Genomic and evolutionary analysis reveals dynamic variations of MKK3 gene, a key regulator for seed dormancy in barley

Authors: TRESSEL, LYDIA - Oak Ridge Institute For Science And Education (ORISE); Caspersen, Ann; Walling, Jason; Gao, Dongying

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/2/2026
Publication Date: 9/1/2026
Citation: Tressel, L.G., Caspersen, A.M., Walling, J.G., Gao, D. 2026. Genomic and evolutionary analysis reveals dynamic variations of MKK3 gene, a key regulator for seed dormancy in barley. The Plant Genome. https://doi.org/10.1002/tpg2.70299.
DOI: https://doi.org/10.1002/tpg2.70299

Interpretive Summary: One of the major events in domesticating wild plants into crops was that their seeds stopped staying dormant for long periods. In barley, this trait is mostly controlled by a gene called MKK3, but it is till poorly understood how this gene varied in wild barley before humans began domesticating it. In this study, we found that certain jumping DNA pieces in barley moved around before humans domesticated the crop, creating many versions of the gene MKK3. These DNA jumps helped copy the entire gene multiple times and even created small fragments of it on other chromosomes. Overall, the study shows that these mobile DNA elements shaped the evolution of MKK3 and led to several independent origins of barley types that sprout easily, which can help breeders develop varieties suited to different environments in the United States and other countries.

Technical Abstract: 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 (Hordeum spontaneum K. Koch) 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 polymerase chain reaction revealed extensive copy number variation of MKK3 and suggested that transposons likely contributed to 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 and 2.5 million years ago. Together, these findings illuminate the dynamic pre-domestication evolution of the MKK3 gene and identify three divergent MKK3 haplotype groups including a unique lineage predominant in Ethiopian germplasm. This study highlights the contribution of transposons to structural diversification and evolutionary differentiation of the MKK3 locus and provides helpful information for understanding the complex history of MKK3 gene in barley and also for improving preharvest sprouting tolerant varieties under distinct natural conditions.