num=3 en-affil= kn-affil=RIKEN, Plant Sci Ctr affil-num=4 en-affil= kn-affil=RIKEN, Plant Sci Ctr affil-num=5 en-affil= kn-affil=Okayama Univ, Bioresources Res Inst affil-num=6 en-affil= kn-affil=Okayama Univ, Bioresources Res Inst affil-num=7 en-affil= kn-affil=Natl Inst Genet affil-num=8 en-affil= kn-affil=Int Rice Res Inst, Crop Res Informat Lab affil-num=9 en-affil= kn-affil=Natl Inst Genet en-keyword=full-length cDNA kn-keyword=full-length cDNA en-keyword=Hordeum vulgare kn-keyword=Hordeum vulgare en-keyword=mRNA kn-keyword=mRNA en-keyword=gene ontology kn-keyword=gene ontology END start-ver=1.4 cd-journal=joma no-vol=23 cd-vols= no-issue=4 article-no= start-page=1249 end-page=1263 dt-received= dt-revised= dt-accepted= dt-pub-year=2011 dt-pub=201104 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Unlocking the Barley Genome by Chromosomal and Comparative Genomics en-subtitle= kn-subtitle= en-abstract= kn-abstract=We used a novel approach that incorporated chromosome sorting, next-generation sequencing, array hybridization, and systematic exploitation of conserved synteny with model grasses to assign; similar to 86% of the estimated; similar to 32,000 barley (Hordeum vulgare) genes to individual chromosome arms. Using a series of bioinformatically constructed genome zippers that integrate gene indices of rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium distachyon in a conserved synteny model, we were able to assemble 21,766 barley genes in a putative linear order. We show that the barley (H) genome displays a mosaic of structural similarity to hexaploid bread wheat (Triticum aestivum) A, B, and D subgenomes and that orthologous genes in different grasses exhibit signatures of positive selection in different lineages. We present an ordered, information-rich scaffold of the barley genome that provides a valuable and robust framework for the development of novel strategies in cereal breeding. en-copyright= kn-copyright= en-aut-name=MayerKlaus F. X. en-aut-sei=Mayer en-aut-mei=Klaus F. X. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=MartisMihaela en-aut-sei=Martis en-aut-mei=Mihaela kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=HedleyPete E. en-aut-sei=Hedley en-aut-mei=Pete E. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=SimkovaHana en-aut-sei=Simkova en-aut-mei=Hana kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=LiuHui en-aut-sei=Liu en-aut-mei=Hui kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=MorrisJenny A. en-aut-sei=Morris en-aut-mei=Jenny A. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=SteuernagelBurkhard en-aut-sei=Steuernagel en-aut-mei=Burkhard kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=TaudienStefan en-aut-sei=Taudien en-aut-mei=Stefan kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=RoessnerStephan en-aut-sei=Roessner en-aut-mei=Stephan kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=GundlachHeidrun en-aut-sei=Gundlach en-aut-mei=Heidrun kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=KubalakovaMarie en-aut-sei=Kubalakova en-aut-mei=Marie kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= en-aut-name=SuchankovaPavla en-aut-sei=Suchankova en-aut-mei=Pavla kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=12 ORCID= en-aut-name=MuratFlorent en-aut-sei=Murat en-aut-mei=Florent kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=13 ORCID= en-aut-name=FelderMarius en-aut-sei=Felder en-aut-mei=Marius kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=14 ORCID= en-aut-name=NussbaumerThomas en-aut-sei=Nussbaumer en-aut-mei=Thomas kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=15 ORCID= en-aut-name=GranerAndreas en-aut-sei=Graner en-aut-mei=Andreas kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=16 ORCID= en-aut-name=SalseJerome en-aut-sei=Salse en-aut-mei=Jerome kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=17 ORCID= en-aut-name=EndoTakashi en-aut-sei=Endo en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=18 ORCID= en-aut-name=SakaiHiroaki en-aut-sei=Sakai en-aut-mei=Hiroaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=19 ORCID= en-aut-name=TanakaTsuyoshi en-aut-sei=Tanaka en-aut-mei=Tsuyoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=20 