BUSCADOR RECOLECTA

Crop Wild Relatives (CWR) are a valuable source of genetic diversity that can be transferred to commercial crops, so their conservation will become a priority in the face of climate change. Bizarrely, in situ conserved CWR populations and the traits one might wish to preserve in them are themselves vulnerable to climate change. In this study, we used a quantitative machine learning predictive approach to project the resistance of CWR populations of lentils to a common disease, lentil rust, caused by fungus Uromyces viciae-fabae. Resistance is measured through a proxy quantitative value, DSr (Disease Severity relative), quite complex and expensive to get. Therefore, machine learning is a convenient tool to predict this magnitude using a well-curated georeferenced calibration set. Previous works have provided a binary outcome (resistant vs. non-resistant), but that approach is not fine enough to answer three practical questions: which variables are key to predict rust resistance, which CWR populations are resistant to rust under current environmental conditions, and which of them are likely to keep this trait under different climate change scenarios. We first predict rust resistance in present time for crop wild relatives that grow up inside protected areas. Then, we use the same models under future climate IPCC (Intergovernmental Panel on Climate Change) scenarios to predict future DSr values. Populations that are rust-resistant by now and under future conditions are optimal candidates for further evaluation and in situ conservation of this valuable trait. We have found that rust-resistance variation as a result of climate change is not uniform across the geographic scope of the study (the Mediterranean basin), and that candidate populations share some interesting common environmental conditions., Peer reviewed

Crop Wild Relatives (CWR) are a valuable source of genetic diversity that can be transferred to commercial crops, so their conservation will become a priority in the face of climate change. Bizarrely, in situ conserved CWR populations and the traits one might wish to preserve in them are themselves vulnerable to climate change. In this study, we used a quantitative machine learning predictive approach to project the resistance of CWR populations of lentils to a common disease, lentil rust, caused by fungus Uromyces viciae-fabae. Resistance is measured through a proxy quantitative value, DSr (Disease Severity relative), quite complex and expensive to get. Therefore, machine learning is a convenient tool to predict this magnitude using a well-curated georeferenced calibration set. Previous works have provided a binary outcome (resistant vs. non-resistant), but that approach is not fine enough to answer three practical questions: which variables are key to predict rust resistance, which CWR populations are resistant to rust under current environmental conditions, and which of them are likely to keep this trait under different climate change scenarios. We first predict rust resistance in present time for crop wild relatives that grow up inside protected areas. Then, we use the same models under future climate IPCC (Intergovernmental Panel on Climate Change) scenarios to predict future DSr values. Populations that are rust-resistant by now and under future conditions are optimal candidates for further evaluation and in situ conservation of this valuable trait. We have found that rust-resistance variation as a result of climate change is not uniform across the geographic scope of the study (the Mediterranean basin), and that candidate populations share some interesting common environmental conditions., Peer reviewed

Crop Wild Relatives (CWR) are a valuable source of genetic diversity that can be transferred to commercial crops, so their conservation will become a priority in the face of climate change. Bizarrely, in situ conserved CWR populations and the traits one might wish to preserve in them are themselves vulnerable to climate change. In this study, we used a quantitative machine learning predictive approach to project the resistance of CWR populations of lentils to a common disease, lentil rust, caused by fungus Uromyces viciae-fabae. Resistance is measured through a proxy quantitative value, DSr (Disease Severity relative), quite complex and expensive to get. Therefore, machine learning is a convenient tool to predict this magnitude using a well-curated georeferenced calibration set. Previous works have provided a binary outcome (resistant vs. non-resistant), but that approach is not fine enough to answer three practical questions: which variables are key to predict rust resistance, which CWR populations are resistant to rust under current environmental conditions, and which of them are likely to keep this trait under different climate change scenarios. We first predict rust resistance in present time for crop wild relatives that grow up inside protected areas. Then, we use the same models under future climate IPCC (Intergovernmental Panel on Climate Change) scenarios to predict future DSr values. Populations that are rust-resistant by now and under future conditions are optimal candidates for further evaluation and in situ conservation of this valuable trait. We have found that rust-resistance variation as a result of climate change is not uniform across the geographic scope of the study (the Mediterranean basin), and that candidate populations share some interesting common environmental conditions., Peer reviewed

