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Homoeologous relationship of rye chromosome arms as detected with wheat PLUG markers

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Abstract

Based on the similarity in gene structure between rice and wheat, the polymerase chain reaction (PCR)-based landmark unique gene (PLUG) system enabled us to design primer sets that amplify wheat genic sequences including introns. From the previously reported wheat PLUG markers, we chose 144 markers that are distributed on different chromosomes and in known chromosomal regions (bins) to obtain rye-specific PCR-based markers. We conducted PCR with the 144 primer sets and the template of the Imperial rye genomic DNA and found that 131 (91.0 %) primer sets successfully amplified PCR products. Of the 131 PLUG markers, 110 (76.4 %) markers showed rye-specific PCR amplification with or without restriction enzyme digestion. We assigned 79 of the 110 markers to seven rye chromosomes (1R to 7R) using seven wheat–rye (cv. Imperial) chromosome addition and substitution lines: 12 to 1R, 8 to 2R, 11 to 3R, 8 to 4R, 16 to 5R, 12 to 6R, and 12 to 7R. Furthermore, we located their positions on the short or long (L) chromosome arm, using 13 Imperial rye telosomic lines of common wheat (except for 3RL). Referring to the chromosome bin locations of the 79 PLUG markers in wheat, we deduced the syntenic relationships between rye and wheat chromosomes. We also discussed chromosomal rearrangements in the rye genome with reference to the cytologically visible chromosomal gaps.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

CTAB:

Cetyltrimethylammonium bromide

EST:

Expressed sequence tag

FISH:

Fluorescence in situ hybridization

GISH:

Genomic in situ hybridization

PCR:

Polymerase chain reaction

PLUG:

PCR-based landmark unique gene

RAPD:

Random amplified polymorphic DNA

RFLP:

Restriction fragment length polymorphism

SCAR:

Sequence-characterized amplified region

SNP:

Single nucleotide polymorphism

SSR:

Simple sequence repeat

STS:

Sequence-tagged site

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Acknowledgments

We are grateful to Dr. Adam J. Lukaszewski, University of California, USA, and to John Innes Centre, Norwich, UK, for providing us the wheat–rye addition and substitution lines used in this study. This is a contribution (no. 6XX) from the Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Japan.

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Authors and Affiliations

  1. Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan

    Jianjian Li, Takashi R. Endo & Shuhei Nasuda

  2. Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, Morioka, Iwate, 020-0198, Japan

    Mika Saito, Goro Ishikawa & Toshiki Nakamura

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  1. Jianjian Li
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  2. Takashi R. Endo
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  3. Mika Saito
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  4. Goro Ishikawa
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  5. Toshiki Nakamura
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  6. Shuhei Nasuda
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Correspondence to Shuhei Nasuda.

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Fig. S1

FISH (green)/GISH (pink) photomicrographs of the mitotic metaphase cells of the wheat-rye addition and substitution (for 3R) lines. FISH probe: pSc200, GISH probe: rye total genomic DNA. Bar = 10 μm (JPEG 233 kb)

High resolution image (TIFF 940 kb)

Fig. S2

Gel images of the PCR products of the 84 PLUG markers assigned to respective rye chromosomes and chromosome arms. Note that PCR products and restriction enzyme-digested PCR products were separated on 1 % and 4 % agarose gels, respectively (JPEG 2053 kb)

High resolution image (TIFF 5078 kb)

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Li, J., Endo, T.R., Saito, M. et al. Homoeologous relationship of rye chromosome arms as detected with wheat PLUG markers. Chromosoma 122, 555–564 (2013). https://doi.org/10.1007/s00412-013-0428-7

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  • DOI: https://doi.org/10.1007/s00412-013-0428-7

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