Leaf firing symptoms and their genetic analysis in a grapevine diversity panel suddenly exposed to a record heatwave

[Lien vers la fiche source] This dataset comes from a panel of 279 grapevine (Vitis Vinifera) cultivars, that was designed to maximize genetic diversity and minimize relatedness among cultivated grapevine while capturing the main low structure in three genetic pools (Nicolas et al., 2016). The panel was studied in summer 2019 on 2-year-old potted plants cultivated outdoors in Montpellier, South France, with 20 plants per cultivar. For each cultivar, all 20 plants were grouped, with 10 plants facing South-West and 10 plants facing North-East. On June 28th a record heatwave occurred over a large art of Europe. After air temperature reached 45°C in our experimental vineyard, some cultivars were largely burnt while others showed no symptoms. The proportion and intensity of leaf firing were scored for all 279 cultivars of the diversity panel on July 2nd, three days after the heatwave. Scoring was based on a visual scale. One score for leaf firing proportion and one score for leaf firing intensity were attributed for the group of 10 plants of each cultivar in each orientation (South-West or North-East). Proportion of leaf firing was scored from 0 to 100% as the proportion of leaves at least partly burnt within the canopy. Intensity of leaf firing was scored as 0, 1, 2, 3, 4 or 5 to describe the extent of the firing within one representative fired leaf (0 when no symptoms, 1 when only leaf margins were affected, up to 5 when the whole leaf was affected). We further calculated the magnitude of symptoms at the canopy level as the product of proportion and intensity. Morphological traits were also studied on the panel. From mid-June to the end of July, we sampled 10 to 14 leaves for each cultivar in order to measure their area. Leaves were chosen as fully expanded and well-irradiated, generally between the tenth and fifteenth phytomers from the apex. They were flattened and cut if necessary to avoid overlap, and then immediately scanned using a flatbed scanner. Leaf area was then obtained through a segmentation procedure in Python. Leaf dry weight was measured after one week in a drying oven (60°C), and leaf mass per area (LMA) was calculated as the ratio between dry weight and area. For leaf area and LMA, the best linear unbiased predictors (BLUPs) of genetic values were estimated using mixed-models. For leaf firing proportion and intensity, each score already consisted in a single average observation for each cultivar and orientation. Along with genotypic data (197,885 SNPs issued from microarray and genotyping-by-sequencing (Flutre et al., 2022) and reduced to 82,868 SNPs after excluding i) SNPs that did not vary across the panel, ii) SNPs with a minor allelic frequency below 5% and iii) duplicated positions), this dataset was used to perform genome wide association studies (GWAS) to detect SNPs associated with leaf firing symptoms or morphological traits. Three GWAS methods were used (MM4LMM, MLMM and varbvs). The ultimate goal of this study was to investigate genomic regions associated to extreme heat tolerance and disclose high-priority candidate genes, and to assess whether these regions co-localized with associations for morphological traits. The associated publication is: Coupel-Ledru A, Westgeest AJ, Albasha R, Millan M, Pallas B, Doligez A, Flutre T, Segura V, This P, Torregrosa L, Simonneau T, Pantin F (2024) Clusters of grapevine genes for a burning world. New Phytologist. DOI: 10.1111/nph.19540.