A MITE Inserted into the Promoter of the Dominant Vrn-A1 Gene in Spring Wheat Contains miR1123

The developmental transition from vegetative to reproductive growth in wheat is mainly controlled by the vernalization gene VRN1. Allelic variation at the VRN-A1 gene on chromosome 5A in hexaploid wheat occurs in the promoter region, where the dominant Vrn-A1 allele contains either an insertion of a miniature inverted-repeat transposable element (MITE) (Vrn-A1a) or a 20-bp deletion (Vrn-A1b) in spring wheat relative to the recessive vrn-A1 allele in winter wheat. Previous models conceptualize that without vernalization the vrn-A1 allele is not expressed due to the presence of a flowering repressor in the binding site of its promoter. When this binding site is impaired in Vrn-1 allele due to either insertion or deletion, the binding site cannot be recognized by the repressor and thus the Vrn-1 alleles are expressed without vernalization. In this study, we found that the MITE in Vrn-A1a possessed sequences of a micro RNA (miR1123) and its imperfect direct repeat. The MITE in Vrn-A1a is a nearly perfect palindrome and can form highly stable hairpin loops when expressed as RNA, which will be recognized by RNA interference enzymatic machinery and processed to form mature miR1123. These findings point to a specific mechanism for the origin and evolution of miR1123 and a regulatory mechanism for developmental genes by miR1123 released from the MITE of Vrn-A1a in wheat.