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


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Article Info

DATE

2006-02-24

AUTHORS

Laura Rossini, Alberto Vecchietti, Letizia Nicoloso, Nils Stein, Simona Franzago, Francesco Salamini, Carlo Pozzi

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. More... »

PAGES

1073-1085

References to SciGraph publications

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  • 2004-09-03. Comparative high resolution map of the six‐rowed spike locus 1 (vrs1) in several populations of barley, Hordeum vulgare L. in HEREDITAS
  • 1993-07. A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome in THEORETICAL AND APPLIED GENETICS
  • 1995-04. The barley Hooded mutation caused by a duplication in a homeobox gene intron in NATURE
  • 2001-12. Map Manager QTX, cross-platform software for genetic mapping in MAMMALIAN GENOME
  • 2001. Generation and Comparison of EST‐Derived SSRs and SNPs in Barley (Hordeum Vulgare L.) in HEREDITAS
  • 2004-01-22. Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat in FUNCTIONAL & INTEGRATIVE GENOMICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s00122-006-0209-2

    DOI

    http://dx.doi.org/10.1007/s00122-006-0209-2

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/16501940


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    35 schema:description 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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    42 FRIZZY PANICLE
    43 MB
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    46 SNP mapping
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