Exploring high throughput secondary trait phenomics to improve grapevine breeding

In recent years characterized by hot dry summers, the implementation of innovative irrigation tools in the vineyard represents a crucial challenge to ensure optimal production and to avoid excess of water consumption. It is known that the grapevine reacts to multiple stresses – i.e., high temperatures and wa- ter shortage – through adaptive mechanisms that are detrimental to the yield. Furthermore, this condi- tion is usually aggravated by high solar radiation, which could negatively affect the phenolic composi- tion of the grapes. Therefore, a cooling system has been developed aiming to reduce bunches’ sunburn damage.

Unmanned Aerial Vehicles (UAVs) are increasingly used to monitor canopy structure and vineyard performance. Compared with traditional remote sensing platforms (e.g. aircraft and satellite), UAVs offer a higher operational flexibility and can acquire ultra-high resolution images in formats such as true color red, green and blue (RGB) and multispectral. Using photogrammetry, 3D vineyard models and normalized difference vegetation index (NDVI) maps can be created from UAV images and used to study the structure and health of grapevine canopies. However, there is a lack of comparison between UAV-based images and ground-based measurements, such as leaf area index (LAI) and canopy porosity.

Making high quality but affordable Pinot noir (PN) wine is challenging in most terroirs and New Zealand’s (NZ) situation is no exception. To increase the probability of making highly typical PN wines producers choose to grow grapes in cool climates on lower fertility soils while adopting labour intensive practices. Stringent yield targets and higher input costs necessarily mean that PN wine cost is high, and profitability lower, in line-priced varietal wine ranges. To understand the reasons why higher yielding vines are perceived to produce wines of lower quality we have undertaken an extensive study of PN in NZ. Since 2018, we established a network of twelve trial sites in three NZ regions to find individual vines that produced acceptable commercial yields (above 2.5kg per vine) and wines of composition comparable to “Icon” labels. Approximately 20% of 660 grape lots (N = 135) were selected from within a narrow juice Total Soluble Solids (TSS) range and made into single vine wines under controlled conditions. Principal Component Analysis of the vine, berry, juice and wine parameters from three vintages found grape berry mass to be most effective clustering variable. As berry mass category decreased there was a systematic increase in the probability of higher berry red colour and total phenolics with a parallel increase in wine phenolics, changed aroma fraction and decreased juice amino acids. The influence of berry size on wine composition would appear stronger than the individual effects of vintage, region, vineyard or vine yield. Our observations support the hypothesis that it is possible to produce PN wines that fall within an “Icon” benchmark composition range at yields above 2.5kg per vine provided that the Leaf Area:Fruit Weight ratio is above 12cm2 per g, mean berry mass is below 1.2g and juice TSS is above 22°Brix.

Conventional molecular analyses provide bulk genomic/transcriptomic data that are unable to reveal the cellular heterogeneity and to precisely define how gene networks orchestrate organ development. We will profile gene expression and identify open chromatin regions at the individual cells level, allowing to define cell-type specific regulatory elements, developmental trajectories and transcriptional networks orchestrating organ development and function. We will perform scRNA-seq and snATAC-seq on leaf/berry protoplasts and nuclei and combine them with the leaf/berry bulk tissues obtained results, where the analysis of transcripts, chromatin accessibility, histone modification and transcription factor binding sites showed that a large fraction of phenotypic variation appears to be determined by regulatory rather than coding variation and that many variants have an organ-specific effect.

Haplotype-resolved genome assemblies were produced for Chasselas and Ugni Blanc, two heterozygous real-field genetic pool Vitis vinifera cultivars by combining high-fidelity long-read sequencing (HiFi) and high‐throughput chromosome conformation capture (Hi-C). The telomere-to-telomere full coverage of the chromosomes allowed us to assemble separately the two haplo-genomes of both cultivars and revealed structural variations between the two haplotypes of a given cultivar.