Application of fiber-FISH in physical mapping of Arabidopsis thaliana

• Published in: Genome Vol. 41; no. 4; pp. 566 - 572
• Main Authors: Jackson, S.A, Wang, M.L, Goodman, H.M, Jiang, J
• Format: Journal Article
• Language: English
• Published: Ottawa, Canada NRC Research Press 01.08.1998; Canadian Science Publishing NRC Research Press
• Subjects: Arabidopsis - genetics; Arabidopsis thaliana; bacterial artificial chromosomes; Chromosome Mapping; Chromosomes; Contig Mapping; cytogenetics; Deoxyribonucleic acid; DNA; DNA libraries; DNA Probes; DNA, Plant - genetics; Fibers; Flowers & plants; Fluorescence; fluorescence in situ hybridization; genetic markers; Genetics; Hybridization; In Situ Hybridization, Fluorescence; loci; nucleic acid hybridization; nucleotide sequences; Plant species; repetitive sequences; Tomatoes
• ISSN: 0831-2796; 1480-3321
• DOI: 10.1139/g98-093

Arabidopsis thaliana has become a model plant species for genetic studies because of its small genome and short juvenility period. However, the small chromosomes of this species are not suitable for classical cytogenetic studies. Here we demonstrate that the fluorescence in situ hybridization (FISH) technique using extended DNA fiber can be a powerful tool in the physical mapping of the A. thaliana genome. Using a refined fiber-FISH technique we were able to measure DNA clusters as long as 1.71 Mb, more than 1% of the A. thaliana genome. Several small DNA loci, including the telomeres and a dispersed repetitive DNA sequence, mil67, were also analyzed with this technique. The results show that without known adjacent DNA markers such small DNA loci cannot be mapped precisely using fiber-FISH. One of the most difficult obstacles in physical mapping by contig assembly is closing the gaps that are present between adjacent contigs. Currently available molecular techniques are not sufficient to accurately estimate physical sizes of these gaps. We isolated bacterial artificial chromosome (BAC) clones bordering gaps 2 and 3 on the physical contig map of A. thaliana chromosome II. The BAC clones were used in fiber-FISH analysis and the physical sizes of the two gaps were estimated as 31 kb and more than 500 kb, respectively. Thus, we have demonstrated that fiber-FISH is an efficient technique for determining the physical size of gaps on molecular contig maps.