Molecular, genetic and transcriptional evidence for a role of VvAGL11 in stenospermocarpic seedlessness in grapevine

Abstract

BackgroundStenospermocarpy is a mechanism through which certain genotypes of Vitis vinifera L. such as Sultanina produce berries with seeds reduced in size. Stenospermocarpy has not yet been characterized at the molecular level.ResultsGenetic and physical maps were integrated with the public genomic sequence of Vitis vinifera L. to improve QTL analysis for seedlessness and berry size in experimental progeny derived from a cross of two seedless genotypes. Major QTLs co-positioning for both traits on chromosome 18 defined a 92-kb confidence interval. Functional information from model species including Vitis suggested that VvAGL11, included in this confidence interval, might be the main positional candidate gene responsible for seed and berry development.Characterization of VvAGL11 at the sequence level in the experimental progeny identified several SNPs and INDELs in both regulatory and coding regions. In association analyses performed over three seasons, these SNPs and INDELs explained up to 78% and 44% of the phenotypic variation in seed and berry weight, respectively. Moreover, genetic experiments indicated that the regulatory region has a larger effect on the phenotype than the coding region. Transcriptional analysis lent additional support to the putative role of VvAGL11's regulatory region, as its expression is abolished in seedless genotypes at key stages of seed development. These results transform VvAGL11 into a functional candidate gene for further analyses based on genetic transformation.For breeding purposes, intragenic markers were tested individually for marker assisted selection, and the best markers were those closest to the transcription start site.ConclusionWe propose that VvAGL11 is the major functional candidate gene for seedlessness, and we provide experimental evidence suggesting that the seedless phenotype might be caused by variations in its promoter region. Current knowledge of the function of its orthologous genes, its expression profile in Vitis varieties and the strong association between its sequence variation and the degree of seedlessness together indicate that the D-lineage MADS-box gene VvAGL11 corresponds to the Seed Development Inhibitor locus described earlier as a major locus for seedlessness. These results provide new hypotheses for further investigations of the molecular mechanisms involved in seed and berry development.

Whole-genome genotyping of grape using a panel of microsatellite multiplex PCRs

“…The availability of the grapevine genome sequence combined with the advent of cheaper and high throughput single nucleotide polymorphism (SNP) genotyping strategies (Gupta et al 2008;Davey et al 2011) were expected to shift the tools of genetic studies in grapevine. However, microsatellites are still the predominant markers contributing to the current knowledge of genetic determinism of the major grapevine traits (Mejía et al 2011;Huang et al 2012;Duchêne et al 2012;Karaagac et al 2012;Doligez et al 2013;Battilana et al 2013;Grzeskowiak et al 2013;Ban et al 2014;Correa et al 2014).…”

Marker assisted selection for seedlessness in table grape breeding

“…1) located on chromosome 18 (Cabezas et al 2006;Costantini et al 2008;Mejía et al 2007, http://www.genoscope.cns.fr/externe/GenomeBrowser/ Vitis/). Recently, Mejía et al (2011) have identified additional microsatellite markers closely linked to SDI, but this information was not available when the study was carried out, 5 years ago. Simultaneous genotyping for the three loci was performed using a multiplex PCR protocol with forward primers labeled with fluorochromes (6-FAM, VIC, and NED for VMC7F2, VVIN16, and UDV-108, respectively) and ABI-Prism 3130 sequencer (Applied Biosystems).…”

“…Although these markers could help to predict seedlessness, the presence of null alleles and the weak linkage with the SDI locus compromises their use in many genetic backgrounds Korpas et al 2009). The third one is the microsatellite VMC7F2 (Cabezas et al 2006), a gene specific marker located 463 bp upstream of the predicted ORF for VvAGL11, proposed as the candidate gene responsible for this major effect QTL (Mejía et al 2011). QTL analyses showed a strong association between the seedlessness donor allele at SDI and a 198-bp allele at this locus.…”

“…However, the 198-bp allele has been found in several seeded cultivars as well (Cabezas et al 2006). The fourth one, which has been recently identified, is the microsatellite p3_VvAGL11: also a gene specific marker in the promoter region of VvAGL11, but for which usefulness has been shown in seedless backgrounds, but not in seeded ones (Mejía et al 2011).…”

“…The seedless phenotype is determined by the presence of a dominant allele at SDI, which has been located on chromosome 18 (Cabezas et al 2006;Costantini et al 2008;Mejía et al 2007). In this region, the MADS-box gene VvAGL11 has been proposed as a candidate for SDI (Costantini et al 2008;Mejía et al 2011) because of its homology with genes of known function that are involved in ovule and seed development and its female flower carpel-specific expression (Díaz-Riquelme et al 2009). …”