ORCID= en-aut-name=ItohTakeshi en-aut-sei=Itoh en-aut-mei=Takeshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=21 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=22 ORCID= en-aut-name=PlatzerMatthias en-aut-sei=Platzer en-aut-mei=Matthias kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=23 ORCID= en-aut-name=MatsumotoTakashi en-aut-sei=Matsumoto en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=24 ORCID= en-aut-name=ScholzUwe en-aut-sei=Scholz en-aut-mei=Uwe kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=25 ORCID= en-aut-name=DolezelJaroslav en-aut-sei=Dolezel en-aut-mei=Jaroslav kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=26 ORCID= en-aut-name=WaughRobbie en-aut-sei=Waugh en-aut-mei=Robbie kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=27 ORCID= en-aut-name=SteinNils en-aut-sei=Stein en-aut-mei=Nils kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=28 ORCID= affil-num=1 en-affil= kn-affil=Helmholtz Ctr Munich affil-num=2 en-affil= kn-affil=Helmholtz Ctr Munich affil-num=3 en-affil= kn-affil=Scottish Crop Res Inst affil-num=4 en-affil= kn-affil=Inst Expt Bot affil-num=5 en-affil= kn-affil=Scottish Crop Res Inst affil-num=6 en-affil= kn-affil=Scottish Crop Res Inst affil-num=7 en-affil= kn-affil=Leibniz Inst Plant Genet & Crop Plant Res affil-num=8 en-affil= kn-affil=Leibniz Inst Age Res Fritz Lipmann Inst affil-num=9 en-affil= kn-affil=Helmholtz Ctr Munich affil-num=10 en-affil= kn-affil=Helmholtz Ctr Munich affil-num=11 en-affil= kn-affil=Inst Expt Bot affil-num=12 en-affil= kn-affil=Inst Expt Bot affil-num=13 en-affil= kn-affil=Univ Clermont Ferrand affil-num=14 en-affil= kn-affil=Leibniz Inst Age Res Fritz Lipmann Inst affil-num=15 en-affil= kn-affil=Helmholtz Ctr Munich affil-num=16 en-affil= kn-affil=Leibniz Inst Plant Genet & Crop Plant Res affil-num=17 en-affil= kn-affil=Univ Clermont Ferrand affil-num=18 en-affil= kn-affil=Kyoto Univ affil-num=19 en-affil= kn-affil=Natl Inst Agrobiol Sci affil-num=20 en-affil= kn-affil=Natl Inst Agrobiol Sci affil-num=21 en-affil= kn-affil=Natl Inst Agrobiol Sci affil-num=22 en-affil= kn-affil=Okayama Univ affil-num=23 en-affil= kn-affil=Leibniz Inst Age Res Fritz Lipmann Inst affil-num=24 en-affil= kn-affil=Natl Inst Agrobiol Sci affil-num=25 en-affil= kn-affil=Leibniz Inst Plant Genet & Crop Plant Res affil-num=26 en-affil= kn-affil=Inst Expt Bot affil-num=27 en-affil= kn-affil=Scottish Crop Res Inst affil-num=28 en-affil= kn-affil=Leibniz Inst Plant Genet & Crop Plant Res END start-ver=1.4 cd-journal=joma no-vol=156 cd-vols= no-issue=1 article-no= start-page=20 end-page=28 dt-received= dt-revised= dt-accepted= dt-pub-year=2011 dt-pub=201105 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Comprehensive Sequence Analysis of 24,783 Barley Full-Length cDNAs Derived from 12 Clone Libraries en-subtitle= kn-subtitle= en-abstract= kn-abstract=Full-length cDNA (FLcDNA) libraries consisting of 172,000 clones were constructed from a two-row malting barley cultivar (Hordeum vulgare 'Haruna Nijo') under normal and stressed conditions. After sequencing the clones from both ends and clustering the sequences, a total of 24,783 complete sequences were produced. By removing duplicates between these and publicly available sequences, 22,651 representative sequences were obtained: 17,773 were novel barley FLcDNAs, and 1,699 were barley specific. Highly conserved genes were found in the barley FLcDNA sequences for 721 of 881 rice (Oryza sativa) trait genes with 50% or greater identity. These FLcDNA resources from our Haruna Nijo cDNA libraries and the full-length sequences of representative clones will improve our understanding of the biological functions of genes in barley, which is the cereal crop with the fourth highest production in the world, and will provide a powerful tool for annotating the barley genome sequences that will become available in the near future. en-copyright= kn-copyright= en-aut-name=MatsumotoTakashi en-aut-sei=Matsumoto en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=TanakaTsuyoshi en-aut-sei=Tanaka en-aut-mei=Tsuyoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=SakaiHiroaki en-aut-sei=Sakai