title: Genome-wide identification of novel genetic markers from RNA sequencing assembly of diverse Aegilops tauschii accessions.
abstract: The wild species in the Triticeae tribe are tremendous resources for crop breeding due to their abundant natural variation. However, their huge and highly repetitive genomes have hindered the establishment of physical maps and the completeness of their genome sequences. To develop molecular markers for the efficient utilization of their valuable traits while avoiding their genome complexity, we assembled RNA sequences of ten representative accessions of Aegilops tauschii, the progenitor of the wheat D genome, and estimated single nucleotide polymorphisms (SNPs) and insertions/deletions (indels). The deduced unigenes were anchored to the chromosomes of Ae. tauschii and barley. The SNPs and indels in the anchored unigenes, covering entire chromosomes, were sufficient for linkage map construction, even in combinations between the genetically closest accessions. Interestingly, the resolution of SNP and indel distribution on barley chromosomes was slightly higher than on Ae. tauschii chromosomes. Since barley chromosomes are regarded as virtual chromosomes of Triticeae species, our strategy allows capture of genetic markers arranged on the chromosomes in order based on the conserved synteny. The resolution of these genetic markers will be comparable to that of the Ae. tauschii whose draft genome sequence is available. Our procedure should be applicable to marker development for Triticeae species, which have no draft sequences available.
authors.affiliation: Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Japan.
authors.forename: Ryo
authors.initials: R
authors.lastname: Nishijima
authors.affiliation: Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Japan. kentaro.yoshida@port.kobe-u.ac.jp.
authors.forename: Kentaro
authors.initials: K
authors.lastname: Yoshida
authors.affiliation: Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan.
authors.forename: Yuka
authors.initials: Y
authors.lastname: Motoi
authors.affiliation: Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan.
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Sato
authors.affiliation: Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Japan.
authors.forename: Shigeo
authors.initials: S
authors.lastname: Takumi
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant / Q000235:genetics; D008040:Genetic Linkage; D005819:Genetic Markers; D018745:Genome, Plant; D001467:Hordeum / Q000235:genetics*; D054643:INDEL Mutation; D010802:Phylogeny; D006109:Poaceae / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D005819:Genetic Markers
keywords: Aegilops tauschii; DNA markers; Hordeum vulgare; RNA sequencing; Synteny