Histological and transcriptomic analyses of lignin biosynthesis in stenospermocarpic seedless and seeded grape ovules

• Comparative histological and transcriptomic analysis of ovule lignification in seedless ‘Zhongpu No.18′ and seeded ‘Muscat Hamburg’ grape cultivars. • Delayed and reduced lignin deposition in ‘Zhongpu No.18′ ovules linked to embryo abortion. • Identification of 12 candidate genes involved in lignin biosynthesis, including key transcription factor MYB (LOC100246160). • Insights into the genetic and developmental basis of seedlessness in grapes, providing valuable targets for seedless breeding strategies. Seedlessness is a highly desirable trait in table and processing grape cultivars. However, the molecular mechanisms underlying stenospermocarpic seedless in grapes remain largely unclear. In this study, the stenospermocarpic seedless cultivar ‘Zhongpu No.18′ (ZP) and the seeded cultivar ‘Muscat Hamburg’ (MH) grapes were chosen for comprehensive histological and transcriptomic analyses to screen the related key genes regulating lignin biosynthesis in grape ovules and explore the relationship between lignin biosynthesis and embryo abortion. We observed that 55–58 days after flowering (DAF) marked a critical transition stage for embryo abortion in ‘ZP’. From 35 to 61 DAF, the lignin content in ‘ZP’ ovules was significantly lower than in ‘MH’. Histological analysis showed that in ‘MH’, the endotesta connected with vascular bundles by 25 DAF, followed by extensive lignin deposition in the endotesta at 35 DAF. In contrast, in ‘ZP’, the connection between endotesta and vascular bundles occurred via the mesotesta from 15 to 64 DAF, with little lignin deposition observed in the mesotesta. This insufficient lignification may impair nutrient transport, leading to embryo abortion in ‘ZP’. Transcriptome profiling revealed that differentially expressed genes (DEGs) between the two cultivars were significantly enriched in lignin biosynthesis-related pathways. Meanwhile, twelve genes potentially involved in grape lignin biosynthesis were identified, among which MYB (LOC100246160), PAL (LOC100233012), and 4CL (LOC100245991) were selected as key candidate genes. Overall, the findings provide valuable insights into the molecular basis of lignin biosynthesis and its role in embryo abortion, providing potential genetic targets to enhance seedlessness traits in grapevine breeding.