Allelic genome structural variations in maize detected by array comparative genome hybridization.
André Beló1, Mary K Beatty, David Hondred
1DuPont Crop Genetics, Route 141, Henry Clay Road, Wilmington, DE 19803, USA. andbelo@gmail.com
TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik
|September 17, 2009
Summary
Copy-number variations (CNVs) are DNA changes impacting large genome segments. This study reveals CNVs are widespread in maize, suggesting they significantly influence plant traits like disease resistance and heterosis.
Area of Science:
- Plant genetics
- Genomics
- Molecular biology
Background:
- Copy-number variations (CNVs), or structural variations (SVs), are DNA polymorphisms affecting large genome segments (>1 kb).
- CNVs have been linked to human diseases but their genomic impact in plants remains largely unexplored.
- Previous studies identified individual structural variations affecting plant traits, but not on a genome-wide scale.
Purpose of the Study:
- To investigate the presence and distribution of CNVs in maize on a genomic scale.
- To assess the frequency and potential origin of CNVs across different maize germplasm subgroups.
- To explore the potential impact of CNVs on maize phenotypes.
Main Methods:
- Utilized array-comparative genome hybridization (aCGH) to compare the genomes of 13 maize inbred lines against the B73 reference genome.
- Analyzed hybridization signal ratios from 60,472 oligonucleotide probes to identify deviations from expected copy-numbers.
- Validated identified CNV regions through further analysis to confirm insertion/deletions and copy-number differences.
Main Results:
- Identified copy-number variations (CNVs) distributed across all chromosome arms in the maize genome.
- Observed CNVs occurring with notable frequency in diverse maize germplasm, indicating an ancient origin.
- Confirmed the presence of both insertion/deletions and copy-number differences within the detected CNV regions.
Conclusions:
- CNVs are a significant feature of the maize genome, present across various inbred lines.
- The widespread distribution and frequency of CNVs suggest they play a crucial role in maize evolution and diversity.
- Detected CNVs likely contribute substantially to plant phenotypes, potentially influencing disease response and heterosis in maize.
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