en-aut-mei=Hiroaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=AmanoNaoki en-aut-sei=Amano en-aut-mei=Naoki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=KanamoriHiroyuki en-aut-sei=Kanamori en-aut-mei=Hiroyuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=KuritaKanako en-aut-sei=Kurita en-aut-mei=Kanako kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=KikutaAri en-aut-sei=Kikuta en-aut-mei=Ari kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=KamiyaKozue en-aut-sei=Kamiya en-aut-mei=Kozue kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=YamamotoMayu en-aut-sei=Yamamoto en-aut-mei=Mayu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=IkawaHiroshi en-aut-sei=Ikawa en-aut-mei=Hiroshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=FujiiNobuyuki en-aut-sei=Fujii en-aut-mei=Nobuyuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= en-aut-name=HoriKiyosumi en-aut-sei=Hori en-aut-mei=Kiyosumi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=12 ORCID= en-aut-name=ItohTakeshi en-aut-sei=Itoh en-aut-mei=Takeshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=13 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=14 ORCID= affil-num=1 en-affil= kn-affil=Natl Inst Agrobiol Sci affil-num=2 en-affil= kn-affil=Natl Inst Agrobiol Sci affil-num=3 en-affil= kn-affil=Natl Inst Agrobiol Sci affil-num=4 en-affil= kn-affil=Natl Inst Agrobiol Sci affil-num=5 en-affil= kn-affil=Inst Soc Techno Innovat Agr Forestry & Fisheries affil-num=6 en-affil= kn-affil=Inst Soc Techno Innovat Agr Forestry & Fisheries affil-num=7 en-affil= kn-affil=Inst Soc Techno Innovat Agr Forestry & Fisheries affil-num=8 en-affil= kn-affil=Inst Soc Techno Innovat Agr Forestry & Fisheries affil-num=9 en-affil= kn-affil=Inst Soc Techno Innovat Agr Forestry & Fisheries affil-num=10 en-affil= kn-affil=Inst Soc Techno Innovat Agr Forestry & Fisheries affil-num=11 en-affil= kn-affil=Hitachi Govt & Publ Corp Syst Engn Ltd affil-num=12 en-affil= kn-affil=Natl Inst Agrobiol Sci affil-num=13 en-affil= kn-affil=Natl Inst Agrobiol Sci affil-num=14 en-affil= kn-affil=Okayama Univ END start-ver=1.4 cd-journal=joma no-vol=3 cd-vols= no-issue=1 article-no= start-page=43 end-page=53 dt-received= dt-revised= dt-accepted= dt-pub-year=1995 dt-pub=1995 dt-online= en-article= kn-article= en-subject= kn-subject= en-title=大麦網斑病抵抗性の選抜効果 kn-title=Selection Effectiveness for the Resistance to Net Blotch in Barley en-subtitle= kn-subtitle= en-abstract=抵抗性と罹病性の両親間の交雑に由来する2組のF2集団とその後代のF3系統を用いて、大麦網斑病における抵抗性の選抜効果を推定した。F3系統の平均値と分散から、病斑指数の分散が小さく、すでに固定した系統が多数存在したので、抵抗性は少数の遺伝子に支配されているとみられた。F2個体とF3系統間の親子相関、親子回帰およびF2の選抜差とF3系統の遺伝獲得量から遺伝率を推定したところ、2組の交雑組合せで抵抗性親の病斑指数は異なっていたにもかかわらず、3種類の遺伝率の推定値はいずれも0.6〜0.8の値を示した。遺伝率が高く、しかも関与する遺伝子数であるため、雑種集団で連続変異を示す場合の大麦網斑病抵抗性の選抜はF2からでも効果的とみられた。 kn-abstract=Selection effectiveness for the resistance to net blotch was estimated by using two sets of F2 and F3 populations derived from the crosses between resistant and susceptible parents. In every F2 and F3 population, disease ratings showed a continuous distribution. As many F3 lines with intermediate resistance had a smaller variance and homozygous genotype, the resistance might be controlled by a few genes. The heritabilities of the disease rating were estimated by correlation coefficients and regression coefficients between each F2 plant and the descended F3 lines. Another estimate for heritability was calculated by the selection differential in the F2 plants and genetic gain in the F3 lines. Despite the different level of resistance in the resistant parents of the two crosses, the three kinds of heritabilities estimated were similar and ranged from 0.6 to 0.8. Because of the fewer number of genes controlling the disease resistance and the higher heritabilities, selection in a early generation may be effective for net blotch resistance in barlcy. en-copyright= kn-copyright= en-aut-name=SatoKazuhiro en-aut-sei=Sato en-aut-mei=Kazuhiro kn-aut-name=佐藤和広 kn-aut-sei=佐藤 kn-aut-mei=和広 aut-affil-num=1 ORCID= en-aut-name=TakedaKazuyoshi en-aut-sei=Takeda en-aut-mei=Kazuyoshi kn-aut-name=武田和義 kn-aut-sei=武田 kn-aut-mei=和義 aut-affil-num=2 ORCID= affil-num=1 en-affil= kn-affil=岡山大学 affil-num=2 en-affil= kn-affil=岡山大学 en-keyword=Net