Comparative Transcriptomic Analysis Reveals Key Pathways and Genes Involved in Late-Acting Self-Incompatibility in Akebia trifoliata

Self-incompatibility (SI) is a key reproductive mechanism in angiosperms that prevents self-fertilization and promotes genetic diversity while limiting breeding efficiency. <i>Akebia trifoliata</i> is a recently domesticated economic crop native to East Asia with medicinal, edible, and oil-producing value. However, its late-acting self-incompatibility (LSI) severely limits genetic improvement and commercial development. To investigate the molecular basis of LSI, we conducted comparative transcriptomic analyses of pistils at 48, 96, 144, 192, and 240 h after self- and cross-pollination, identifying 1552, 2954, 1302, 814, and 1978 differentially expressed genes (DEGs), respectively. DEGs were consistently enriched in mitogen-activated protein kinase (MAPK) signaling, plant hormone signal transduction, and ubiquitin-mediated proteolysis pathways, with clear transcriptional differences before and after 96 h. Compared with cross-pollinated pistils, self-pollinated pistils showed restricted pollen tube spread, and genes related to pollen recognition and tube development showed differential expression at 48 and 96 h, indicating that LSI probably occurs within the pollen tube. Collectively, these results indicate that pistils of <i>A. trifoliata</i> exhibit distinct early responses to self- and cross-pollination, and that DEG-enriched pathways are similar to those involved in <i>S-RNase</i>-mediated SI. These results provide new insights into the molecular basis of LSI and suggest potential targets for overcoming the SI barrier.