Apomixis is a unique reproductive process that produces fertile offspring without the combination of sperm and egg cells. This process perfectly reproduces maternal DNA, making it possible to fix heterosis during reproduction. Malus shizongensis is a newly discovered species that is closely related to Malus hupehensis Rehd. After de-male bagging, it was found that the fruit set rate reached 78.7%. Preliminary analysis indicated that M. shizongensis have apomictic reproductive characteristics. In this work, we employed paraffin sectioning and electron scanning microscopy to explore apomixis in M. shizongensis during the development of male–female gametes and embryo sacs. Stigma fluorescence assays showed that pollen germination was normal, but less pollen entered the ovaries. Additionally, analysis of anthers indicated the presence of dysplasia and paraffin sectioning revealed that the pollen mother cells were aborted due to abnormal disintegration of the tapetum layer. Taken together, our results indicate that the primary causes of apomixis in M. shizongensis are anther dysplasia and male gamete development failure, resulting in reduced pollen tube entry into ovaries and reduced reproduction of female gametes. In conclusion, this study provide a theoretical basis and technical supports for apple stock breeding and apple industry development.
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