blotch kn-keyword=Net blotch en-keyword=Pyrenophora teres kn-keyword=Pyrenophora teres en-keyword=Selection kn-keyword=Selection en-keyword=Barley kn-keyword=Barley en-keyword=Disease resistance kn-keyword=Disease resistance END start-ver=1.4 cd-journal=joma no-vol=2 cd-vols= no-issue=1 article-no= start-page=123 end-page=134 dt-received= dt-revised= dt-accepted= dt-pub-year=1994 dt-pub=1994 dt-online= en-article= kn-article= en-subject= kn-subject= en-title=カクヤリグサ科一年生雑草における数量分類学的研究 kn-title=Numerical Taxonomic Study in Annual Cyperaceous Weeds en-subtitle= kn-subtitle= en-abstract=カヤツリグサ科の3種の雑草カヤツリグサ(C.microiria Steud.)12系統、コゴメガヤツリ(Cyperus iria L.)12系統およびチャガヤツリ(C.amuricus Maxim.)6系統を岡山県、鳥取県および東京都なら採集して倉敷で栽培し、形態的特性、バイオマスおよび種子生産性など21形質を調査した。各形質を分散分析したところ系統間差はいずれも有意であったが、種間の値は多くの形質で重複し、単一形質による種の判別は困難であった。21形質間の相関行列を主成分分析したところ、上位3主成分の累積寄与率は83%と大きく、第1主成分(37%)は小穂の形態と種子生産性、第2主成分(28%)は生長量、第3主成分(18%)は種子重と小穂密度とそれぞれ関係が深いとみられた。第1主成分と第3主成分によって供試30系統は3群に分けられ、各群はそれぞれの種と一致した。さらに、第2主成分と第3主成分によってカヤツリグサ種内の系統は主として生長量の異なる3群に分類できた。クラスター分析によって供試30系統は4つの大きな群に分けられた。一番目の群には、C.amuricusの全系統、二番目の群にはC.microiriaの3系統、三番目の群にはC.microiriaの残りの系統、および最後のクラスターにはC.iriaの全系統が含まれた。従って、C.microiriaha形態的および生態的形質において異なる2ないし3の生態型から成ると考えられた。このように数量分類学あるいは多変量解析はカヤツリグサ科の雑草の種間ならびに種内の分類に極めて有効な解析法であることが示された。 kn-abstract=Three species of Cyperaceous weeds, Cyperus iria (12 strains), C. microiria(12 strains) and C. amuricus (6 strains), were collected from different sites of Okayama, Tottori and Tokyo prefectures, and various morphological characters, biomass and seed production were observed on the plants which were cultivated at Kurashiki. The analysis of variance showed a significant difference among the strains in each character. However, the species overlapped with each other in most morphological characters. Prinipal component analysis on the 21 characters showed that 83% of the total variation could be explained by the first three components: the first component (37%) was regarded as factors concerning spikelet and seed production; the second component (28%) was regarded as factors concerned the size of vegetative parts; the third component (18%) was largely affected by seed weight and floret density. Scatter diagram on the first and third principal components showed that the 30 strains of three species divided into three groups, and strains in each group correspond to the three species without exception. Based on the second and third principal components, strains of C. microiria were further divided into three sub-groups according to size of vegetative parts. Using the cluster analysis, 30 strains of these species were divided into four large clusters; the first was composed of C. amuricus strains, the second was of three strains of C. microiria, the third included the remaining strains of C. microiria, and the last cluster was composed of C. iria strains. It may be concluded that C. microiria is composed of two or three ecotypes which are different in morphological and reproductive traits. en-copyright= kn-copyright= en-aut-name=Muhamad AhmadChozin en-aut-sei=Muhamad Ahmad en-aut-mei=Chozin kn-aut-name=Muhamad AhmadChozin kn-aut-sei=Muhamad Ahmad kn-aut-mei=Chozin aut-affil-num=1 ORCID= en-aut-name=SatouKazuhiro en-aut-sei=Satou en-aut-mei=Kazuhiro kn-aut-name=佐藤和広 kn-aut-sei=佐藤 kn-aut-mei=和広 aut-affil-num=2 ORCID= en-aut-name=YasudaShozo en-aut-sei=Yasuda en-aut-mei=Shozo kn-aut-name=安田昭三 kn-aut-sei=安田 kn-aut-mei=昭三 aut-affil-num=3 ORCID= affil-num=1 en-affil= kn-affil=岡山大学 affil-num=2 en-affil= kn-affil=岡山大学 affil-num=3 en-affil= kn-affil=岡山大学 en-keyword=Cyperus iria kn-keyword=Cyperus iria en-keyword=Cyperus microiria kn-keyword=Cyperus microiria en-keyword=Cyperus amuricus kn-keyword=Cyperus amuricus en-keyword=Numerical taxonomy kn-keyword=Numerical taxonomy en-keyword=Speciation kn-keyword=Speciation END start-ver=1.4 cd-journal=joma no-vol=2 cd-vols= no-issue=1 article-no= start-page=111 end-page=122 dt-received= dt-revised= dt-accepted= dt-pub-year=1994 dt-pub=1994 dt-online= en-article= kn-article= en-subject= kn-subject= en-title=Comparison of Resistance to Powdery Mildew between Wild Barley (Hordeum spontaneum C. Koch) kn-title=オオムギの野生種(Hordeum spontaneum C. Koch)と在来種におけるうどんこ病抵抗性の比較 en-subtitle= kn-subtitle= en-abstract=病原菌の変異による抵抗性品種の罹病化は耐病性育種の大きな問題である。