Proteomic Analysis of Pollen–Stigma Interaction between Vitis rotundifolia and Vitis vinifera

Muscadine grape (Vitis rotundifolia) is highly resistant to many diseases and insects that attack european grape (Vitis vinifera). However, distant hybridization incompatibility between V. rotundifolia (female) and V. vinifera (male) impedes the utilization of V. rotundifolia in grape breeding. This study used fourth-dimension label-free protein quantitation to detect the key genes and pathways in the V. rotundifolia stigma after self-pollination (V. rotundifolia × V. rotundifolia) and cross-pollination (V. rotundifolia × V. vinifera). A histological analysis showed that pollen tube growth in the stigma of V. rotundifolia was arrested 8 hours after cross-pollination, but not after self-pollination. A proteomic analysis identified 32 differentially expressed proteins (DEPs) in the stigma of V. rotundifolia between self-pollination and cross-pollination. A heatmap analysis grouped these DEPs into four clusters. The top gene ontology terms were ATPase-coupled transmembrane transporter activity, extracellular region, DNA replication, and cellular carbohydrate biosynthetic process. A Kyoto Encyclopedia of Genes and Genomes analysis revealed that these DEPs participated in DNA replication and starch and sucrose metabolism pathways. The downregulated A5AY88, D7TJ35, D7SU26, F6HJI1, and F6GUE7 may have a role in cross incompatibility. This study revealed the cross incompatibility of grapes at histological and proteomic levels.