Loss‐of‐Function Mutation in <i>TaZIP4‐B2</i> and <i>TaMSH7‐3D</i> Fuels Karyotypic Variation, Phenotypic Diversity, and Enables Rapid Evolution of Tolerance to Salinity Stress

Allopolyploid species often contain specific genes dedicated to suppressing meiotic homoeologous pairing. In common wheat, TaZIP4-B2 and TaMSH7-3D fulfil this role. Nevertheless, to what extent the loss-of-function of these genes may lead to meiotic breakdown in wheat itself and hence generate karyotypic heterogeneity remains incompletely understood. Here, we show that CRISPR/Cas9-generated loss-of-function mutation of either or both TaZIP4-B2 and TaMSH7-3D leads to disrupted meiosis, triggering widespread karyotypic instability including both numerical and structural chromosomal variations (NCVs and SCVs). NCVs predominantly occurred in the D subgenome, involving preferential gains of 2A/4B/5D and losses of 6A/5B/2D, while frequencies of SCVs among subgenomes followed the order of subgenomes D > A > B, with 6A/5B/2D showing the most rearrangements. Notably, karyotypic variation in Tazip4-B2/Tamsh7-3D double mutants showed initial rapid accumulation followed by gradual stabilization across generations. Karyotypic heterogeneity caused extensive phenotypic diversity, including several key agronomic traits. Notably, Tazip4-B2/Tamsh7-3D double mutant showed more intercalary insertional translocations than the classical ph1b deletion mutant, suggesting its advantage in alien genetic introgression. Moreover, tolerance to strong salinity emerged in progenies of the mutants due to karyotypic variation. Our findings demonstrate that the loss-of-function mutation of TaZIP4-B2/TaMSH7-3D promotes rapid karyotype variability, phenotypic diversity, and environmental adaptability in wheat itself, suggesting a novel possibility for wheat improvement by karyotypic renovation.