Gene copy number evolution during tetraploid cotton radiation
1Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
Heredity
|February 18, 2010
Summary
Duplication-resistant (DR) genes are preferentially restored to low copy numbers after polyploidization in cotton. This study reveals gene loss and divergence, particularly in the D genome, contributing to trait variation.
Area of Science:
- Plant genomics
- Evolutionary biology
- Molecular genetics
Background:
- Gene duplication and loss are non-random processes following polyploidization.
- Duplication-resistant (DR) genes are identified by their convergent restoration to a singleton state after multiple genome duplications.
- Understanding the timing of DR gene restoration is crucial for comprehending genome evolution.
Purpose of the Study:
- To investigate the copy number and restoration timeframe of DR genes in cotton.
- To compare gene loss rates between DR genes and randomly selected genes in polyploid cotton.
- To explore genome-specific divergence patterns in tetraploid cotton.
Main Methods:
- Selection of 27 cotton homologs of Arabidopsis DR genes based on Pfam domains.
- Southern hybridization and sequence analysis to determine gene copy numbers in diploid and tetraploid cotton species.
- BAC sequencing to confirm gene loss events.
- Analysis of 5' sequence divergence in relation to gene copy number.
Main Results:
- DR genes exhibited significantly lower copy numbers compared to randomly selected cotton ESTs.
- Three DR genes showed loss of D genome-derived homoeologs in some tetraploid cotton species.
- Gene loss in polyploid cotton was confirmed by BAC sequencing in two instances.
- Divergence in 5' sequences of DR genes correlated with gene copy number.
Conclusions:
- Genes with Pfam domains associated with duplication resistance in Arabidopsis are also preferentially restored to low copy number in recent polyploid cotton.
- The D genome progenitor in tetraploid cotton appears to undergo more gene copy number divergence than the A genome.
- Gene loss and D subgenome-biased alterations in gene expression may contribute to quantitative trait variation in tetraploid cotton.
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