Comparative Study of Gametogenesis and Genomic Signatures Associated with Pollen Sterility in a Seedless Mutant of Grapevine (Vitis vinifera L.)

Abstract

The demand for seedless grapes for consumption as fresh and dried fruits is very high. In grapevine (Vitis vinifera L.), seedlessness arises through two different mechanisms: stenospermocarpy and parthenocarpy. However, the major regulators of seed development and their target genes in grapes have not yet been fully characterized. In the present study, the seeded grape hybrid ARI-516 and its seedless mutant were used to investigate the molecular mechanisms controlling the seedless trait in grapes. The study of gametogenesis revealed that pollen grains in the seedless mutant exhibited abnormal morphology, extremely low viability, and complete inability to germinate. In addition, the size of the macrogametophyte in the seedless mutant was significantly smaller than that observed in ARI-516. A transcriptomic comparison was performed at three developmental stages: pre-flowering (E-L 15), anthesis (E-L 23), and berry set (E-L 31), to examine altered developmental processes in the seedless mutant and ARI-516. The downregulated genes in the seedless mutant were mainly enriched in biological pathways related to male gametophyte development, which may lead to pollen sterility. The RNA-seq results were further validated by qRT-PCR. Additionally, genome sequencing data were used to identify induced mutations in the seedless mutant, revealing three homozygous and 25 heterozygous InDels in genes associated with male gametophyte development. The combined results of RNA-seq and genome sequencing suggest that parthenocarpic seedlessness in the ARI-516 seedless mutant arises from abnormalities in developmental and physiological processes involved in pollen formation, maturation, and germination. The study also demonstrated the downregulation of transcription factors and their target genes associated with cell division, gibberellin biosynthesis and signalling, cell wall development, and pollen germination. Overall, this research represents an important effort to identify candidate genes associated with parthenocarpic pollen sterility in grapes using a genomic approach.