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Gene identification in a complex chromosomal continuum by local genomic cross-referencing
Z Avramova1, A Tikhonov, P SanMiguel
1Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
The Plant Journal : for Cell and Molecular Biology
|December 1, 1996
Summary
Identifying genes in complex plant genomes is challenging. This study uses conserved DNA sequences and grass genome collinearity to efficiently locate genes in sorghum using maize DNA probes.
Area of Science:
- Genomics
- Molecular Biology
- Plant Science
Background:
- Higher plant genomes are complex, featuring repetitive DNA and low-copy sequences, complicating gene identification.
- Mobile repetitive DNA with RNA homology can further obscure gene mapping within chromosomal regions.
Purpose of the Study:
- To develop and validate efficient methods for gene identification in complex plant genomes.
- To utilize genic sequence conservation and grass genome collinearity as tools for gene discovery.
Main Methods:
- A bacterial artificial chromosome (BAC) clone from sorghum was isolated using a maize Adh1 probe.
- The sorghum BAC DNA was hybridized against a contiguous DNA sequence from maize flanking Adh1.
- Cross-hybridization patterns were analyzed to distinguish genes from repetitive elements and retrotransposons.
Main Results:
- Low-copy-number sequences from maize hybridized to the sorghum BAC, while repetitive sequences did not.
- A cross-hybridizing low-copy sequence was identified as a gene; a non-hybridizing one was a retrotransposon (Reina).
- Orthologous regions showed collinearity between sorghum and maize genomes, though more compressed in sorghum.
Conclusions:
- Genomic cross-referencing via hybridization of orthologous clones is an effective and rapid method for gene identification.
- This technique aids in understanding genome organization and comparative genomics between grass species.