Use of cDNA-AFLP for transcript profiling in narrow genetic pools; for example, cucumber (Cucumis sativus L.)

Abstract

A cDNA-AFLP transcript profiling was employed to examine three representative tissues (seedling, ovary and leaf) of nine Korean cucumber (Cucumis sativus L.) F1 hybrids. Differential accumulation of transcript-derived fragments (TDFs) was detected in 92 profiles. Genetic distance-based cluster analysis partitioned these hybrids into four main groupings, consistent with their phenotypic relationships. Although several polymorphic profiles were confirmed by reverse transcriptase polymerase chain reaction (RT-PCR) analysis, many were not reproducible, indicating that a large portion of the observed polymorphisms were based on sequence variation of transcripts rather than expression of variation. Thus, it is proposed that cDNA-AFLP profiling be based on a dual descriptor system (sequence and expression). Data indicate that such a system would provide an efficient genetic marker system for identifying polymorphisms in narrow genetic pools. © 2006 Blackwell Verlag.