Abstract
Background: Seedlessness in grape (Vitis vinifera) is an important commercial trait for both the fresh and drying markets. However, despite numerous studies, the mechanisms and key genes regulating grape seedlessness are mostly unknown.Results: In this study, we sequenced the genomes of the V. vinifera seeded cultivar ‘Red Globe’, the seedless cultivar ‘Centennial’, as well as the derived hybrids. Nonsynonymous SNPs were identified by genome sequencing and analyzed with published transcriptome data. Nonsynonymous SNPs were found in genes which were differential expressed during seeded and seedless grape ovule development, and corresponding Gene Ontology and pathway enrichment were conducted. A potential QTL region associated with seed size was characterized based on SNP-index for both seedless and seeded progeny. Expression analysis of SNP associated candidate genes during ovule development in multiple seeded and seedless grape cultivars were conducted and 3 SNP were further subjected to SNaPshot analysis in 40 progeny for validation.Conclusion: In summary, nonsynonymous SNPs happened in genes related seed development, which identified to be protein kinase, transcription factors, cytochrome P450 and showed differential expression during seeded and seedless grape ovule development. These nonsynonymous SNP associated genes were mainly involved in biological processes like hormone balance, seed coat and endosperm development, reproductive organ development, oxidation and reduction, senescence and cell death. Based on SNP-index and expression pattern analysis, candidate genes in the QTL region were identified and a SNP in G8 showed 67.5% efficiency in the grape progeny validation. Overall, the data cast light on the differences of seed development between seeded and seedless progeny in genomic level, which provides valuable resources for future functional study and grape breeding.
Transcriptional changes during ovule development in two genotypes of litchi (Litchi chinensis Sonn.) with contrast in seed size
