Laser capture microdissection‐based spatiotemporal transcriptomes uncover regulatory networks during seed abortion in seedless Ponkan (Citrus reticulata)

SUMMARY Seed abortion is an important process in the formation of seedless characteristics in citrus fruits. However, the molecular regulatory mechanism underlying citrus seed abortion is poorly understood. Laser capture microdissection‐based RNA‐seq combined with Pacbio‐seq was used to profile seed development in the Ponkan cultivars ‘Huagan No. 4’ (seedless Ponkan) (Citrus reticulata) and ‘E'gan No. 1’ (seeded Ponkan) (C. reticulata) in two types of seed tissue across three developmental stages. Through comparative transcriptome and dynamic phytohormone analyses, plant hormone signal, cell division and nutrient metabolism‐related processes were revealed to play critical roles in the seed abortion of ‘Huagan No. 4’. Moreover, several genes may play indispensable roles in seed abortion of ‘Huagan No. 4’, such as CrWRKY74, CrWRKY48 and CrMYB3R4. Overexpression of CrWRKY74 in Arabidopsis resulted in severe seed abortion. By analyzing the downstream regulatory network, we further determined that CrWRKY74 participated in seed abortion regulation by inducing abnormal programmed cell death. Of particular importance is that a preliminary model was proposed to depict the regulatory networks underlying seed abortion in citrus. The results of this study provide novel insights into the molecular mechanism across citrus seed development, and reveal the master role of CrWRKY74 in seed abortion of ‘Huagan No. 4’. Significance Statement The seedless character of citrus has important economic value and is favored by consumers, but the formation process of its internal mechanism still lacks understanding. In this study, the molecular mechanism of seed abortion in seedless Ponkan caused by abnormal programmed cell death was preliminarily analyzed by functional genomics, cytological morphological observation, physiological and biochemical assays, as well as stable genetic transformation.