永続性のある抵抗性品種を育成するための遺伝資源を得る目的で、病原菌と長期間共進化してきた野生オオムギ(Hordeum spontaneum)と在来種のうどんこ病抵抗性を評価した。材料はH.spontaneum162系統ならびにこれらと産地を同じくする在来品種145系統である。接種には日本のうどんこ病菌H1,h4,h9の他に人為的交雑によって育成した7菌株を加えた10菌株を用いた。第1葉の反応を免疫的抵抗性(i)、高度抵抗性(R)、中度抵抗性(M)および罹病性(S)に分類した。その結果、以下のことが明らかとなった。1)抵抗性(i,R,M)を示す系統の頻度は大部分の菌株において野生種の方が高かった。2)野生種の抵抗性は在来種よりも多数の菌株に対して有効であった。3)クラスター分析の結果、野生種の大部分が同一のグループに属し、在来品種は多くのサブグループに属することが明らかにされた。4)これらの事実から、オオムギの野生種はうどんこ病抵抗性育種の遺伝資源として在来種と同等あるいはそれ以上に有用であるとみられた。 kn-abstract=A total of 162 strains of wild barley, Hordeum spontaneum C. Koch originating from Iran, Iraq, Turkey and Central Asia, were tested for resistance to powdery mildew. Then, the variation of resistance was compared with that of 145 local varieties of cultivated barley (Hordeum vulgare L.) originating from the same region of the wild barley collection. Ten different isolates of the parasite with Japanese origin were separately inoculated onto the first leaves of the host plants. The infection types were classified into the following: i, immunelike; R, highly resistant; M, moderately resistant; and S, highly susceptible. Resistant strains with i, R or M infection type were more frequent among wild barleys as compared with the cultivated forms. It is noteworthy that among these three resistant reactions,the M type was most frequent in the wild barley. To compare the degree of resistance to a total of 10 isolates, the resistance score was calculated in each of the wild and cultivated strains as the following: Scores 1,2,3 and 4 were given to the infection types of i, R, M and S, respectively, and the mean score for 10 isolates was calculated. Wild barley showed significantly low resistance scores as compared with those of cultivated barley. This was also confirmed by the cluster analysis; the cluster with more resistance to 10 isolates consisted of many strains of wild barley. Next, the resistance of wild barley was characterized by their broader effective ranges to different isolates. According to the x2 test for independence of reactions to two different isolates, the resistant factor(s) involved in wild barley was confirmed to be rather non-specific to the parasite. It was concluded that H. spontaneum may be useful genetic resources for the breeding of resistance to powdery mildew as well as local varieties. en-copyright= kn-copyright= en-aut-name=FukuyamaToshinori en-aut-sei=Fukuyama en-aut-mei=Toshinori kn-aut-name=福山利範 kn-aut-sei=福山 kn-aut-mei=利範 aut-affil-num=1 ORCID= en-aut-name=HetaHideo en-aut-sei=Heta en-aut-mei=Hideo kn-aut-name=部田英雄 kn-aut-sei=部田 kn-aut-mei=英雄 aut-affil-num=2 ORCID= en-aut-name=SatoKazuhiro en-aut-sei=Sato en-aut-mei=Kazuhiro kn-aut-name=佐藤和広 kn-aut-sei=佐藤 kn-aut-mei=和広 aut-affil-num=3 ORCID= en-aut-name=TakedaKazuyoshi en-aut-sei=Takeda en-aut-mei=Kazuyoshi kn-aut-name=武田和義 kn-aut-sei=武田 kn-aut-mei=和義 aut-affil-num=4 ORCID= affil-num=1 en-affil= kn-affil=岡山大学 affil-num=2 en-affil= kn-affil=岡山大学 affil-num=3 en-affil= kn-affil=岡山大学 affil-num=4 en-affil= kn-affil=岡山大学 en-keyword=Hordeum spontaneum kn-keyword=Hordeum spontaneum en-keyword=Barley kn-keyword=Barley en-keyword=Powdery mildew kn-keyword=Powdery mildew en-keyword=Resistance kn-keyword=Resistance END start-ver=1.4 cd-journal=joma no-vol=2 cd-vols= no-issue=1 article-no= start-page=91 end-page=102 dt-received= dt-revised= dt-accepted= dt-pub-year=1994 dt-pub=1994 dt-online= en-article= kn-article= en-subject= kn-subject= en-title=Sources of Resistance to Net Blotch in Barley Germplasm kn-title=大麦網斑病における抵抗性遺伝資源 en-subtitle= kn-subtitle= en-abstract=日本ならびにカナダで採取した大麦網斑病菌4菌株を、岡山大学資源生物科学研究所大麦系統保存施設の保有する2,200あまりの品種に接種して、各菌株に対する抵抗性遺伝子源を評価すると共に病原性の分化を検討した。結果の概要は以下の通りである。1)3回にわたって44品種に4菌株を接種した予備試験の結果、病斑指数の品種変異は極めて大きく、品種の抵抗性に対する接種時期の影響は小さかった。2)供試4菌株に対するオオムギ品種の抵抗性の頻度分布はいずれも連続的で、そのピークは抵抗性側であった。各菌株間の病斑指数は有意な正の相関関係にあり、菌株間の病原性の分化は小さかった。3)各菌株に対する抵抗性遺伝資源はエチオピア、北アフリカおよび朝鮮半島に多かった。一方、日本で採取した2菌株に対する罹病性の品種はトルコおよびヨーロッパに多いのに対して、カナダで採取した菌株に対する罹病性の品種はネパールに多かった。また、ネパールに由来する品種の病斑指数は、日本の2菌株に対しては抵抗性と罹病性の2群に分かれたが、カナダの2菌株に対しては連続的な分布を示した。特に、カナダの菌株WRS102に対するネパール由来の品種の反応は、強度の抵抗性を示す品種がなく、ピークが罹病性側に片寄っており、日本の菌株に対する反応とは大きく異なった。4)日本で採取したK105とカナダで採取したWRS102の病斑指数の菌株間相関係数は、4菌株の組合せの中で最も小さく、K105とWRS102の病原性は多少分化していた。