Abstract
In cultivated barley (Hordeum vulgare ssp. vulgare), six-rowed spikes produce three times as many seeds per spike as do two-rowed spikes. The determinant of this trait is the Mendelian gene vrs1, located on chromosome 2H, which is syntenous with rice (Oryza sativa) chromosomes 4 and 7. We exploited barley–rice micro-synteny to increase marker density in the vrs1 region as a prelude to its map-based cloning. The rice genomic sequence, covering a 980 kb contig, identified barley ESTs linked to vrs1. A high level of conservation of gene sequence was obtained between barley chromosome 2H and rice chromosome 4. A total of 22 EST-based STS markers were placed within the target region, and the linear order of these markers in barley and rice was identical. The genetic window containing vrs1 was narrowed from 0.5 to 0.06 cM, which facilitated covering the vrs1 region by a 518 kb barley BAC contig. An analysis of the contig sequence revealed that a rice Vrs1 orthologue is present on chromosome 7, suggesting a transposition of the chromosomal segment containing Vrs1 within barley chromosome 2H. The breakdown of micro-collinearity illustrates the limitations of synteny cloning, and stresses the importance of implementing genomic studies directly in the target species.
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Acknowledgements
We thank M. Sameri, S. Okamura, M. Chono, J. Song and Y. Nagamura for their help and advice. We also thank M. Matsuoka, Y. Turuspekov and P. Azhaguvel for useful discussions. We thank R. Koebner for linguistic assistance in the preparation of this manuscript. The financial support of the Ministry of Agriculture, Forestry and Fisheries of Japan is acknowledged (Rice Genome Project MP1113b and Green Techno Project GD3006). M. Pourkheirandish was a research fellow supported by Japan International Research Center for Agricultural Sciences (JIRCAS).
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Pourkheirandish, M., Wicker, T., Stein, N. et al. Analysis of the barley chromosome 2 region containing the six-rowed spike gene vrs1 reveals a breakdown of rice–barley micro collinearity by a transposition. Theor Appl Genet 114, 1357–1365 (2007). https://doi.org/10.1007/s00122-007-0522-4
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DOI: https://doi.org/10.1007/s00122-007-0522-4