High resolution diel transcriptomes of autotetraploid potato reveal expression and sequence conservation among rhythmic genes

Background Photoperiodic changes in diel cycles of gene expression are
pervasive in plants. The timing of circadian regulators, together with
light signals, regulate multiple photoperiod-dependent responses such as
growth, flowering or tuber formation. However, for most genes, the
importance of cyclic mRNA levels is less clear. We analyzed the diel
transcriptome of modern cultivated potato, a highly heterozygous
autotetraploid. Clonal propagation and limited meiosis have led to the
accumulation of deleterious alleles, making tetraploid potato an ideal
model system to investigate the conservation of cyclic expression and
cyclic genes during artificial selection and clonal propagation. Results
Our results indicate that rhythmic alleles of cultivated potato were more
highly expressed than non-rhythmic genes and were highly co-expressed not
only under diel cycles but also across tissues, developmental stages, and
stress conditions. Moreover, the smaller ratio of non-synonymous to
synonymous differences within rhythmic versus non-rhythmic allelic groups
indicates that cyclic genes, in general, have more conserved core
functions than non-cyclic genes. In accordance with this observation,
fully rhythmic allelic groups were highly enriched in photosynthesis and
ribosome biogenesis genes, which have core functions in plants.
Furthermore, we investigated differences in cyclic expression patterns
between photoperiod identifying potential regulators of the strong
photoperiodic change in phase of expression for ribosome biogenesis and
pathogen response genes. Finally, analyses of genes involved in tuber
formation suggests that the regulation of CO gene transcription is not the
only factor enabling tuberization under long days in modern cultivated
potato. Conclusions This study not only provides high quality diel
transcriptomic datasets of cultivated potato but also provides important
insight on the role of allelic diversity in rhythmic expression in plants.