terclim by ICS banner
IVES 9 IVES Conference Series 9 Reduced bunch compactness in a clone of Tempranillo associates with a complex reciprocal translocation detected by long-read sequencing genomics

Reduced bunch compactness in a clone of Tempranillo associates with a complex reciprocal translocation detected by long-read sequencing genomics

Abstract

Grapevine cultivars are vegetatively propagated to maintain their varietal attributes. However, spontaneous somatic variation emerges during prolonged periods of vegetative growth, providing an opportunity for the natural improvement of traditional grapevine cultivars. Notably, reduction in bunch compactness is a favorable trait in viticulture, offering advantages such as decreased susceptibility to bunch fungal diseases, and a more uniform ripening of berries. To unravel the genetic and developmental mechanisms behind bunch compactness variation, we examined a somatic variant of Tempranillo Tinto cultivar with loose bunches. We found that the mutant clone exhibits a ~50% reduction in pollen viability compared to typical Tempranillo clones. By aligning Illumina and Nanopore whole-genome sequencing reads to a diploid genome assembly of Tempranillo, we identified genome structural variations (SV) specific of this clone: translocation events involving chromosomes 1-3, 7-11, and 8-17. The presence of the SV breakpoints was validated using PCR and Sanger sequencing. The analysis of self-cross progeny of the mutant clone showed that low pollen viability and reduced number of seeds per berry co-segregate with the SV event between specific haplotypes of chromosomes 1 and 3, suggesting a causal effect for this rearrangement. Inspection of Nanopore read alignments identified that the SV 1-3 event corresponds to a complex reciprocal translocation with duplications at the breakpoints of the two involved chromosomes. Considering that heterozygous reciprocal translocations associate with partially incompatible chromosome pairing during meiosis, we propose that this type of SV decreases fruit set rate by lowering gamete viability, ultimately reducing bunch compactness.

DOI:

Publication date: June 14, 2024

Issue: Open GPB 2024

Type: Article

Authors

Pablo Carbonell-Bejerano1*, Noelia Alañón1, Yolanda Ferradás1,2, Nuria Mauri1,3, José Miguel Martínez-Zapater1, Javier Ibáñez1*

1 Instituto de Ciencias de la Vid y del Vino (ICVV, CSIC-CAR-UR), Departamento de Viticultura, Logroño, Spain
2 Departamento de Biología Funcional, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
3 Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Cerdanyola del Vallès, Barcelona, Spain

Contact the author*

Keywords

bunch compactness, clonal variation, genome structural variation, pollen viability, reciprocal translocation

Tags

IVES Conference Series | Open GPB | Open GPB 2024

Citation

Related articles…

What are the optimal ranges and thresholds for berry solar radiation for flavonoid biosynthesis?

In wine grape production, canopy management practices are applied to control the source-sink balance and improve the cluster microclimate to enhance berry composition. The aim of this study was to identify the optimal ranges of berry solar radiation exposure (exposure) for upregulation of flavonoid biosynthesis and thresholds for their degradation, to evaluate how canopy management practices such as leaf removal, shoot thinning, and a combination of both affect the grapevine (Vitis vinifera L. cv. Cabernet Sauvignon) yield components, berry composition, and flavonoid profile under context of climate change. First experiment assessed changes in the grape flavonoid content driven by four degrees of exposure. In the second experiment, individual grape berries subjected to different exposures were collected from two cultivars (Cabernet Sauvignon and Petit Verdot). The third experiment consisted of an experiment with three canopy management treatments (i) LR (removal of 5 to 6 basal leaves), (ii) ST (thinned to 24 shoots per vine), and (iii) LRST (a combination of LR and ST) and an untreated control (UNT). Berry composition, flavonoid content and profiles, and 3-isobutyl 2-methoxypyrazine were monitored during berry ripening. Although increasing canopy porosity through canopy management practices can be helpful for other purposes, this may not be the case of flavonoid compounds when a certain proportion of kaempferol was achieved. Our results revealed different sensitivities to degradation within the flavonoid groups, flavonols being the only monitored group that was upregulated by solar radiation. Within different canopy management practices, the main effects were due to the ST. Under environmental conditions given in this trial, ST and LRST hastened fruit maturity; however, a clear improvement of the flavonoid compounds (i.e., greater anthocyanin) was not observed at harvest. Methoxypyrazine berry content decreased with canopy management practices studied. Although some berry traits were improved (i.e. 2.5° Brix increase in berry total soluble solids) due to canopy management practices (ST), this resulted in a four-fold increase in labor operations cost, two-fold decrease in yield with a 10-fold increase in anthocyanin production cost per hectare that should be assessed together as the climate continues to get hot.

Function, barriers, and the environmental benefits of reuse bottle system for wine

With 0.3 to 0.7 kg CO2eq per 0.75 L wine, the glass bottle is the main contributor to the carbon footprint of a bottle of wine.

Dynamic agrivoltaics, climate protection for grapevine driven by artificial intelligence

The year-on-year rise in temperatures and the increase in extreme weather events due to climate change are already having an impact on agriculture. Among the perennial fruit species, grapevine is already negatively impacted by these events through an acceleration of its phenology, more damage from late frosts or through an increase in the sugar level of the berries (and therefore the alcoholic degree of the wine) and a decrease of acidity, impacting the wine quality. Sun’Agri, in partnership with INRAE, Chambre d’agriculture du Vaucluse, Chambre d’agriculture des Pyrénées-Orientales and IFV, developed a protection system based on dynamic agrivoltaics to protect grapevine. It consists of photovoltaic solar panels positioned above the crop, high enough not to impede the passage of agricultural machinery, and tiltable from +/- 90° to adjust the level of shading on the vineyard. These smart louvers, driven by artificial intelligence (physical models & plant growth models), are steered according to the plant’s needs and provide real climate protection.

NEW INSIGHTS INTO THE FATE OF MARKERS INVOLVED IN FRESH MUSHROOM OFF-FLAVOURS DURING ALCOHOLIC FERMENTATION

The fresh mushroom off-flavour (FMOff) has been appearing in wines since the 2000s. Some C8 compounds such as 1-octen-3-one, 1-octen-3-ol, 1-hydroxyoctan-3-one, 3-octanol and others are involved in this specific off-flavour [1-3]. At the same time, glycosidic precursors of some FMOff compounds have been identified in musts contaminated by Crustomyces subabruptus [4], highlighting the role of aroma precursors in this specific taint. However, the fate of these volatile molecules and glycosidic fractions during fermentation is not well known.

Beyond classical statistics – data fusion coupled with pattern recognition

AIM: Patterns in data obtained from wine chemical and sensory evaluations are difficult to infer using classical statistics.