Transcriptional and epigenetic dynamics underlying semigamy and haploid induction in Gossypium barbadense

Semigamy is a rare fertilization anomaly in plants that enables haploid induction (HI), a valuable strategy for accelerating crop breeding; however, its molecular basis remains largely unexplored. We investigated transcriptional and epigenetic mechanisms underlying semigamy mutant VSg in island cotton (Gossypium barbadense), which exhibits a high haploid induction rate during double fertilization. We combined cytological observations with time-resolved transcriptome profiling and whole-genome bisulfite sequencing across key fertilization stages. This integrative approach captured dynamic molecular changes associated with gamete nuclear fusion and early zygotic development. Compared with the wild-type, which displayed rapid polar nuclei fusion and normal free nuclear endosperm formation, the semigamy mutant showed delayed polar nuclei fusion and impaired sperm-egg nuclear fusion. Transcriptomic analyses identified differentially expressed genes enriched in membrane fusion processes, while epigenomic profiling revealed dynamic DNA methylation changes in genes encoding transmembrane proteins, cyclins, and kinesins, suggesting disrupted regulation of membrane dynamics and cell cycle progression. These results indicate that coordinated transcriptional and epigenetic regulation of nuclear fusion and cell cycle pathways underlie semigamy-induced developmental arrest and haploid induction. The study provides mechanistic insights into fertilization biology and highlights semigamy as a promising system for improving haploid breeding strategies in crops.