Theoretical and Applied Genetics

, Volume 118, Issue 3, pp 499–514

Localization of anchor loci representing five hundred annotated rice genes to wheat chromosomes using PLUG markers


  • Goro Ishikawa
    • Tohoku National Agriculture Research Center
    • Tohoku National Agriculture Research Center
  • Taizo Ashida
    • Graduate School of AgricultureKyoto University
  • Mika Saito
    • Tohoku National Agriculture Research Center
  • Shuhei Nasuda
    • Graduate School of AgricultureKyoto University
  • Takashi R. Endo
    • Graduate School of AgricultureKyoto University
  • Jianzhong Wu
    • National Institute of Agrobiological Sciences
  • Takashi Matsumoto
    • National Institute of Agrobiological Sciences
Original Paper

DOI: 10.1007/s00122-008-0916-y

Cite this article as:
Ishikawa, G., Nakamura, T., Ashida, T. et al. Theor Appl Genet (2009) 118: 499. doi:10.1007/s00122-008-0916-y


PCR-based Landmark Unique Gene (PLUG) markers are EST-PCR markers developed based on the orthologous gene conservation between rice and wheat, and on the intron polymorphisms among the three orthologous genes derived from the A, B and D genomes of wheat. We designed a total of 960 primer sets from wheat ESTs that showed high similarity with 951 single-copy rice genes. When genomic DNA of Chinese Spring wheat was used as a template, 872 primer sets amplified one to five distinct products. Out of these 872 PLUG markers, 531 were assigned to one or more chromosomes by nullisomic-tetrasomic analysis. For each wheat chromosome, the number of loci detected ranged from 32 for chromosome 6A to 73 for chromosome 7D, with an average of 48 loci per chromosome. Several novel synteny perturbations were identified using deletion bin-mapping of markers. Furthermore, we demonstrated that PLUG markers can be used as probes to simultaneously identify BAC clones that contain homoeologous regions from all three genomes.

Supplementary material

122_2008_916_MOESM1_ESM.xls (290 kb)
Supplementary material 1 PLUG primer sequences, wheat ESTs and rice genes, and summary of PCR and mapping results. In the ‘no. of products’ column, ‘m’ indicates the primer set amplified multiple non-specific products. S, H and T in the ‘detection’ column indicate that the product from the specific genome can be distinguished by size polymorphism of the PCR product, or of the HaeIII-digested or TaqI-digested product, respectively. Asterisks in the last columns indicate markers correspond to the probes used in the NSF deletion-bin mapping project ( (XLS 289 kb)
122_2008_916_MOESM2_ESM.xls (69 kb)
Supplementary material 2 Aneuploid lines of Chinese Spring used in this study. The NBRP-Wheat strain ID designation is shown. Lines used in this study, and those used by Qi et al. (2003) are indicated, and updated FL values based on each study are given. (XLS 69 kb)
122_2008_916_MOESM3_ESM.pdf (4.4 mb)
Supplementary material 3 Gel-documentation for the nullisomic-tetrasomic analysis of the 154 PLUG markers used in deletion-bin mapping. Rose, yellow and blue asterisks in the photos indicate that the band is derived from the A, B or D genome, respectively. PCR products and restriction enzyme-digested PCR products were separated on 1% and 4% agarose gels, respectively. (PDF 4469 kb)
122_2008_916_MOESM4_ESM.pdf (72 kb)
Supplementary material 4 Comparative maps of wheat and rice orthologous chromosomes. Arrows beside the rice chromosomes indicate centromere positions. The C-banding patterns and deletion breakpoints of Chinese Spring chromosomes were taken from Endo and Gill (1996). (PDF 72 kb)

Copyright information

© Springer-Verlag 2008