Candidate genes for barley mutants involved in plant architecture: an in silico approach |
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Authors: | Laura Rossini Alberto Vecchietti Letizia Nicoloso Nils Stein Simona Franzago Francesco Salamini Carlo Pozzi |
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Institution: | (1) Dipartimento di Produzione Vegetale, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy;(2) Fondazione Parco Tecnologico Padano, Località Cascina Codazza, Via Einstein, 26900 Lodi, Italy;(3) Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany |
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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.
Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users. |
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