Mass cloning of differential and nondifferential transcript-derived fragments from cDNA-AFLP experiments in sunflower

We have developed a 1-step procedure for cloning multiple bands obtained through cDNA-amplified fragment length polymorphism (AFLP) experiments. This protocol enables us to clone differential and nondifferential transcript-derived fragments (TDFs) in the same experiment. It consists of a mass cloning of cDNA-AFLP amplification products, identification of clones of interest with electrophoresis, and characterization through sequencing. The entire experiment can be performed in 1 wk because of the reduced time and effort needed for cloning, and it can be applied to any PCR method that produces complex band patterns. This method, tested on a comparison of gene expression between globular and heart embryo stages in sunflower embryogenesis, enabled us to clone 10 differential TDFs in the same experiment.