SPET-based linkage maps for traits associated with berry texture and seedlessness in grapevine

Abstract

Berry texture and seed size are major components of grapevine fruit quality, influencing both consumer perception and technologicalperformance; however, the genetic bases of these traits remain incompletely understood. In this study, Single Primer Enrichment Technology (SPET)–based high-resolution linkage mapping was used to dissect the genetic architecture of berry texture, berry color, and seed traits in a grapevine F₁ population of 200 individuals derived from crossing the seeded red wine cultivar Raboso Veronese and theseedless white table grape Sultanina. Dense pseudo-testcross genetic maps were independently constructed for both parents, each including over 1,200 molecular markers, and integrated with an extensive automated phenotyping dataset encompassing berry color, 28 texture-related traits, and 12 seed traits.

Quantitative trait locus (QTL) analysis confirmed major, known loci associated with berry color on chromosome 2 and with berry texture and seedlessness on chromosome 18. In addition, several minor-effect QTLs for berry texture components were detected in bothgenotypes: in Raboso Veronese they were found on chromosomes 11, 17, and 18, while in Sultanina they were detected on chromosomes4 and 11. Although each of these loci individually explained a limited proportion of phenotypic variance, their combined effectscontributed to the fine-scale modulation of berry mechanical properties.

Candidate gene analysis within QTL confidence intervals revealed contrasting, genotype-specific genetic architectures. In Raboso Veronese, berry texture was mainly associated with structural genes involved in cell wall remodeling and sugar transport. In Sultanina, regulatory genes related to hormonal signaling and transcriptional control, including the seedlessness-related locus VvAGL11 and genesencoding NAC, AP2/ERF, SAUR, and F-box proteins, played a predominant role in coordinating berry texture and seed development.

Despite moderate map inflation likely resulting from residual genotyping inaccuracies inherent to highly heterozygous genomes, strongcollinearity between genetic and physical marker positions supported the reliability of marker ordering and QTL localization.

Overall, this study represents the first application of SPET for linkage mapping in grapevine and provides novel insights into the genetic mechanisms underlying berry texture and seed traits, offering valuable targets for functional validation and marker-assisted breeding.