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

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.

本数据集来源于包含279个葡萄（Vitis Vinifera）品种的品种组，该品种组旨在最大化栽培葡萄的遗传多样性、最小化品种间亲缘关系，同时涵盖三个基因池中的主要低结构（Nicolas等，2016）。

2019年夏季，在法国南部蒙彼利埃室外栽培的2年生盆栽植株上对该品种组进行了研究，每个品种包含20株植株。每个品种的20株植株分为两组：10株朝向西南，10株朝向东北。

6月28日，欧洲大部分地区遭遇了创纪录的热浪。当实验葡萄园的气温达到45℃后，部分品种出现大面积叶片灼烧，而其他品种则无症状。

热浪过后3天（7月2日），对多样性品种组的279个品种进行了叶片灼烧（leaf firing）比例和强度的评分。评分采用目视尺度。针对每个品种、每个朝向的10株植株组，分别评定叶片灼烧比例和强度得分。叶片灼烧比例按冠层内至少部分灼烧的叶片占比计，评分范围为0至100%。叶片灼烧强度采用0-5分制，描述代表性灼烧叶片的灼烧程度：0表示无症状，1表示仅叶缘受影响，最高5分表示整叶受影响。

我们进一步通过比例与强度的乘积计算冠层水平的症状严重程度。

此外，还对品种组的形态性状进行了研究。6月中旬至7月底，每个品种取样10-14片叶片以测量叶面积。所选叶片为完全展开且光照良好的叶片，通常位于顶端第10至15个植物节段（phytomer）之间。叶片经压平（必要时切割以避免重叠）后，立即用平板扫描仪扫描。随后通过Python中的分割程序获取叶面积。

叶片在60℃干燥箱中放置一周后测量干重，叶面积比质量（LMA）为干重与面积的比值。对于叶面积和LMA，采用混合模型（mixed-models）估计遗传值的最佳线性无偏预测值（BLUPs）。对于叶片灼烧比例和强度，每个品种、每个朝向的得分已为单一平均观测值。

结合基因型数据（197,885个单核苷酸多态性（SNP）来自微阵列和测序分型（genotyping-by-sequencing）（Flutre等，2022），经筛选后保留82,868个SNP：排除i）在品种组中无变异的SNP、ii）次要等位基因频率（minor allelic frequency）低于5%的SNP、iii）重复位置的SNP），该数据集用于开展全基因组关联研究（GWAS），以检测与叶片灼烧症状或形态性状相关的SNP。采用了三种GWAS方法：MM4LMM、MLMM和varbvs。本研究的最终目标是探究与极端耐热性相关的基因组区域，揭示高优先级候选基因，并评估这些区域是否与形态性状的关联区域共定位。

相关出版物为：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.