なお、K105に抵抗性でWRS102に罹病性の品種は25品種であり、そのうち20品種がネパール由来で、かつ、そのほとんどが小穂脱落性東亜型を示した。従ってK105に抵抗性でWRS102に罹病性の遺伝子は、ネパールの東亜型品種に偏在しているとみられる。 kn-abstract=Net blotch caused by a fungus Pyrenophora teres Drechs. is a common disease in barley. Its source of resistance has been screened by many researchers by field evaluations or seedling tests inoculating a single isolatc. Since the pathogcnic variation of isolates has been reported in net blotch, resistance of the varieties to the disease may be different among the isolates with different pathogenicities. In this study, the pathogenic variation was examined and the varietal variation of the resistance was evaluated by inoculating with four P. teres isolates collected from Japan and Canada to more than 2,200 barley varieties of the world collection preserved at the Barley Germplasm Center of Okayama University. A preliminary inoculation test showed that the disease rating was affected little by the inoculation seasons. Disease ratings of varieties showed a continuous variation with a single mode in the resistant range in each of the four isolates. However, the correlation coefficient between Japanese isolate K105 and Canadian isolate WRS102 was as low as 0.55, indicating a slight pathogenic differentiation between these isolates. Significant correlation coefficients (r=.55~.78) among the ratings of isolates indicated that the pathogenicity to the varieties was rather similar and that the pathogenic differentiation was small among the four isolates tested. In general, varieties from Ethiopia, North Africa and Korea were more resistant than those from other regions. Varieties from Turkey and Europe were susceptible to Japanese isolates, while Nepalese varieties were susceptible to Canadian isolates. Twenty of 25 varieties which were resistant to the isolate K105 but susceptible to the isolate WR102 were from Nepal and most of those were Oriental-type (Bt bt2) in brittleness of rachis. These findings revealed an example of regional concentration of resistant gene in net blotch. en-copyright= kn-copyright= en-aut-name=SatoKazuhiro en-aut-sei=Sato en-aut-mei=Kazuhiro kn-aut-name=佐藤和広 kn-aut-sei=佐藤 kn-aut-mei=和広 aut-affil-num=1 ORCID= en-aut-name=TakedaKazuyoshi en-aut-sei=Takeda en-aut-mei=Kazuyoshi kn-aut-name=武田和義 kn-aut-sei=武田 kn-aut-mei=和義 aut-affil-num=2 ORCID= affil-num=1 en-affil= kn-affil=岡山大学 affil-num=2 en-affil= kn-affil=岡山大学 en-keyword=Barley kn-keyword=Barley en-keyword=Net blotch kn-keyword=Net blotch en-keyword=Disease resistance kn-keyword=Disease resistance en-keyword=Genetic resources kn-keyword=Genetic resources en-keyword=Race differentiation kn-keyword=Race differentiation END start-ver=1.4 cd-journal=joma no-vol=2 cd-vols= no-issue=1 article-no= start-page=63 end-page=68 dt-received= dt-revised= dt-accepted= dt-pub-year=1994 dt-pub=1994 dt-online= en-article= kn-article= en-subject= kn-subject= en-title=Genetic Analysis of Large Trichome in Barley Leaf Blade kn-title=オオムギの葉の剛毛に関する遺伝子分析 en-subtitle= kn-subtitle= en-abstract=岡山大学資源生物科学研究所大麦系統保存施設が保有するオオムギのうち約2,300品種を対象として、葉身の表面に生じる毛(trichome)の変異体を検索した。1)2,300品種のうち9品種(0.4%)が葉身の表面に剛毛を生じた。2)通常の品種では毛茸の鈎状部分の長さが約10μmであるのに対して剛毛型の品種では約40μmであった。Pub遺伝子による長毛はこれよりはるかに長く、剛毛型とは明らかに異なった。3)剛毛型は優性の1遺伝子(Ltr,large trichome)に支配されており、連鎖分析の結果、第7染色体にLtr-s-fsの順に配列されることが明らかになった。 kn-abstract=The inheritance and linkage relationship of a new hairiness trait "large trichome" was investigated in barley. Although the size of large trichome is about four times that of normal one, the character can not be recognized with the naked eye. However, it is easily identified by the roughness of leaf touch. The large trichomes develop on both sides of the leaf blades. The direction of trichome is both acropetal and basipetal. It is clearly distinguished from the extremely long trichome controlled by Pub gene. About 2,300 varieties of our Barley Germplasm Center were screened by the leaf touch to find nine varieties with large trichome. Two of them were six-rowed local variety from Pakistan, and other seven were two-rowed varieties from Europe and Japan. All of them were hulled type. Crosses of six large trichome varieties with a normal Japanese variety resulted in the large trichome