Comparative Transcriptomics Identifies Dormancy‐Related Differentially Expressed Genes and Differential Pathways Involved in Late and Early Flowering of Prunus dulcis

Abstract

Almond ( Prunus dulcis ), one of the world's most important nut crops, is highly vulnerable to adverse weather conditions, particularly spring frost, making flowering time a critical determinant of yield and production stability. To investigate the molecular basis of flowering‐time variation, comparative transcriptome analyses were performed on two early‐flowering and two late‐flowering almond cultivars at the popcorn stage. The analysis identified several candidate genes exhibiting contrasting expression patterns between the flowering groups. Notably, dormancy‐associated genes, including dormancy‐associated MADS‐box ( DAM ), dormancy‐related genes ( DRM ), and auxin repressor proteins ( ARP ), showed higher expression in late‐flowering cultivars, while multiple transcription factor families, including bHLH, NAC, MYB, WRKY, B3, C3H, C2H2, and M‐type MADS‐box proteins, were associated with regulatory pathways related to dormancy release and floral development. These expression patterns are consistent with previously reported dormancy‐associated mechanisms in Prunus species and identify candidate genes potentially associated with delayed flowering. De novo transcriptome assembly generated 100,126 unigenes, from which 52,305 coding sequences were predicted. Functional annotation across multiple public databases identified 15,514 consistently annotated coding sequences, and 763 expressed sequence‐derived simple sequence repeats (SSRs) with suitable flanking regions were identified as potential molecular markers. This study provides a valuable transcriptomic resource for almond and identifies candidate genes and regulatory pathways associated with flowering‐time variation. These findings improve our understanding of the molecular mechanisms underlying flowering phenology. Furthermore, provide a foundation for future functional studies and marker‐assisted breeding aimed at developing late‐flowering almond cultivars with improved resilience to spring frost.