Chromosomal Swap in Tempranillo Clone VP11 Cuts Fertility but Boosts Disease Resistance

A recent genetic study has identified the cause behind a unique trait in VP11, a commercial clone of the Tempranillo grape variety. Researchers from the Vitigen group at the Instituto de Ciencias de la Vid y del Vino (ICVV) in Spain have discovered that VP11’s loose grape clusters and reduced fruit set are linked to a specific chromosomal rearrangement. This finding could have significant implications for viticulture, especially in regions where disease pressure and fruit quality are major concerns.

VP11 was originally selected from an old vine in Elvillar, Álava, Spain, for its loose bunches, which are associated with more uniform berry ripening and lower incidence of diseases such as bunch rot. Compared to conventional Tempranillo clones, VP11 produces about 50% less viable pollen and fewer seeds per berry, indicating reduced fertility in both male and female gametes.

To understand the genetic basis of these traits, the research team performed whole-genome sequencing using long-read technology. They compared the genome of VP11 to a reference Tempranillo genome they had previously assembled. The analysis revealed eleven large structural changes in VP11’s DNA, including three inter-chromosomal events. Among these was a complex reciprocal translocation—an exchange of segments between two chromosomes.

Further genetic analysis showed that this translocation is directly responsible for the reduction in gamete viability. In self-pollinated offspring of VP11, only those individuals inheriting both chromosomes involved in the translocation survived. Gametes with an unbalanced chromosomal content, inheriting only one of the translocated chromosomes, were not viable. This explains why VP11 has lower pollen viability and fewer seeds per berry.

The study also found that while VP11’s loose bunches are mainly due to fewer berries per cluster—a result of reduced fruit set—other factors such as flower sex type can influence bunch compactness in grapevines. However, in VP11’s genetic background, the effect of flower sex on bunch compactness was less pronounced than in control clones.

The researchers suggest that in vegetatively propagated crops like grapevine, mutations that reduce gamete fertility can be beneficial if they lead to agronomic advantages such as looser clusters and healthier fruit. In sexually propagated crops, such mutations would likely be eliminated because they compromise reproductive success. But in grapevines, which are propagated by cuttings to maintain varietal identity, these mutations can persist and even be selected for if they improve crop quality or disease resistance.

The discovery highlights the value of long-read sequencing technologies for detecting complex structural variants in highly heterozygous crops like grapevine. It also demonstrates how somatic mutations—genetic changes that occur during a plant’s lifetime—can contribute to intra-varietal diversity and improvement without altering key characteristics of elite cultivars.

VP11 is now used commercially for high-quality wine production due to its favorable cluster structure. The findings from this study could inform future breeding and selection strategies aimed at improving grapevine resilience and fruit quality under changing environmental conditions.

The full results of this research were published on January 27, 2026, in BMC Plant Biology (Volume 26: Article 348). The study was led by Noelia Alañón-Sánchez and colleagues from ICVV and collaborating institutions. Data from the genome sequencing have been made publicly available through the European Nucleotide Archive under accession number PRJEB97948.

This work underscores how advances in genomics are helping scientists unravel the genetic mechanisms behind important agricultural traits. For growers and winemakers facing challenges from climate change and disease pressure, understanding these mechanisms could offer new tools for maintaining yield and quality while reducing reliance on chemical controls.