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Transcriptional and epigenetic reprogramming during androgenesis in Brassica Rapa [ChIP-seq]

ABSTRACT: Stress-induced reprogramming of unicellular microspores can redirect their developmental fate from gametophyte formation to embryogenesis, a process termed androgenesis or microspore embryogenesis, which provides a powerful tool for haploid breeding in agriculture. However, the molecular basis of genotype-dependent variation in embryogenic competence and induction efficiency remains poorly understood, limiting its widespread application in crop improvement.In this study, we investigated the transcriptional and epigenetic reprogramming during microspore embryogenesis in Brassica rapa, focusing on the induction process and early embryogenesis stages. Our research aims to elucidate the molecular mechanisms underlying cell fate transition and the regulation of induction efficiency

ORGANISM(S): Brassica rapa

PROVIDER: GSE298089 | GEO | 2026/05/29

REPOSITORIES: GEO

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Project description:Microspore embryogenesis is a process in which immature male gametophytes are induced to form embryo-like structures that can regenerate into doubled haploid (DH) plants following chromosome doubling. By producing complete homozygosity in a single generation, DH technology accelerates cultivar development and is particularly valuable for breeding resilient crops under increasing biotic and abiotic stresses. However, bread wheat remains largely recalcitrant to microspore embryogenesis, with strong genotype dependence limiting its broad application in breeding programs. To investigate the molecular basis of this variation, we performed a comparative transcriptomic time-course in two spring wheat cultivars with contrasting embryogenic responses: Nanda (highly responsive) and Sadash (recalcitrant). Dynamic gene expression reprogramming was observed during embryogenesis, with Nanda showing distinct enrichment of biological processes linked to epigenetic regulation, including nucleosome assembly, chromatin remodeling, and chromatin organization, while the integration of stress perception, hormonal signaling, cytoskeletal and cell wall remodeling, and targeted metabolic shifts collectively establishes the cellular environment necessary for successful microspore embryogenesis. Differentially expressed gene (DEG) hotspots suggested possible structural variation underlying the divergent responses between genotypes. Machine learning highlighted potential biomarkers, notably a histone deacetylase gene TRAESCS1D02G454400 located within a DEG-enriched region. Subgenome-specific analysis further revealed pronounced suppression of B-subgenome homoeologs in Sadash, 65% of which overlapped with DEGs from the genotype comparison. These findings highlight the central role of epigenetic regulation, homoeolog expression bias, and genotype-specific genomic variation in determining embryogenic efficiency. These insights also provide new molecular targets and biomarkers to overcome recalcitrance and enhance the utility of microspore embryogenesis in wheat DH breeding pipelines.

Project description:Sugarcane (Saccharum spp. hybrid) is an economically important crop that is widely grown for its sucrose content, and somatic embryogenesis is a promising approach for efficient micropropagation and genetic transformation in this context. The induction of somatic embryogenesis is controlled by various genes and proteins involved in hormonal pathways and stress responses, which act as key regulators of in vitro cellular reprogramming. In this study, we employed a temporal proteomic approach to investigate the underlying molecular mechanisms governing sugarcane embryogenic callus formation in response to 2,4-dichlorophenoxyacetic acid (2,4-D) during induction. Comprehensive proteomic profiling revealed 996 differentially accumulated proteins (DAPs) across at least one pairwise comparison among time points (0, 7, 14 and 21 days) during callus induction. These DAPs were classified into different clusters on the basis of their accumulation profile. Our study advances the understanding of the molecular mechanisms of somatic embryogenesis in sugarcane, highlighting the regulation of key proteins during this process. Proteins involved in photosynthesis and starch accumulation were not detected during callus induction. In contrast, proteins involved in embryogenesis, histone epigenetic regulation, hormone responses and protein post-translational modification accumulate during callus induction. The predicted interactions between the TOPLESS protein and auxin response proteins (SKP1, CUL1 and CAND1 proteins) are associated with increased accumulation of the histone deacetylase HDT2 protein, a regulator of chromatin condensation, during embryogenic callus initiation. Moreover, proteomic analysis revealed a temporal reduction in methylation cycle enzymes during callus induction, whereas global DNA methylation (GDM) showed only a slight, non-significant increase, suggesting that additional regulatory layers are involved in embryogenic competence. The identified protein dynamics provide valuable targets for refining somatic embryogenesis protocols and advancing their biotechnological applications in sugarcane.

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Transcriptional and epigenetic reprogramming during androgenesis in Brassica Rapa [ChIP-seq]

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