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PMID: 12225588 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Fine mapping in tomato using microsynteny with the Arabidopsis genome: the Diageotropica (Dgt) locus.

Genome biology ·Vol. 3 ·No. 9 ·2002-08-28 ·Pages research0049

Oh K, Hardeman K, Ivanchenko MG, Ellard-Ivey M, Nebenführ A, White TJ, Lomax TL

Abstract

The Arabidopsis thaliana genome sequence provides a catalog of reference genes applicable to comparative microsynteny analysis of other species, facilitating map-based cloning in economically important crops. We have applied such an analysis to the tomato expressed sequence tag (EST) database to expedite high-resolution mapping of the Diageotropica (Dgt) gene within the distal end of chromosome 1 in tomato (Lycopersicon esculentum). A BLAST search of the Arabidopsis database with nucleotide sequences of markers that flank the tomato dgt locus revealed regions of microsynteny between the distal end of chromosome 1 in tomato, two regions of Arabidopsis chromosome 4, and one on chromosome 2. Tomato ESTs homeologous to Arabidopsis gene sequences within those regions were converted into co-dominant molecular markers via cleaved amplified polymorphic sequence (CAPS) analysis and scored against an informative backcross mapping population. Six new microsyntenic EST (MEST) markers were rapidly identified in the dgt region, two of which further defined the placement of the Dgt gene and permitted the selection of a candidate tomato bacterial artificial chromosome clone for sequence analysis. Microsynteny-based comparative mapping combined with CAPS analysis of recombinant plants rapidly and economically narrowed the dgt mapping region from 0.8 to 0.15 cM. This approach should contribute to developing high-density maps of molecular markers to target-specific regions for positional cloning and marker-assisted selection in a variety of plants.

Keywords
Non-programmatic
MeSH Terms
Arabidopsis/genetics Chromosome Mapping/methods Chromosomes, Artificial, Bacterial Chromosomes, Plant Expressed Sequence Tags Gene Order Genes, Plant Genetic Markers Genome, Plant Lycopersicon esculentum/genetics Random Amplified Polymorphic DNA Technique Synteny
Chemicals
Genetic Markers
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Oh KwangChul
Department of Botany and Plant Pathology and the Center for Gene Research and Biotechnology, Oregon State University, Corvallis, OR 97331-2902, USA.
Hardeman Kristine
Ivanchenko Maria G
Ellard-Ivey Mary
Nebenführ Andreas
White T J
Lomax Terri L
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/gb-2002-3-9-research0049
Published
2002-08-28
Epub
2002-00-28
Pages
research0049
Language
English
Region
England
NLM ID
100960660
PMCID
PMC126874
Subset
IM
External Links
PubMed source DOI: 10.1186/gb-2002-3-9-research0049 PMC Full Text View journal details
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