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Chromosomal rearrangements play essential roles in crop evolution, and different types of rearrangements have been identified in various cultivars belonging to Triticeae. However, it has not been reported whether chromosome rearrangements also occur within the same cultivar. We screened 33 plants of a Chinese modern cultivar Aikang58 (AK58) using non‐denaturing fluorescence in situ hybridization technique and found two with reciprocal translocation 3BL‐6BL and 3BS‐6BS present, thereafter designated as AK58T. The breakpoint positions of AK58T were different from previous 3B‐6B translocation, indicating newly reported translocations in common wheat. The genetic similarity between AK58 and AK58T was greater than 99.8% by wheat 55K chip array analysis. Our results showed no significant phenotype difference in five developmental periods or seven seed traits between the two lines under speed breeding conditions. However, the F1 hybrids between AK58 and AK58T severely suffered from low seedset due to the documented occurrence of multivalent formation during meiosis. Screening of 41 F2 progenies identified eight types of chromosomal variations that affected agronomic traits and decreased the fertility. Therefore, we reported that chromosomal rearrangements within the same cultivar could be hidden by high phenotype and genotype similarity, and concluded that these types of hidden variations may lead to severe fertility penalty once outcross occurred.

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