Unraveling the Deep Genetic Architecture for Seedlessness in Grapevine and the Development and Validation of a New Set of Markers for VviAGL11-Based Gene-Assisted Selection

Abstract

Seedless inheritance has been considered a quasi-monogenic trait based on the VvAGL11 gene. An intragenic simple sequence repeat (SSR) marker, p3_VvAGL11, is currently used to opportunely discard seeded progeny, which represents up to 50% of seedlings to be established in the field. However, the rate of false positives remains significant, and this lack of accuracy might be due to a more complex genetic architecture, some intrinsic flaws of p3_VvAGL11, or potential recombination events between p3_VvAGL11 and the causal SNP located in the coding region. The purpose of this study was to update the genetic architecture of this trait in order to better understand its implications in breeding strategies. A total of 573 F1 individuals that segregate for seedlessness were genotyped with a 20K SNP chip and characterized phenotypically during four seasons for a fine QTL mapping analysis. Based on the molecular diversity of p3_VvAGL11 alleles, we redesigned this marker, and based on the causal SNP, we developed a qPCR-HRM marker for high-throughput and a Tetra-ARMS-PCR for simple predictive analyses. Up to 10 new QTLs were identified that describe the complex nature of seedlessness, corresponding to small but stable effects. The positive predictive value, based on VvAGL11 alone (0.647), was improved up to 0.814 when adding three small-effect QTLs in a multi-QTL additive model as a proof of concept. The new SSR, 5U_VviAGL11, is more informative and robust, and easier to analyze. However, we demonstrated that the association can be lost by intragenic recombination and that the e7_VviAGL11 SNP-based marker is thus more reliable and decreases the occurrence of false positives. This study highlights the bases of prediction failure based solely on a major gene and a reduced set of candidate genes, in addition to opportunities for molecular breeding following further and larger validation studies.

Structural and molecular characterization of theRpv3locus towards the development of KASP markers for downy mildew resistance in grapevine (Vitisspp.)

“…The co-localization of the Rpv3 locus and the SdI locus (Seed development Inhibitor) gave us the opportunity to test molecular markers that were already established for seedlessness assisted selection. These markers (UDV108, VMC7F2, VVIN16, P2_VVAGL11 and P3_VVAGL11) are known for their efficiency (>80% accuracy) as tools for assisted selection of apirenic grapevines (Doligez et al 2002; Cabezas et al 2006; Mejía et al 2011; Ocarez et al 2020). For this analysis, we performed the phenotypic characterization of resistant genotypes on ‘Villard Blanc’ X ‘Villard Blanc’ population after a P. viticola challenge assay (see Materials and Methods - Fig.4).…”

Mechanisms and Candidate Genes for Seed and Fruit Set in Grapevine

“…In 1996, [32] proposed that three independent recessive genes, which are regulated by a major dominant inhibitor locus named SDI (Seed Development Inhibitor, according to [33]), control seed development. Different QTL (quantitative trait locus) studies located SDI on linkage group (LG) 18, explaining up to 70% of the phenotypic variance in seed content [34][35][36][37][38][39][40]. Based on genetic linkage and putative homology, the seed morphogenesis regulator gene AGAMOUS-LIKE 11 (VvAGL11) was proposed as the SDI candidate gene [37,38].…”

“…This tool has been successfully applied to studies of genetic diversity, relationships and structure as well as to QTL and association mapping (e.g. [40,57,[108][109][110][111]).…”

VviAGL11 self-regulates and targets hormone- and secondary metabolism-related genes during seed development

“…The mutated seedless version has a partial dominance over seeded alleles, allowing breeding for seedlessness based in heterozygous seedlings. Moreover, sequence data on the regulative region of VviAGL11 showed low recombination rates between the promoter and the CDS regions, thus suggesting the existence of a Linkage disequilibrium in that region [ 12 ]. The existence of incomplete dominance of some alleles in the promoter region has been also observed [ 5 , 10 , 12 ].…”

“…Moreover, sequence data on the regulative region of VviAGL11 showed low recombination rates between the promoter and the CDS regions, thus suggesting the existence of a Linkage disequilibrium in that region [ 12 ]. The existence of incomplete dominance of some alleles in the promoter region has been also observed [ 5 , 10 , 12 ]. Besides this genetic and transcriptional data confirming a major role of VviAGL11 in grape stenospermocarpy, no functional evidence nor a working mechanism has yet been defined.…”