title: Characterization of a mini core collection of Japanese wheat varieties using single-nucleotide polymorphisms generated by genotyping-by-sequencing.
abstract: A core collection of Japanese wheat varieties (JWC) consisting of 96 accessions was established based on their passport data and breeding pedigrees. To clarify the molecular basis of the JWC collection, genome-wide single-nucleotide polymorphism (SNP) genotyping was performed using the genotyping-by-sequencing (GBS) approach. Phylogenetic tree and population structure analyses using these SNP data revealed the genetic diversity and relationships among the JWC accessions, classifying them into four groups; "varieties in the Hokkaido area", "modern varieties in the northeast part of Japan", "modern varieties in the southwest part of Japan" and "classical varieties including landraces". This clustering closely reflected the history of wheat breeding in Japan. Furthermore, to demonstrate the utility of the JWC collection, we performed a genome-wide association study (GWAS) for three traits, namely, "days to heading in autumn sowing", "days to heading in spring sowing" and "culm length". We found significantly associated SNP markers with each trait, and some of these were closely linked to known major genes for heading date or culm length on the genetic map. Our study indicates that this JWC collection is a useful set of germplasm for basic and applied research aimed at understanding and utilizing the genetic diversity among Japanese wheat varieties.
authors.affiliation: Plant Genome Research Unit, National Institute of Agrobiological Sciences , 2-1-2, Kan-non-dai, Tsukuba, Ibaraki 305-8602 , Japan.
authors.forename: Fuminori
authors.initials: F
authors.lastname: Kobayashi
authors.affiliation: Bioinformatics Research Unit, National Institute of Agrobiological Sciences , 2-1-2, Kan-non-dai, Tsukuba, Ibaraki 305-8602 , Japan.
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Tanaka
authors.affiliation: Plant Genome Research Unit, National Institute of Agrobiological Sciences , 2-1-2, Kan-non-dai, Tsukuba, Ibaraki 305-8602 , Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Kanamori
authors.affiliation: Plant Genome Research Unit, National Institute of Agrobiological Sciences, 2-1-2, Kan-non-dai, Tsukuba, Ibaraki 305-8602, Japan; Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki 305-8634, Japan.
authors.forename: Jianzhong
authors.initials: J
authors.lastname: Wu
authors.affiliation: Advanced Genomics Laboratory, National Institute of Agrobiological Sciences , 1-2, Owashi, Tsukuba, Ibaraki 305-8634 , Japan.
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Katayose
authors.affiliation: Plant Genome Research Unit, National Institute of Agrobiological Sciences, 2-1-2, Kan-non-dai, Tsukuba, Ibaraki 305-8602, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Ten-noh-dai, Tsukuba, Ibaraki 305-8572, Japan.
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Handa
keywords: Japan; core collection; genetic diversity; genome-wide association study (GWAS); genotyping-by-sequencing (GBS); wheat