Supplementary Table 1 Trunk diameters measured in 2017 before starting the experiment of the central 16 vines of each treatment. The analysis of variance was performed at P < 0.05. ns = not significant; * = significant differences. Supplementary Table 2 Summary of all the vine measurements carried out in the experiment, which vines were used, when they were taken and what were the objectives of each measurement. Supplementary Table 3 Parameters used to calculate respiration and the reference from which they were extracted and adapted. For fruit respiration Q10 = 2 was assumed. In Escalona et al., 2012, shoot respiration was presented in nmol O2/gDW. We assumed a respiratory quotient = 1. Supplementary Table 4 Environmental conditions in and out of the whole canopy gas exchange chamber. Note that on 29th May temperature and VPD in the chamber for CFlate were high values since a pipe obturation occurred for one hour. Supplementary Table 5 Maximum net carbon exchange per leaf area (maxNCEch) and net carbon exchange (NCEch), measured through whole canopy gas exchange chamber, and net carbon exchange modelled (NCEm). Supplementary Table 6 Inputs required to estimate net carbon exchange model in the experimental zone for the days in which open-top whole canopy gas exchange chambers were operating. Note that not all the measurements included a whole day data since data were adjusted for the time the vine was in the whole canopy gas exchange chamber. Supplementary Figure 1 Scheme of the experimental design on an NDVI map performed in year 2016 with an airborne (all the methodology was described in Bellvert et al., 2020). The different numbers are he replicates of each treatment. The distance between vines of the same replicate of different treatments is represented in red. Supplementary Figure 2 Open-top whole canopy gas exchange chamber used to validate the net carbon exchange model. Supplementary Figure 3 Linear regression between modelled net carbon exchange (NCEm) and measured using an open-top whole-canopy gas exchange chamber (NCEch) (R2 = 0.95, y=1.03x- 1.98, RMSE = 5.8; NSE = 0.95). Black circles indicate measurements conducted before applying the treatments and includes vines from all three treatments in 2019. Measurements after the forcing date correspond to Control (blue), CFearly (green) and CFlate (orange). The grey dotted line means 1:1 relation., Elevated temperatures during berry ripening have been shown to affect grape quality. The crop forcing technique (summer pruning that ‘force’ the vine to start a new cycle) has been shown to improve berry quality by delaying the harvest date. However, yield is typically reduced on forced vines, which is attributed to vine low carbon availability soon after forcing and likely incomplete inflorescence formation. The present study aims to estimate the carbon balance of forced vines and evaluate vine responses to changes in carbon patterns due to forcing. Three treatments were studied on Tempranillo cultivar: non-forced vines (Control), vines forced shortly after fruit set (CFearly) and vines forced one month later at the beginning of bunch closure (CFlate). Whole canopy net carbon exchange was modelled and validated using two whole canopy gas exchange chambers. In addition, non-structural carbohydrate reserves at budburst, forcing date and harvest, were analysed. Yield, yield components and vegetative growth were also evaluated. Harvest date was delayed by one and two months in the CFearly and CFlate, respectively, which increased must acidity. However, yield was lower in the forced treatments compared to the Control (49% lower for CFearly and 82% for CFlate). In the second year, at the time when CFearly and CFlate dormant buds were unlocked (forced budburst), forced vines had significantly lower non-structural carbohydrates than Control vines at budburst. Although the time elapsed from budburst to reach maximum net carbon exchange was longer for the Control treatment (80 days) than for the forced treatments (about 40 days), average daily net carbon exchange until harvest was comparable between Control (60.9 g CO2/vine/day) and CFearly (55.9 g CO2/vine/day), but not for CFlate (38.7 g CO2/vine/day). In addition, the time elapsed from budburst to harvest was shorter in forced treatments (about 124 days) than for the Control (172 days). As a result, the cumulative net carbon exchange until harvest was reduced by 35% (CFearly) and 55% (CFlate) in the forced treatments. However, no differences in carbon reserves at harvest were observed between treatments partly helped by the higher source:sink ratio observed in forced than Control vines., Peer reviewed

TABLE S1. Country of origin of the landraces lines and pedigree of ICARDA’s breeding lines of the tested accessions for herbicide tolerance., Peer reviewed

