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A microcolinearity study at the earliness per se gene Eps-A m 1 region reveals an ancient duplication that preceded the wheat–rice divergence

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Abstract

Wheat flowering is controlled by numerous genes, which respond to environmental signals such as photoperiod and vernalization. Earliness per se (Eps) genes control flowering time independently of these environmental cues and are responsible for the fine tuning of flowering time. We recently mapped the Eps-A m 1 gene on the end of Triticum monococcum chromosome arm 1AmL. As a part of our efforts to clone Eps-A m 1 we developed PCR markers flanking this gene within a 2.7 cM interval. We screened more than one thousand gametes with these markers and identified 27 lines with recombination between them. Recombinant lines were used to generate a high-density map and to investigate the microcolinearity between wheat and rice in this region. We mapped ten genes from a 149 kb region located at the distal part of rice chromosome 5 (cdo393 – Ndk3) on a 3.7 cM region on wheat chromosome one. This region is part of an ancient duplication between rice chromosomes 5 and 1. Genes present in both rice chromosomes were less similar to each other than to the closest wheat orthologues, suggesting that this duplication preceded the divergence between wheat and rice. This hypothesis was supported by the presence of 18 loci duplicated both in rice chromosomes 5 and 1 and in the colinear wheat chromosomes from homoeologous groups 1 and 3. Independent gene deletions in wheat and rice lineages explain the alternations of colinearity between rice chromosome 5 and wheat chromosomes 1 and 3. Colinearity between the end of rice chromosome 5 and wheat chromosome 1 was also interrupted by a small inversion, and several non-colinear genes. These results suggest that the distal region of the long arm of wheat chromosome 1 was involved in numerous changes that differentiated wheat and rice genomes. This comparative study provided sufficient markers to saturate the Eps-A m 1 gene region and to precisely map this gene within a 0.9 cM interval flanked by the VatpC and Smp loci.

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Acknowledgements

This project was supported by the National Research Initiative of the USDA Cooperative State Research, Education and Extension Service, grant number 2003-00703. The authors thank Lenka Valarikova for excellent technical assistance.

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  1. A. M. Linkiewicz

    Present address: Department of Biotechnology and Cytogenetics, Plant Breeding and Acclimatization Institute Radzików, 05-870, Blonie, Poland

Authors and Affiliations

  1. Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA

    M. Valárik, A. M. Linkiewicz & J. Dubcovsky

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  1. M. Valárik
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Correspondence to J. Dubcovsky.

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Communicated by P. Langridge

Sequencesobtained in this study: DQ196178, DQ196179, DQ196180, DQ196181, DQ196182, DQ196183, DQ196184, DQ196185, DQ196186, DQ196187, DQ196488, DQ198537, DQ308530, DQ308531, DQ308532, DQ308533, DQ308534, DQ308535, DQ308536, DQ308537, DQ308538, DQ308539, DQ308540

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Valárik, M., Linkiewicz, A.M. & Dubcovsky, J. A microcolinearity study at the earliness per se gene Eps-A m 1 region reveals an ancient duplication that preceded the wheat–rice divergence. Theor Appl Genet 112, 945–957 (2006). https://doi.org/10.1007/s00122-005-0198-6

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