Comparative Fluorescence in Situ Hybridization Mapping of a 431-kb Arabidopsis thaliana Bacterial Artificial Chromosome Contig Reveals the Role of Chromosomal Duplications in the Expansion of the Brassica rapa Genome

Abstract Comparative genome studies are important contributors to our understanding of genome evolution. Most comparative genome studies in plants have been based on genetic mapping of homologous DNA loci in different genomes. Large-scale comparative physical mapping has been hindered by the lack of efficient and affordable techniques. We report here the adaptation of fluorescence in situ hybridization (FISH) techniques for comparative physical mapping between Arabidopsis thaliana and Brassica rapa. A set of six bacterial artificial chromosomes (BACs) representing a 431-kb contiguous region of chromosome 2 of A. thaliana was mapped on both chromosomes and DNA fibers of B. rapa. This DNA fragment has a single location in the A. thaliana genome, but hybridized to four to six B. rapa chromosomes, indicating multiple duplications in the B. rapa genome. The sizes of the fiber-FISH signals from the same BACs were not longer in B. rapa than those in A. thaliana, suggesting that this genomic region is duplicated but not expanded in the B. rapa genome. The comparative fiber-FISH mapping results support that chromosomal duplications, rather than regional expansion due to accumulation of repetitive sequences in the intergenic regions, played the major role in the evolution of the B. rapa genome.

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High-resolution physical mapping in Arabidopsis thaliana and tomato by fluorescence in situ hybridization to extended DNA fibres

The Plant Journal ◽

10.1046/j.1365-313x.1996.09030421.x ◽

1996 ◽

Vol 9 (3) ◽

pp. 421-430 ◽

Cited By ~ 143

Author(s):

Paul F. Fransz ◽

Carlos Alonso-Blanco ◽

Tsvetana B. Liharska ◽

Anton J.M. Peeters ◽

Pim Zabel ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

In Situ Hybridization ◽

High Resolution ◽

Fluorescence In Situ Hybridization ◽

Physical Mapping ◽

Extended Dna Fibres

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Physical mapping of DNA repetitive sequences to mitotic and meiotic chromosomes of Brassica oleracea var. alboglabra by fluorescence in situ hybridization

Heredity ◽

10.1046/j.1365-2540.1998.00432.x ◽

1998 ◽

Vol 81 (6) ◽

pp. 666-673 ◽

Cited By ~ 37

Author(s):

Susan J Armstrong ◽

Paul Fransz ◽

David F Marshall ◽

Gareth H Jones

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Brassica Oleracea ◽

Physical Mapping ◽

Repetitive Sequences ◽

Meiotic Chromosomes ◽

Dna Repetitive Sequences

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Application of fiber-FISH in physical mapping of Arabidopsis thaliana

Genome ◽

10.1139/g98-093 ◽

1998 ◽

Vol 41 (4) ◽

pp. 566-572 ◽

Cited By ~ 46

Author(s):

Scott A Jackson ◽

Ming Li Wang ◽

Howard M Goodman ◽

Jiming Jiang

Keyword(s):

Arabidopsis Thaliana ◽

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Physical Mapping ◽

Molecular Techniques ◽

Fish Analysis ◽

Contig Assembly ◽

Fish Technique ◽

Bac Clones

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 fibers 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, mi167, 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 the 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. Key words: fluorescence in situ hybridization, DNA fibers, physical mapping, genome analysis.

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Physical mapping of the 5S ribosomal RNA genes in Arabidopsis thaliana by multi-color fluorescence in situ hybridization with cosmid clones

The Plant Journal ◽

10.1046/j.1365-313x.1997.12010031.x ◽

1997 ◽

Vol 12 (1) ◽

pp. 31-37 ◽

Cited By ~ 73

Author(s):

Minoru Murata ◽

J.S. Heslop-Harrison ◽

Fusao Motoyoshi

Keyword(s):

Arabidopsis Thaliana ◽

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Ribosomal Rna ◽

Physical Mapping ◽

Ribosomal Rna Genes ◽

5S Ribosomal Rna ◽

Rna Genes

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Physical mapping of barley genes using an ultrasensitive fluorescence in situ hybridization technique

Genome ◽

10.1139/g03-084 ◽

2004 ◽

Vol 47 (1) ◽

pp. 179-189 ◽

Cited By ~ 29

Author(s):

J L Stephens ◽

S E Brown ◽

N L.V Lapitan ◽

D L Knudson

Keyword(s):

In Situ Hybridization ◽

Hordeum Vulgare ◽

Fluorescence In Situ Hybridization ◽

Linkage Map ◽

Physical Mapping ◽

Physical Map ◽

Primary Objective ◽

Hybridization Technique ◽

Hordeum Vulgare L

The primary objective of this study was to elucidate gene organization and to integrate the genetic linkage map for barley (Hordeum vulgare L.) with a physical map using ultrasensitive fluorescence in situ hybridization (FISH) techniques for detecting signals from restriction fragment length polymorphism (RFLP) clones. In the process, a single landmark plasmid, p18S5Shor, was constructed that identified and oriented all seven of the chromosome pairs. Plasmid p18S5Shor was used in all hybridizations. Fourteen cDNA probes selected from the linkage map for barley H. vulgare 'Steptoe' × H. vulgare 'Morex' (Kleinhofs et al. 1993) were mapped using an indirect tyramide signal amplification technique and assigned to a physical location on one or more chromosomes. The haploid barley genome is large and a complete physical map of the genome is not yet available; however, it was possible to integrate the linkage map and the physical locations of these cDNAs. An estimate of the ratio of base pairs to centimorgans was an average of 1.5 Mb/cM in the distal portions of the chromosome arms and 89 Mb/cM near the centromere. Furthermore, while it appears that the current linkage maps are well covered with markers along the length of each arm, the physical map showed that there are large areas of the genome that have yet to be mapped.Key words: Hordeum vulgare, barley, physical mapping, FISH, cDNA, genetics, linkage, chromosome, BACs.

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