CmRT1, a Ty3-gypsy-like retrotransposon in Castanea mollissima,is associated with a short-catkin mutation

Summary

Retrotransposons are major components of the genomes of most eukaryotic organisms and have resulted in the introduction of desirable traits in many crops, including fruit trees. Here, we describe a Ty3-gypsy-like retrotransposon associated with a short-catkin mutant in Chinese chestnut (Castanea mollissima), resulting in catkins that are < 20% the length of normal staminate catkins. A partial sequence of the retrotransposon, named CmRT1, detected by amplified fragment length polymorphism (AFLP) analysis, and its complete sequence were determined from the genome of Chinese chestnut (Castanea mollissima) using improved Tail-PCR. CmRT1 was 10,067 bp in length and shared high homology in its predicted amino acid sequence and motifs with other Ty3/gypsy-like retrotransposons. The 5’ long terminal repeat (LTR) of CmRT1 contained a TATA box and several cis-elements that were predicted to be important for processes involving abscisic acid, gibberellic acid, and auxins and in stress-mediated responses. Further characterisation of the transposition event that led to the short-catkin phenotype was performed using two pairs of primers that aligned with the flanking region of the LTRs. The expected PCR bands were observed only in genomic DNA from plants that showed the mutation. Finally, cloning and real-time qPCR analysis of an NADP-dependent alkenal double-bond reductase (CmADBR) target gene that was adjacent to CmRT1, revealed that CmADBR expression was significantly down-regulated in the short-catkin mutant. Taken together, these results suggest that the CmRT1 retrotransposon is responsible for the short-catkin phenotype.