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Candidate genes for barley mutants involved in plant architecture: an in silico approach

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Abstract

To individuate candidate genes (CGs) for a set of barley developmental mutants, a synteny approach comparing the genomes of barley and rice has been introduced. Based on map positions of mutants, sequenced RFLP markers linked to the target loci were selected. The markers were mapped in silico by BLAST searches against the rice genome sequence and chromosomal regions syntenous to barley target intervals were identified. Rice syntenous regions were defined for 15 barley chromosomal intervals hosting 23 mutant loci affecting plant height (brh1; brh2; sld4), shoot and inflorescence branching (als; brc1; cul-2, -3, -5, -15, -16; dub1; mnd6; vrs1), development of leaves (lig) and leaf-like organs (cal-b19, -C15, -d4; lks5; suKD-25; suKE-74; suKF-76; trd; trp). Annotation of 110 Mb of rice genomic sequence made it possible to screen for putative CGs which are listed together with the reasons supporting mutant–gene associations. For two loci, CGs were identified with a clear probability to represent the locus considered. These include FRIZZY PANICLE, a candidate for the brc1 barley mutant, and the rice ortholog of maize Liguleless1 (Lg1), a candidate for the barley lig locus on chromosome 2H. For this locus, the validity of the approach was supported by the PCR-amplification of a genomic fragment of the orthologous barley sequence. SNP mapping located this fragment on chromosome 2H in the region hosting the lig genetic locus.

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Acknowledgements

We are grateful to David Horner for help with phylogenetic analysis and automation of in silico synteny analyses. This research was supported by a grant to F.S. from the Ministero dell’Istruzione, dell’Università e della Ricerca (MIUR), FIRB project FUNCTIONMAP (RBAU01MHMR_002).

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Authors and Affiliations

  1. Dipartimento di Produzione Vegetale, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy

    Laura Rossini, Letizia Nicoloso, Simona Franzago & Francesco Salamini

  2. Fondazione Parco Tecnologico Padano, Località Cascina Codazza, Via Einstein, 26900, Lodi, Italy

    Alberto Vecchietti, Francesco Salamini & Carlo Pozzi

  3. Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Gatersleben, Germany

    Nils Stein

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  1. Laura Rossini
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  2. Alberto Vecchietti
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  3. Letizia Nicoloso
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  4. Nils Stein
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  5. Simona Franzago
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  6. Francesco Salamini
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  7. Carlo Pozzi
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Correspondence to Carlo Pozzi.

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Communicated by J. W. Snape

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Rossini, L., Vecchietti, A., Nicoloso, L. et al. Candidate genes for barley mutants involved in plant architecture: an in silico approach. Theor Appl Genet 112, 1073–1085 (2006). https://doi.org/10.1007/s00122-006-0209-2

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  • DOI: https://doi.org/10.1007/s00122-006-0209-2

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