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.

Nallatt Ocarez,Carlo Bergamini,Maria Francesca Cardone,Antonio Domenico Marsico,Nilo Mejía,Reynaldo Núñez,Rocco Perniola,Nicolás Jiménez

doi:10.3390/genes11020151

Nallatt Ocarez, Carlo Bergamini + Show 6 more

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https://doi.org/10.3390/genes11020151

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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.

Highlights

Table grapes are a consumable product developed by breeding activities that deal with global demands coming from producers, plant nurseries, and consumers [1]
Considering the additive effect of QTLs, we developed a simple predictive model that includes the simultaneous evaluation of multiple QTLs, represented by the multiple single nucleotide polymorphisms (SNPs) used as cofactors in the multiple QTL mapping analysis
The hypothesis proposed by Bouquet and Danglot [10] regarding the inheritance of seedlessness controlled by a major dominant locus and three independent minor loci still seems to be valid, and the genetic architecture reveals that seedlessness is a complex trait controlled by the VviAGL11 gene as the dominant major locus and by up to 11 stable and small-effect QTLs

Summary

Introduction

Table grapes are a consumable product developed by breeding activities that deal with global demands coming from producers, plant nurseries, and consumers [1]. Selection, based on a phenotypic evaluation of traits such as berry size, berry skin color, and bunch size, is simple but requires the plant to achieve maturity (2–3 years after crosses were made) [6]. Assisted selection, based on DNA molecular markers, can be applied from the very early stages of seedling development and with total independence from the fruit developmental and ripening process [7]. This approach is currently being applied in several breeding programs, especially for quasi-monogenic traits that are subject to negative selection, such as seedlessness or fungal disease resistance, through discarding of undesirable plants

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