LOX-A4 shapes Triticum urartu gene pools and contributions to the A subgenome of polyploid wheat

Lipoxygenases (LOXs) play vital roles in plant growth and defense. In this study, through genomic and molecular analyses, we discover a major LOX gene (LOX-A4) differentially expressed in Triticum urartu (Tu), the diploid progenitor of A subgenome in polyploid wheat. Compared to Tu accessions carrying wild type gene (LOX-A4W), those bearing mutant allele (LOX-A4m) show better growth but lower stress tolerance. These differences concur with a wider geographical distribution of LOX-A4m accessions than LOX-A4W materials in the Fertile Crescent. Interestingly, only mutant LOX-A4 alleles are detected in 3,516 worldwide tetraploid and hexaploid wheat lines; restoring LOX-A4W expression in common wheat inhibits growth but enhances stress tolerance. Furthermore, genome-wide identity-by-state analysis reveals that polyploid wheat A subgenome is more related to the A genome in 13 LOX-A4m Tu accessions. Thus, our work provides evidence that LOX gene variation shapes plant gene pools and their contributions to polyploid genome formation via regulating growth-defense trade-offs. Triticum urartu is the diploid progenitor of polyploid wheat A subgenome. Here, the authors report an improved genome assembly of T. urartu and uncover a lipoxygenase gene that shapes T. urartu gene pools and their contributions to polyploid wheat A subgenome by regulating growth-defense trade offs.