Molecular marker-assisted selection (MAS) can significantly accelerate and improve the efficiency of the breeding process in seedless grape cultivars.  In this study, we developed the KASP_VviAGL11 and VviAGL11_410 markers based on a single nucleotide polymorphism (SNP) site (Chr18: 26889437 (A/C)) of the VviAGL11 gene, and compared them with previously reported SSR markers p3_VvAGL11 and 5U_VviAGL11 by testing 101 cultivars and 81 F₁ hybrid progenies.  The results showed that both of the proposed markers obtained 100% accuracy rates in detecting allele A, which was closely associated with the seedless trait in grapes, while p3_VvAGL11 and 5U_VviAGL11 had lower accuracy rates due to their tendency to produce false positives.  After careful evaluation of the technical advantages and disadvantages associated with these markers, we concluded that KASP_VviAGL11 was superior in terms of simplicity, cost-effectiveness, efficiency, and accuracy.  Thus, we optimized the process of molecular MAS for seedless grapes, focusing on the KASP_VviAGL11 marker as a central component, to provide key technical support for the development of new seedless grape cultivars.

We aimed to develop a set of single nucleotide polymorphism (SNP) markers that can be used to distinguish the main cultivated grape (Vitis L.) cultivars in China and provide technical support for domestic grape cultivar protection, cultivar registration, and market rights protection.  A total of 517 high-quality loci were screened from 4 241 729 SNPs obtained by sequencing 304 grape accessions using specific locus amplified fragment sequencing, of which 442 were successfully designed as Kompetitive Allele Specific PCR (KASP) markers.  A set of 27 markers that completely distinguishes 304 sequenced grape accessions was determined by using the program, and 26 effective markers were screened based on 23 representative grape cultivars.  Finally, a total of 46 out of 48 KASP markers, including 22 markers selected by the research group in the early stage, were re-screened based on 348 grape accessions.  Population structure, principal component, and cluster analyses all showed that the 348 grape accessions were best divided into two populations.  In addition, cluster analysis subdivided them into six subpopulations.  According to genetic distance, V. labrusca, V. davidii, V. heyneana, and V. amurensis were far from V. vinifera, while V. vinifera×V. labrusca and V. amurensis×V. vinifera were somewhere in between these two groups.  Furthermore, a core set of 25 KASP markers could distinguish 95.69% of the 348 grape accessions, and the other 21 markers were used as extended markers.  Therefore, SNP molecular markers based on KASP typing technology provide a new way for mapping DNA fingerprints in grape cultivars.  With high efficiency and accuracy and low cost, this technology is more competitive than other current identification methods.  It also has excellent application prospects in the grape distinctness, uniformity, and stability (DUS) test, as well as in promoting market rights protection in the near future.

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.  In this study, we sequenced the genomes of the V. vinifera seeded cultivar ‘Red Globe’, the seedless cultivar ‘Centennial Seedless’, and the derived hybrids.  Nonsynonymous single nucleotide polymorphisms (SNPs) were identified by genome sequencing and analyzed using published transcriptome data.  Nonsynonymous SNPs occurred in genes related to seed development, which were identified as protein kinases, transcription factors, and cytochrome P450s and showed differential expression during ovule development in both seeded and seedless grapes.  These nonsynonymous SNP-associated genes were mainly involved in biological processes such as hormone balance, seed coat and endosperm development, reproductive organ development, oxidation and reduction, senescence and cell death.  A potential quantitative trait locus (QTL) region associated with seed size was characterized based on the SNP-index, and expression analysis of candidate genes in the QTL region during ovule development in multiple seeded and seedless grape cultivars were conducted.  Three SNPs were further subjected to SNaPshot analysis and one SNP in G8 showed 67.5% efficiency in the grape progeny validation.  Overall, the data obtained in this study shed light on the differences in seed development between seeded and seedless progeny at the genomic level, which provides valuable resources for future functional studies and grape breeding.