- THIS ARTICLE
- Full Text
- Full Text (PDF)
- Supporting Information
-
All Versions of this Article:
genetics.109.106591v1
183/3/1153 most recent - Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Email this article to a friend
- Related articles in Genetics
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
- Reprints & Permissions
- GOOGLE SCHOLAR
- Articles by Thumma, B. R.
- Articles by Southerton, S. G.
- PUBMED
- PubMed Citation
- Articles by Thumma, B. R.
- Articles by Southerton, S. G.
Originally published as Genetics Published Articles Ahead of Print on September 7, 2009.
Genetics, Vol. 183, 1153-1164, November 2009, Copyright © 2009
doi:10.1534/genetics.109.106591
Identification of a Cis-Acting Regulatory Polymorphism in a Eucalypt COBRA-Like Gene Affecting Cellulose Content
Bala R. Thumma*,1,
Bronwyn A. Matheson*,
Deqiang Zhang*,2,
Christian Meeske*,
Roger Meder*,
Geoff M. Downes
and
Simon G. Southerton*
* Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Canberra, Australian Capital Territory 2601, Australia and CSIRO Sustainable Ecosystems, Hobart, Tasmania 7001, Australia
1 Corresponding author: CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia.
E-mail: reddy.thumma{at}csiro.au
Populations with low linkage disequilibrium (LD) offer unique opportunities to study functional variants influencing quantitative traits. We exploited the low LD in forest trees to identify functional polymorphisms in a Eucalyptus nitens COBRA-like gene (EniCOBL4A), whose Arabidopsis homolog has been implicated in cellulose deposition. Linkage analysis in a full-sib family revealed that EniCOBL4A is the most strongly associated marker in a quantitative trait locus (QTL) region for cellulose content. Analysis of LD by genotyping 11 common single-nucleotide polymorphisms (SNPs) and a simple sequence repeat (SSR) in an association population revealed that LD declines within the length of the gene. Using association studies we fine mapped the effect of the gene to SNP7, a synonymous SNP in exon 5, which occurs between two small haplotype blocks. We observed patterns of allelic expression imbalance (AEI) and differential binding of nuclear proteins to the SNP7 region that indicate that SNP7 is a cis-acting regulatory polymorphism affecting allelic expression. We also observed AEI in SNP7 heterozygotes in a full-sib family that is linked to heritable allele-specific methylation near SNP7. This study demonstrates the potential to reveal functional polymorphisms underlying quantitative traits in low LD populations.
Related articles in Genetics:
ISSUE HIGHLIGHTS
Genetics 2009 183: NP.
 |