Genetic dissection of transcriptional regulation by cDNA-AFLP

Plant J. 2006 Feb;45(3):439-46. doi: 10.1111/j.1365-313X.2005.02630.x.


This study demonstrates that cDNA-AFLP is a powerful gel-based genome-scale transcript profiling technique to generate quantitative gene expression profiles for eQTL mapping. We used cDNA-AFLP to monitor the relative abundance of 912 transcripts across 50 Arabidopsis thaliana recombinant inbred lines. Estimates for heritability of cDNA-AFLP intensity polymorphisms were high, with a median of 0.30 and an interquartile range of 0.21-0.44. A total of 198 expression polymorphisms were significantly linked to specific chromosomal regions (P < 0.05). Both cis- and trans-acting loci correlated with the variation in gene expression levels were found. Some of the trans-acting loci correlated to multiple expression polymorphisms, suggesting trans-acting alleles with widespread transcriptional effects. Here, we have illustrated that cDNA-AFLP constitutes a powerful transcript profiling method that can be utilized for 'multifactorial genomics' analysis of any plant or animal species for which segregating populations and molecular marker maps are available.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics
  • Chromosome Mapping
  • DNA, Complementary* / metabolism
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation, Plant*
  • Genomics / methods
  • Phenotype
  • Polymerase Chain Reaction / methods
  • Polymorphism, Genetic*
  • Quantitative Trait Loci*
  • RNA, Messenger / analysis
  • Transcription, Genetic


  • DNA, Complementary
  • RNA, Messenger