Comparative analysis of the genetic variability within the Q-type C2H2 zinc-finger transcription factors in the economically important cabbage, canola and Chinese cabbage genomes.

BACKGROUND

and encompass many economically important vegetable and oil crops; such as cabbage, broccoli, canola and Chinese cabbage. The genome sequencing of these species allows for gene discovery with an eye towards discerning the natural variability available for future breeding. The Q-type C2H2 zinc-finger protein (ZFP) transcription factors contain zinc finger motifs with a conserved QALGGH as part of the motif and they may play a critical role in the plants response to stress. While they may contain from one to five ZF domains (ZFD) this work focuses on the ZFPs that contain two zinc-fingers, which bind to the promoter of genes, and negatively regulate transcription via the EAR motif. and are diploid and evolved into distinct species about 3.7 million years ago. is polyploid and formed by fusion of the diploids about 7500 years ago.

RESULTS

This work identifies a total of 146 Q-type C2H2-ZFPs with 37 in , 35 in and 74 in . The level of sequence similarity and arrangement of these genes on their chromosomes have mostly remained intact in , when compared to the chromosomes inherited from either or . In contrast, the difference between the protein sequences of the orthologs of and is greater and their organization on the chromosomes is much more divergent. In general, the 146 proteins are highly conserved especially within the known motifs. Differences within subgroups of ZFPs were identified. Considering that has twice the number of these proteins in its genome, RNA-Seq data was mined and the expression of 68 of the 74 genes was confirmed.

CONCLUSION

Alignment of these proteins gives a snapshot of the variability that may be available naturally in species. The aim is to study how different ZFPs bind different genes or how dissimilar EAR motifs alter the negative regulation of the genes bound to the ZFP. Results from such studies could be used to enhance tolerance in future breeding programs.