Quantitative transcript analysis in plants: improved first-strand cDNA synthesis

Gene expression profiling via LongSAGE in a non-model plant species: a case study in seeds of Brassica napus

BACKGROUND

Serial analysis of gene expression (LongSAGE) was applied for gene expression profiling in seeds of oilseed rape (Brassica napus ssp. napus). The usefulness of this technique for detailed expression profiling in a non-model organism was demonstrated for the highly complex, neither fully sequenced nor annotated genome of B. napus by applying a tag-to-gene matching strategy based on Brassica ESTs and the annotated proteome of the closely related model crucifer A. thaliana.

RESULTS

Transcripts from 3,094 genes were detected at two time-points of seed development, 23 days and 35 days after pollination (DAP). Differential expression showed a shift from gene expression involved in diverse developmental processes including cell proliferation and seed coat formation at 23 DAP to more focussed metabolic processes including storage protein accumulation and lipid deposition at 35 DAP. The most abundant transcripts at 23 DAP were coding for diverse protease inhibitor proteins and proteases, including cysteine proteases involved in seed coat formation and a number of lipid transfer proteins involved in embryo pattern formation. At 35 DAP, transcripts encoding napin, cruciferin and oleosin storage proteins were most abundant. Over both time-points, 18.6% of the detected genes were matched by Brassica ESTs identified by LongSAGE tags in antisense orientation. This suggests a strong involvement of antisense transcript expression in regulatory processes during B. napus seed development.

CONCLUSION

This study underlines the potential of transcript tagging approaches for gene expression profiling in Brassica crop species via EST matching to annotated A. thaliana genes. Limits of tag detection for low-abundance transcripts can today be overcome by ultra-high throughput sequencing approaches, so that tag-based gene expression profiling may soon become the method of choice for global expression profiling in non-model species.

Genetic and epigenetic alterations after hybridization and genome doubling

Hybridization and polyploidization are now recognized as major phenomena in the evolution of plants, promoting genetic diversity, adaptive radiation and speciation. Modern molecular techniques have recently provided evidence that allopolyploidy can induce several types of genetic and epigenetic events that are of critical importance for the evolutionary success of hybrids: (1) chromosomal rearrangements within one or both parental genomes contribute toward proper meiotic pairing and isolation of the hybrid from its progenitors; (2) demethylation and activation of dormant transposable elements may trigger insertional mutagenesis and changes in local patterns of gene expression, facilitating rapid genomic reorganisation; (3) rapid and reproducible loss of low copy DNA sequence appears to result in further differentiation of homoeologous chromosomes; and (4) organ-specific up- or down-regulation of one of the duplicated genes, resulting in unequal expression or silencing one copy. All these alterations also have the potential, while stabilizing allopolyploid genomes, to produce novel expression patterns and new phenotypes, which together with increased heterozygosity and gene redundancy might confer on hybrids an elevated evolutionary potential, with effects at scales ranging from molecular to ecological. Although important advances have been made in understanding genomic responses to allopolyploidization, further insights are still expected to be gained in the near future, such as the direction and nature of the diploidization process, functional relevance of gene expression alterations, molecular mechanisms that result in adaptation to different ecologies/habitats, and ecological and evolutionary implications of recurrent polyploidization.