type F1s, suggesting the dominant nature of the trait. The large trichome line Hokuiku 17 was crossed with various linkage testres to study the mode of inheritance and the linkage relationship of the gene. In the F2 populations, the large trichome was controlled by a single dominant gene named Ltr (large trichome), which was independentiy inherited from the following marker genes; br and gl-5 on chromosome 1; li and ν on chromosome 2; uz on chromosome 3; K and gl-3 on chromosome 4; trd on chromosome 5; ο on chromosome 6. On the other hand, from the cross between Hokuiku 17 and OUL166, Ltr was found to be linked with s and fs on chromosome 7. Although the allelism test has not been completed, the very low frequency of the large trichome type (9/2,300) indicates that the variant resulted from a recent mutation event, or the fitness of the variant is low in the natural and/or artificial selection. en-copyright= kn-copyright= en-aut-name=SatoKazuhiro en-aut-sei=Sato en-aut-mei=Kazuhiro kn-aut-name=佐藤和広 kn-aut-sei=佐藤 kn-aut-mei=和広 aut-affil-num=1 ORCID= en-aut-name=TakedaKazuyoshi en-aut-sei=Takeda en-aut-mei=Kazuyoshi kn-aut-name=武田和義 kn-aut-sei=武田 kn-aut-mei=和義 aut-affil-num=2 ORCID= affil-num=1 en-affil= kn-affil=岡山大学 affil-num=2 en-affil= kn-affil=岡山大学 en-keyword=Barley kn-keyword=Barley en-keyword=Trichome kn-keyword=Trichome en-keyword=Linkage analysis kn-keyword=Linkage analysis END start-ver=1.4 cd-journal=joma no-vol=1 cd-vols= no-issue=1 article-no= start-page=75 end-page=90 dt-received= dt-revised= dt-accepted= dt-pub-year=1992 dt-pub=1992 dt-online= en-article= kn-article= en-subject= kn-subject= en-title=Establishment of a Seedling Test for Resistance to Net Blotch in Barley and a Search for Resistant Varieties kn-title=大麦網斑病における幼苗検定法の確立と抵抗性品種の検索 en-subtitle= kn-subtitle= en-abstract=A seedling test was developed and used to evaluate the resistance to net blotch of more than five thousand barley varieties preserved in the Barley Germplasm Center, Okayama University. 1) Disease ratings (Tekauz 1985) of varieties varied depending on the temperatures after inoculation. However, these was no change for rank of varietal resistance in the temperature range from 15 to 25℃, which covers the normal growing temperature for barley. 2) There was little variation in the level of seedling resistance of varieties under different levels of fertilizer application. 3) A high positive correlation was observed in the disease ratings obtained after second-leaf and fourth-leaf stage inoculations of the 2,230 barley varieties. Inoculation at the second leaf stage was superior to fourth leaf inoculation since it resulted in a wide range of disease ratings and required a shorter testing period. 4) The disease ratings observed appeared to be a stable genetic character sine the error standard deviations were only 0.4 to 0.8 in plots and 0.5 to 1.0 in plants, when four or five plants per plot were tested. 5) The disease ratings of 5, 102 varieties when tested with isolate K105 showed continuous variation with a mode in the resistant range. By comparing the average disease ratings for varieties from different regions, resistance was found to be higher in the Ethiopean and Koreaan barleys and lower in European, Tukish and South-east Asian types. However. there were obvious difference between varieties within a region, such as between two-rowed and six-rowed varieties from Japan and between covered and naked varieties from Nepal. 6) When varieties were classified into the principal morphological or physiological types of barley, the two-rowed, spring habit, and western-type in rachis brittleness showed significantly lower levels of resistance than the contrasting types for each of these classifications. In particular, the group having two-rowed, spring-habit, western-type, covered characteristics, which was common among malting barley varieties had lower resistance, while a group of six-rowed, autumn-habit, naked barleys showed higher resistance. Comparisons using isogenic pairs for row-types and hull-types did not reveal any obvious differences between each pair, indicating that the differences between groups were not probably due to the pleiotropic or likage effects of genes but to the different genetic backgrounds of these varieties. kn-abstract=大麦網斑病は糸状菌の1種であるPyrenophora teres Drechs.