title: A high-density genetic map with array-based markers facilitates structural and quantitative trait locus analyses of the common wheat genome.
abstract: The large genome and allohexaploidy of common wheat have complicated construction of a high-density genetic map. Although improvements in the throughput of next-generation sequencing (NGS) technologies have made it possible to obtain a large amount of genotyping data for an entire mapping population by direct sequencing, including hexaploid wheat, a significant number of missing data points are often apparent due to the low coverage of sequencing. In the present study, a microarray-based polymorphism detection system was developed using NGS data obtained from complexity-reduced genomic DNA of two common wheat cultivars, Chinese Spring (CS) and Mironovskaya 808. After design and selection of polymorphic probes, 13,056 new markers were added to the linkage map of a recombinant inbred mapping population between CS and Mironovskaya 808. On average, 2.49 missing data points per marker were observed in the 201 recombinant inbred lines, with a maximum of 42. Around 40% of the new markers were derived from genic regions and 11% from repetitive regions. The low number of retroelements indicated that the new polymorphic markers were mainly derived from the less repetitive region of the wheat genome. Around 25% of the mapped sequences were useful for alignment with the physical map of barley. Quantitative trait locus (QTL) analyses of 14 agronomically important traits related to flowering, spikes, and seeds demonstrated that the new high-density map showed improved QTL detection, resolution, and accuracy over the original simple sequence repeat map.
authors: Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe 657-8501, Japan.
authors: Julio Cesar Masaru
authors: JC
authors: Iehisa
authors: Core Research Division, Organization of Advanced Science and Technology, Kobe University, Kobe, Japan.
authors: Ryoko
authors: R
authors: Ohno
authors: Bio Research Laboratory, TOYOTA Motor Corporation, Toyota, Aichi 471-8572, Japan.
authors: Tatsuro
authors: T
authors: Kimura
authors: Bio Research Laboratory, TOYOTA Motor Corporation, Toyota, Aichi 471-8572, Japan.
authors: Hiroyuki
authors: H
authors: Enoki
authors: Bio Research Laboratory, TOYOTA Motor Corporation, Toyota, Aichi 471-8572, Japan.
authors: Satoru
authors: S
authors: Nishimura
authors: Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe 657-8501, Japan.
authors: Yuki
authors: Y
authors: Okamoto
authors: Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
authors: Shuhei
authors: S
authors: Nasuda
authors: Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe 657-8501, Japan takumi@kobe-u.ac.jp.
authors: Shigeo
authors: S
authors: Takumi
mesh_terms: D002874:Chromosome Mapping; D003198:Computer Simulation; D008040:Genetic Linkage; D005819:Genetic Markers; D018745:Genome, Plant; D001467:Hordeum / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D011110:Polymorphism, Genetic; D040641:Quantitative Trait Loci; D014908:Triticum / Q000235:genetics*
chemical_list: D005819:Genetic Markers
keywords: QTL analysis; array-based genotyping; chromosomal synteny; high-density genetic map; next-generation sequencing