Supplementary Figure S1. Light micrographs of Aporcelaimus vorax Thorne & Swanger, 1936 (New York population, female). (a) anterior region in lateral, median view; (b) same in submedian view; (c) same in surface view; (d, j) anterior genital branch; (e) pharyngo-intestinal junction; (f) uterine egg; (g, h) vagina; (i) posterior body region; (k, l) caudal region. (Scale bars: a-c = 10 μm; d, I, j = 100 μm; e, g, h, k, l = 20 μm; f = 50 μm.). Supplementary Figure S2. Light micrographs of Aporcelaimus vorax Thorne & Swanger, 1936 (Utah population, female). (a-c, g, k) anterior region in lateral, median view, white arrow head pointing at a mucro located behind the odontophore base; (d) posterior genital branch; (e, f) anterior region in lateral, surface view; (h) vagina; (i) posterior body region; (j) caudal region. (Scale bars: a, g, k, h, j = 20 μm; b, c, e, f = 10 μm; d, i = 100 μm.). Supplementary Figure S3. Phylogenetic relationships of Epacrolaimus declinatoaculeatus with species of Dorylaimida. Bayesian 50% majority rule consensus tree as inferred from cytochrome c oxidase subunit I (COI) mtDNA gene sequence alignment under the TIM1 + I+ G model (−lnL = 1794.5284; AIC = 3649.056880; freqA = 0.2733; freqC = 0.1679; freqG =0.2093; freqT = 0.3495; R(a) = 1.0000; R(b) = 23.6308; R(c) = 18.0225; R(d) = 18.0225; R(e) = 59.8927; R(f) = 1.0000; Pinva = 0.4440; and Shape = 2.0240). Posterior probabilities more than 0.70 are given for appropriate clades. Newly obtained sequences in this study are shown in bold, and coloured box indicate clade association of the studied species. Scale bar = expected changes per site. Supplementary Table S1. Morphometrics of previous records of Epacrolaimus declinatoaculeatus (Kreis, 1924) Andrássy, 2000 (= Aporcelaimus vorax Thorne & Swanger, 1936). Measurements in μm except L in mm. [See printed text for additional information.], Peer reviewed

The use of more salt stress-tolerant vine rootstocks can be a sustainable strategy for adapting traditional grapevine cultivars to future conditions. However, how the new M1 and M4 rootstocks perform against salinity compared to conventional ones, such as the 1103-Paulsen, had not been previously assessed under real field conditions. Therefore, a field trial was carried out in a young ‘Tempranillo’ (Vitis vinifera L.) vineyard grafted onto all three rootstocks under a semi-arid and hot-summer Mediterranean climate. The vines were irrigated with two kinds of water: a non-saline Control with EC of 0.8 dS m–1 and a Saline treatment with 3.5 dS m–1. Then, various physiological parameters were assessed in the scion, and, additionally, gene expression was studied by high throughput sequencing in leaf and berry tissues. Plant water relations evidenced the osmotic effect of water quality, but not that of the rootstock. Accordingly, leaf-level gas exchange rates were also reduced in all three rootstocks, with M1 inducing significantly lower net photosynthesis rates than 1103-Paulsen. Nevertheless, the expression of groups of genes involved in photosynthesis and amino acid metabolism pathways were not significantly and differentially expressed. The irrigation with saline water significantly increased leaf chloride contents in the scion onto the M-rootstocks, but not onto the 1103P. The limitation for leaf Cl– and Na+ accumulation on the scion was conferred by rootstock. Few processes were differentially regulated in the scion in response to the saline treatment, mainly, in the groups of genes involved in the flavonoids and phenylpropanoids metabolic pathways. However, these transcriptomic effects were not fully reflected in grape phenolic ripeness, with M4 being the only one that did not cause reductions in these compounds in response to salinity, and 1103-Paulsen having the highest overall concentrations. These results suggest that all three rootstocks confer short-term salinity tolerance to the scion. The lower transcriptomic changes and the lower accumulation of potentially phytotoxic ions in the scion grafted onto 1103-Paulsen compared to M-rootstocks point to the former being able to maintain this physiological response in the longer term. Further agronomic trials should be conducted to confirm these effects on vine physiology and transcriptomics in mature vineyards., Peer reviewed

The use of more salt stress-tolerant vine rootstocks can be a sustainable strategy for adapting traditional grapevine cultivars to future conditions. However, how the new M1 and M4 rootstocks perform against salinity compared to conventional ones, such as the 1103-Paulsen, had not been previously assessed under real field conditions. Therefore, a field trial was carried out in a young ‘Tempranillo’ (Vitis vinifera L.) vineyard grafted onto all three rootstocks under a semi-arid and hot-summer Mediterranean climate. The vines were irrigated with two kinds of water: a non-saline Control with EC of 0.8 dS m–1 and a Saline treatment with 3.5 dS m–1. Then, various physiological parameters were assessed in the scion, and, additionally, gene expression was studied by high throughput sequencing in leaf and berry tissues. Plant water relations evidenced the osmotic effect of water quality, but not that of the rootstock. Accordingly, leaf-level gas exchange rates were also reduced in all three rootstocks, with M1 inducing significantly lower net photosynthesis rates than 1103-Paulsen. Nevertheless, the expression of groups of genes involved in photosynthesis and amino acid metabolism pathways were not significantly and differentially expressed. The irrigation with saline water significantly increased leaf chloride contents in the scion onto the M-rootstocks, but not onto the 1103P. The limitation for leaf Cl– and Na+ accumulation on the scion was conferred by rootstock. Few processes were differentially regulated in the scion in response to the saline treatment, mainly, in the groups of genes involved in the flavonoids and phenylpropanoids metabolic pathways. However, these transcriptomic effects were not fully reflected in grape phenolic ripeness, with M4 being the only one that did not cause reductions in these compounds in response to salinity, and 1103-Paulsen having the highest overall concentrations. These results suggest that all three rootstocks confer short-term salinity tolerance to the scion. The lower transcriptomic changes and the lower accumulation of potentially phytotoxic ions in the scion grafted onto 1103-Paulsen compared to M-rootstocks point to the former being able to maintain this physiological response in the longer term. Further agronomic trials should be conducted to confirm these effects on vine physiology and transcriptomics in mature vineyards., Peer reviewed

