Integrated Transcriptomic Analysis Identifies Candidate Regulators Associated with Coconut Zygotic Embryo Development and Haustorium Maturation

Coconut zygotic embryo germination supports seedling establishment through coordinated embryo growth, tissue differentiation, and nutrient acquisition. A distinctive feature is the cotyledonary haustorium, which develops within the endosperm and transfers stored reserves to the growing seedling. However, transcriptional changes linking early germination to haustorium maturation and their relationships with phytohormone dynamics remain poorly understood. Here, we show that integrated time-resolved RNA sequencing, transcription factor (TF) and co-expression analyses, functional enrichment, and phytohormone profiling across 1–8 weeks after germination (WAG), including shoot/root (SR) and haustorium (Ha) tissues, reveal distinct developmental programs. We identified 792 core differentially expressed genes (DEGs), which formed four expression clusters. Cluster 4 was associated with early embryo development and included transcription factor (TF) modules involving VP1, ABI4, ARF1, BBM2, TCP4, ERF003, GRF2, and GRF6. In contrast, Cluster 1 increased during haustorium development and was enriched in hormone signaling, flavonoid biosynthesis, and cutin, suberine, and wax biosynthesis. MIF1, HOX16, and CPC showed high co-expression network connectivity. Hormone profiling showed relatively high auxin- and cytokinin-related metabolites early, progressive abscisic acid (ABA) increases, elevated ABA, indole-3-acetic acid (IAA), jasmonic acid (JA), jasmonoyl-isoleucine (JA-Ile), and salicylic acid (SA) in 6WAG-Ha, and increased methyl jasmonate (MeJA) and salicylic acid glucoside (SAG) in 8WAG-Ha. These findings reveal transcription factors and phytohormones during zygotic embryo germination, providing new understanding and reference to genetic transformation and somatic embryogenesis in coconut and other palm crops.