の感染によって葉身、葉鞘等に網目状の病斑を生じ、子実の登熟低下によって減収する共に、ビールオオムギにおいては醸造品質であるエキス分が低下する重要病害である。本病害は世界各地のオオムギ栽培地帯のうち主として温暖・湿潤な地域に分布しており(Shipton et al.1973)、近年、連作や灌漑によって被害が増大しつつある(Mathre 1982)。我国においては従来からその存在が確認されていたものの、登熟後期の活性の衰えた葉に生じる病害として重要性は認識されていなかった。しかし、最近、北海道、鳥取県、鹿児島県などのビールオオムギ栽培地帯で局所的な激発事例が確認されている。(佐藤、未発表)。本病害に対する防除法としては種子消毒ならびに殺菌剤の茎葉撒布が有効であるが、その効果は完全ではない。また、茎葉撒布はコストが高く、環境汚染の問題もあるので、最も有効で経済的かつ安全な防除法は抵抗性品種を栽培することと言っても良い。従来、本病害の積極的な抵抗性育種は行われていなかったが、最近は抵抗性を有する品種も育成されている(Metcalfe 1987)。抵抗性品種を育成するためには、遺伝資源ならびに雑種後代を効率よく評価、選抜するための検定方法を確立しなければならない。本病抵抗性の検定方法としては幼苗検定法、圃場検定法が考案されて広く用いられているが(Buchannon and McDonald 1965, Holtmeyer and Webster 1981)、環境条件の変化によって抵抗性が変動する事例が報告されているので(Khan and Boyd 1970, Tekauz 1986)、抵抗性を確実に評価するための安定した検定条件を設定する必要がある。抵抗性に関する遺伝資源についてはSchaller and Wiebe (1952)、Dessouki et al.(1965)およびBuchannon and McDonald (1965)等がそれぞれ数千品種を評価し、中国東北部、トルコおよびエチオピアなどに抵抗性の遺伝資源が豊富であること報告している。それらの品種のいくつかについては、抵抗性の遺伝子分析が行われており(Bockelman et al. 1977, Davis et al. 1990)、本病抵抗性育種の交配親として使用されている(Tekazu and Buchannon 1977, Moseman and Smith 1985)。岡山大学資源生物科学研究所大麦系統保存施設は世界的にも貴重なと東アジアの遺伝資源をはじめ五千余の保存品種を有するが、著者らは大麦網斑病の幼苗検定法を確立し、これらの品種の抵抗性を評価したので報告する。 en-copyright= kn-copyright= en-aut-name=SatoKazihiro en-aut-sei=Sato en-aut-mei=Kazihiro kn-aut-name=佐藤和広 kn-aut-sei=佐藤 kn-aut-mei=和広 aut-affil-num=1 ORCID= en-aut-name=TakedaKazuyoshi en-aut-sei=Takeda en-aut-mei=Kazuyoshi kn-aut-name=武田和義 kn-aut-sei=武田 kn-aut-mei=和義 aut-affil-num=2 ORCID= affil-num=1 en-affil= kn-affil=岡山大学 affil-num=2 en-affil= kn-affil=岡山大学 END start-ver=1.4 cd-journal=joma no-vol=1 cd-vols= no-issue=2 article-no= start-page=147 end-page=158 dt-received= dt-revised= dt-accepted= dt-pub-year=1993 dt-pub=1993 dt-online= en-article= kn-article= en-subject= kn-subject= en-title=日本とカナダの春播オオムギから採取した大麦網斑病菌株の病原性の変異 kn-title=Pathogenic Variation of Pyrenophora teres Isolates Collected from Japanese and Canadian Spring Barley en-subtitle= kn-subtitle= en-abstract=北海道およびカナダの春播オオムギがら採取した22の大麦網斑病菌株(Pyrenophora teres Drechs.)を世界各地のオオムギ38品種に幼苗接種し、病斑指数によって病原性の変異を検討した。分散分析の結果、菌株の病原力ならびに品種の抵抗性には有意差が認められたが、菌株と品種の交互作用は統計的には有意でなかった。各菌株の反応をFinlay-Wilkinson(1963)の回帰分析によって解析したところ、北海道とカナダの菌株で病原性反応に差が認められた。この傾向はカナダの菌株のうち、通常のNet typeの菌株よりも斑点状病斑を示すSpot typeの菌株で顕著であった(Fig.1)。さらに、菌株と品種の交互作用を詳細に解析するために相互作用と相乗交互作用モデル(AMMIモデル)を適用して交互作用に関する主成分分析を行った結果、各菌株は日本のNet type、カナダのNet type、カナダのSpot typeの3群に分けられた(Fig.1)。各菌株について群間ならびに群内の相関係数を算出したところ(Table5)、Net typeの菌株相互の相関係数は0.601〜0.969と相対的に高かったが、一部の菌株と品種の組合わせでは抵抗性反応の逆転がみられた(Fig.4)。一方、Spot typeの菌株とNet typeの菌株の相関係数は0.302〜0.538と低く、両者の病原性は多少異なることが示された。このような一部の菌株と品種の間に認められる弱い交互作用は、抵抗性を支配する主働遺伝子の特異的な反応が、いわゆる圃場抵抗性を支配する微働遺伝子の作用によって修飾された結果と考えられる。 kn-abstract=Twenty-two isolates of Pyrenophora teres Drechs. collected from Japanese and Canadian spring barleys were inoculated to 38 barley varieties having various genetic backgrounds. The analysis of variance for the discase ratings showed that there were significant differences both in the virulence of isolates and the resistance of varieties. However, the interaction among isolates and varieties was not statistically significant. Both Finlay-Wilkinson regression analysis and principal component analysis by Additive Main effects and Multiplicative Interaction effects(AMMI)model classified the isolates into three groups,which were different in origins and sympton types. A spot tyte isolate was distinguished from net type isolates by its generally high virulence. A slight pathogenic differentiation was suggested between Japanese and Canadian net type isolates. en-copyright= kn-copyright= en-aut-name=SatoKazuhiro en-aut-sei=Sato en-aut-mei=Kazuhiro kn-aut-name=佐藤和広 kn-aut-sei=佐藤 kn-aut-mei=和広 aut-affil-num=1 ORCID= en-aut-name=TakedaKazuyoshi en-aut-sei=Takeda en-aut-mei=Kazuyoshi kn-aut-name=武田和義 kn-aut-sei=武田 kn-aut-mei=和義 aut-affil-num=2 ORCID= affil-num=1 en-affil= kn-affil=岡山大学 affil-num=2 en-affil= kn-affil=岡山大学 en-keyword=Hordeum vulgare kn-keyword=Hordeum vulgare en-keyword=Pyrenophora teres kn-keyword=Pyrenophora teres en-keyword=Barley kn-keyword=Barley en-keyword=Net blotch kn-keyword=Net blotch en-keyword=Race differentiation kn-keyword=Race differentiation END