The use of more salt stress-tolerant vine rootstocks can be a sustainable strategy for adapting traditional grapevine cultivars to future conditions. However, how the new M1 and M4 rootstocks perform against salinity compared to conventional ones, such as the 1103-Paulsen, had not been previously assessed under real field conditions. Therefore, a field trial was carried out in a young ‘Tempranillo’ (Vitis vinifera L.) vineyard grafted onto all three rootstocks under a semi-arid and hot-summer Mediterranean climate. The vines were irrigated with two kinds of water: a non-saline Control with EC of 0.8 dS m–1 and a Saline treatment with 3.5 dS m–1. Then, various physiological parameters were assessed in the scion, and, additionally, gene expression was studied by high throughput sequencing in leaf and berry tissues. Plant water relations evidenced the osmotic effect of water quality, but not that of the rootstock. Accordingly, leaf-level gas exchange rates were also reduced in all three rootstocks, with M1 inducing significantly lower net photosynthesis rates than 1103-Paulsen. Nevertheless, the expression of groups of genes involved in photosynthesis and amino acid metabolism pathways were not significantly and differentially expressed. The irrigation with saline water significantly increased leaf chloride contents in the scion onto the M-rootstocks, but not onto the 1103P. The limitation for leaf Cl– and Na+ accumulation on the scion was conferred by rootstock. Few processes were differentially regulated in the scion in response to the saline treatment, mainly, in the groups of genes involved in the flavonoids and phenylpropanoids metabolic pathways. However, these transcriptomic effects were not fully reflected in grape phenolic ripeness, with M4 being the only one that did not cause reductions in these compounds in response to salinity, and 1103-Paulsen having the highest overall concentrations. These results suggest that all three rootstocks confer short-term salinity tolerance to the scion. The lower transcriptomic changes and the lower accumulation of potentially phytotoxic ions in the scion grafted onto 1103-Paulsen compared to M-rootstocks point to the former being able to maintain this physiological response in the longer term. Further agronomic trials should be conducted to confirm these effects on vine physiology and transcriptomics in mature vineyards., Peer reviewed

Supplemental table S1: Primers and probes used for grapevine gene expression analysis., The use of more salt stress-tolerant vine rootstocks can be a sustainable strategy for adapting traditional grapevine cultivars to future conditions. However, how the new M1 and M4 rootstocks perform against salinity compared to conventional ones, such as the 1103-Paulsen, had not been previously assessed under real field conditions. Therefore, a field trial was carried out in a young ‘Tempranillo’ (Vitis vinifera L.) vineyard grafted onto all three rootstocks under a semi-arid and hot-summer Mediterranean climate. The vines were irrigated with two kinds of water: a non-saline Control with EC of 0.8 dS m–1 and a Saline treatment with 3.5 dS m–1. Then, various physiological parameters were assessed in the scion, and, additionally, gene expression was studied by high throughput sequencing in leaf and berry tissues. Plant water relations evidenced the osmotic effect of water quality, but not that of the rootstock. Accordingly, leaf-level gas exchange rates were also reduced in all three rootstocks, with M1 inducing significantly lower net photosynthesis rates than 1103-Paulsen. Nevertheless, the expression of groups of genes involved in photosynthesis and amino acid metabolism pathways were not significantly and differentially expressed. The irrigation with saline water significantly increased leaf chloride contents in the scion onto the M-rootstocks, but not onto the 1103P. The limitation for leaf Cl– and Na+ accumulation on the scion was conferred by rootstock. Few processes were differentially regulated in the scion in response to the saline treatment, mainly, in the groups of genes involved in the flavonoids and phenylpropanoids metabolic pathways. However, these transcriptomic effects were not fully reflected in grape phenolic ripeness, with M4 being the only one that did not cause reductions in these compounds in response to salinity, and 1103-Paulsen having the highest overall concentrations. These results suggest that all three rootstocks confer short-term salinity tolerance to the scion. The lower transcriptomic changes and the lower accumulation of potentially phytotoxic ions in the scion grafted onto 1103-Paulsen compared to M-rootstocks point to the former being able to maintain this physiological response in the longer term. Further agronomic trials should be conducted to confirm these effects on vine physiology and transcriptomics in mature vineyards., Peer reviewed