Transcriptomic Profiling and Identification of Candidate Genes Governing Fruit Spine in Spinach (Spinacia oleracea L.)

Fruit spine formation in spinach (Spinacia oleracea L.) affects seed processing and mechanized sowing, yet its molecular basis underlying this trait remains unclear. Therefore, we performed comparative transcriptome analysis of two contrasting genotypes, Sp35 (spiny) and Sp34 (spineless), at early morphogenesis and late developmental stages. RNA-seq analysis identified 3002 differentially expressed genes (DEGs) at the early developmental stage and 2737 DEGs at the later stage. Intersection analysis revealed that 1080 DEGs were differentially expressed in both stages, suggesting that these shared genes may play particularly important roles. Functional enrichment analysis of these 1080 shared DEGs revealed involvement in cell wall biogenesis, phenylpropanoid biosynthesis, and carbohydrate metabolism, highlighting roles for secondary cell wall formation and lignification in spine development. To identify the key regulatory gene, weighted gene co-expression network analysis (WGCNA) was conducted and found a significantly correlated gene module. In this co-expression gene module, a MYB transcription factor SOV2g002850 occupies a central position. Additionally, several MADS-box genes and WRKY regulatory genes were also identified in the co-expression network. Overall, this study provides a comprehensive transcriptomic framework for spinach spine development and identifies candidate genes for future functional validation and breeding.