Transposons Triggered Dynamic Evolution of MKK3 Gene, a Key Regulator for Seed Dormancy in Barley

Barley (Hordeum vulgare L.) is an important crop in the world and its seed dormancy is primarily controlled by a Mitogen-Activated Protein Kinase Kinase 3 (MKK3) gene. Although kinase activity of MKK3 and its roles in barley post-domestication have been widely studied, the pre-domestication evolution of MKK3 and the spread of nondormant alleles among global barley varieties remain largely unexplored. In this study, we analyzed MKK3 sequences in barley and its wild progenitor (H. spontaneum) and identified two polymorphic miniature inverted-repeat transposable elements (MITEs). Comparative analyses indicated that the insertions/excision of the MITEs predated the current estimates of barley domestication. Examination of the barley pangenomes coupled with droplet digital (dd) PCR revealed extensive copy number variation of MKK3 and suggested that transposons likely drove tandem amplification of the MKK3 gene on chromosome 5H. Additionally, approximately 1-Kb MKK3 sequences were found on chromosomes 1H and 6H. Further analysis indicated that these short MKK3 sequences were captured by a CACTA transposon that also contained fragments from four other expressed genes. The acquisition of MKK3 was estimated to be between 1.9-2.5 million years ago. Together, these findings illuminate the dynamic pre-domestication evolution of the MKK3 gene and suggest three independent origins of highly nondormant barley worldwide including a unique lineage predominant in Ethiopian germplasm. This study reveals the pivotal roles of transposons in MKK3 evolution and provide helpful information for understanding the complex history of MKK3 gene in barley and also for improving preharvest sprouting (PSH) tolerant varieties under distinct natural conditions.