Research

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

KwangChul Oh¹, Kristine Hardeman^1,2, Maria G Ivanchenko¹, Mary Ellard-Ivey^1,3, Andreas Nebenführ^1,4, TJ White¹ and Terri L Lomax¹

¹  Department of Botany and Plant Pathology and the Center for Gene Research and Biotechnology, Oregon State University, Corvallis, OR 97331-2902, USA

²  Monsanto-Mystic Research, 62 Maritime Drive, Mystic, CT 06355, USA

³  Department of Biology, Pacific Lutheran University, Tacoma, WA 98447-0003, USA

⁴  Department of Botany, University of Tennessee, Knoxville, TN 37996-1100, USA

author email corresponding author email

Genome Biology 2002, 3:research0049.1-0049.11doi:10.1186/gb-2002-3-9-research0049

Published:	28 August 2002

Subject areas: Plant biology, Genome studies, Genetics, Methods, Model organisms

Abstract

Background

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).

Results

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.

Conclusions

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.