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DNA Res. 2014 Jun 27. pii: dsu020. [Epub ahead of print]

A High-Density Genetic Map with Array-Based Markers Facilitates Structural and Quantitative Trait Locus Analyses of the Common Wheat Genome.

Author information

  • 1Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe 657-8501, Japan.
  • 2Core Research Division, Organization of Advanced Science and Technology, Kobe University, Kobe, Japan.
  • 3Bio Research Laboratory, TOYOTA Motor Corporation, Toyota, Aichi 471-8572, Japan.
  • 4Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
  • 5Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe 657-8501, Japan takumi@kobe-u.ac.jp.


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.

© The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.


QTL analysis; array-based genotyping; chromosomal synteny; high-density genetic map; next-generation sequencing

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