title: Genetic diversity and phylogeny of Japanese sake-brewing rice as revealed by AFLP and nuclear and chloroplast SSR markers.
abstract: Japanese rice ( Oryza sativa L.) cultivars that are strictly used for the brewing of sake (Japanese rice wine) represent a unique and traditional group. These cultivars are characterized by common traits such as large grain size with low protein content and a large, central white-core structure. To understand the genetic diversity and phylogenetic characteristics of sake-brewing rice, we performed amplified fragment length polymorphism and simple sequence repeat analyses, using 95 cultivars of local and modern sake-brewing rice together with 76 cultivars of local and modern cooking rice. Our analysis of both nuclear and chloroplast genome polymorphisms showed that the genetic diversity in sake-brewing rice cultivars was much smaller than the diversity found in cooking rice cultivars. Interestingly, the genetic diversity within the modern sake-brewing cultivars was about twofold higher than the diversity within the local sake-brewing cultivars, which was in contrast to the cooking cultivars. This is most likely due to introgression of the modern cooking cultivars into the modern sake-brewing cultivars through breeding practices. Cluster analysis and chloroplast haplotype analysis suggested that the local sake-brewing cultivars originated monophyletically in the western regions of Japan. Analysis of variance tests showed that several markers were significantly associated with sake-brewing traits, particularly with the large white-core structure.
authors.affiliation: Laboratory of Plant Genetics, Department of Biological and Environmental Science, Faculty of Agriculture, and Graduate School of Science and Technology, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan.
authors.forename: Z
authors.initials: Z
authors.lastname: Hashimoto
authors.forename: N
authors.initials: N
authors.lastname: Mori
authors.forename: M
authors.initials: M
authors.lastname: Kawamura
authors.forename: T
authors.initials: T
authors.lastname: Ishii
authors.forename: S
authors.initials: S
authors.lastname: Yoshida
authors.forename: M
authors.initials: M
authors.lastname: Ikegami
authors.forename: S
authors.initials: S
authors.lastname: Takumi
authors.forename: C
authors.initials: C
authors.lastname: Nakamura
mesh_terms: D000704:Analysis of Variance; D016000:Cluster Analysis; D018556:Crops, Agricultural / Q000235:genetics*; D018742:DNA, Chloroplast / Q000235:genetics; D014644:Genetic Variation; D005843:Geography; D006239:Haplotypes / Q000235:genetics; D007564:Japan; D018598:Minisatellite Repeats / Q000235:genetics; D021141:Nucleic Acid Amplification Techniques; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D012150:Polymorphism, Restriction Fragment Length; D013045:Species Specificity
chemical_list: D018742:DNA, Chloroplast