Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era

Identification of the polymorphisms controlling quantitative traits remains a challenge for plant geneticists. Multiparent advanced generation intercross (MAGIC) populations offer an alternative to traditional linkage or association mapping populations by increasing the precision of quantitative trait loci (QTL) mapping. Here, we present the first tomato MAGIC population and highlight its potential for the valorization of intraspecific variation, QTL mapping and causal polymorphism identification. The population was developed by crossing eight founder lines, selected to include a wide range of genetic diversity, whose genomes have been previously resequenced. We selected 1536 SNPs among the 4 million available to enhance haplotype prediction and recombination detection in the population. The linkage map obtained showed an 87% increase in recombination frequencies compared to biparental populations. The prediction of the haplotype origin was possible for 89% of the MAGIC line genomes, allowing QTL detection at the haplotype level. We grew the population in two greenhouse trials and detected QTLs for fruit weight. We mapped three stable QTLs and six specific of a location. Finally, we showed the potential of the MAGIC population when coupled with whole genome sequencing of founder lines to detect candidate SNPs underlying the QTLs. For a previously cloned QTL on chromosome 3, we used the predicted allelic effect of each founder and their genome sequences to select putative causal polymorphisms in the supporting interval. The number of candidate polymorphisms was reduced from 12 284 (in 800 genes) to 96 (in 54 genes), including the actual causal polymorphism. This population represents a new permanent resource for the tomato genetics community.     

Light‐dependent regulation of ascorbate in tomato by a monodehydroascorbate reductase localized in peroxisomes and the cytosol

Ascorbate is a powerful antioxidant in plants, and its levels are an important quality criteria in commercial species. Factors influencing these levels include environmental variations, particularly light, and the genetic control of its biosynthesis, recycling and degradation. One of the genes involved in the recycling pathway encodes a monodehydroascorbate reductase (MDHAR), an enzyme catalysing reduction of the oxidized radical of ascorbate, monodehydroascorbate, to ascorbate. In plants, MDHAR belongs to a multigene family. Here, we report the presence of an MDHAR isoform in both the cytosol and peroxisomes and show that this enzyme negatively regulates ascorbate levels in Solanum lycopersicum (tomato). Transgenic lines overexpressing MDHAR show a decrease in ascorbate levels in leaves, whereas lines where MDHAR is silenced show an increase in these levels in both fruits and leaves. Furthermore, the intensity of these differences is light dependent. The unexpected effect of this MDHAR on ascorbate levels cannot be explained by changes in the expression of Smirnoff–Wheeler pathway genes, or the activity of enzymes involved in degradation (ascorbate peroxidase) or recycling of ascorbate (dehydroascorbate reductase and glutathione reductase), suggesting a previously unidentified mechanism regulating ascorbate levels.     

The genetic and functional analysis of flavor in commercial tomato: the FLORAL4 gene underlies a QTL for floral aroma volatiles in tomato fruit

Tomato (Solanum lycopersicum L.) has become a popular model for genetic studies of fruit flavor in the last two decades. In this article we present a study of tomato fruit flavor, including an analysis of the genetic, metabolic and sensorial variation of a collection of contemporary commercial glasshouse tomato cultivars, followed by a validation of the associations found by quantitative trait locus (QTL) analysis of representative biparental segregating populations. This led to the identification of the major sensorial and chemical components determining fruit flavor variation and detection of the underlying QTLs. The high representation of QTL haplotypes in the breeders’ germplasm suggests that there is great potential for applying these QTLs in current breeding programs aimed at improving tomato flavor. A QTL on chromosome 4 was found to affect the levels of the phenylalanine‐derived volatiles (PHEVs) 2‐phenylethanol, phenylacetaldehyde and 1‐nitro‐2‐phenylethane. Fruits of near‐isogenic lines contrasting for this locus and in the composition of PHEVs significantly differed in the perception of fruity and rose‐hip‐like aroma. The PHEV locus was fine mapped, which allowed for the identification of FLORAL4 as a candidate gene for PHEV regulation. Using a gene‐editing‐based (CRISPR‐CAS9) reverse‐genetics approach, FLORAL4 was demonstrated to be the key factor in this QTL affecting PHEV accumulation in tomato fruit.     

Direct analysis of pollen fitness by flow cytometry: implications for pollen response to stress

Sexual reproduction in flowering plants depends on the fitness of the male gametophyte during fertilization. Because pollen development is highly sensitive to hot and cold temperature extremes, reliable methods to evaluate pollen viability are important for research into improving reproductive heat stress (HS) tolerance. Here, we describe an approach to rapidly evaluate pollen viability using a reactive oxygen species (ROS) probe dichlorodihydrofluorescein diacetate (i.e. H₂DCFDA‐staining) coupled with flow cytometry. In using flow cytometry to analyze mature pollen harvested from Arabidopsis and tomato flowers, we discovered that pollen distributed bimodally into ‘low‐ROS’ and ‘high‐ROS’ subpopulations. Pollen germination assays following fluorescence‐activated cell sorting revealed that the high‐ROS pollen germinated with a frequency that was 35‐fold higher than the low‐ROS pollen, supporting a model in which a significant fraction of a flower's pollen remains in a low metabolic or dormant state even after hydration. The ability to use flow cytometry to quantify ROS dynamics within a large pollen population was shown by dose‐dependent alterations in DCF‐fluorescence in response to oxidative stress or antioxidant treatments. HS treatments (35°C) increased ROS levels, which correlated with a ~60% reduction in pollen germination. These results demonstrate the potential of using flow cytometry‐based approaches to investigate metabolic changes during stress responses in pollen.     

Lethal and sublethal behavioural responses of saline water beetles to acute heat and osmotic stress

1. As species' physiological breadth determines their potential to deal with environmental changes, and influences individuals' survival and the persistence of populations, information about lethal and sublethal responses could be fundamental for conservation purposes. 2. We used a standard experimental approach to explore mortality and behavioural avoidance responses (i.e. flight and emersion from the water) to a combination of acute heat and osmotic stress on six species of saline water beetles (belonging to Enochrus, Nebrioporus, and Ochthebius genera). 3. Heat stress affected survival and behavioural responses in all of the species, whereas osmotic stress and the interaction between both stressors only showed significant effects for the Ochthebius genus. Behavioural and survival patterns were highly interrelated across the stress gradients. The Enochrus and Nebrioporus studied species showed maximum avoidance activity at 35–40 °C, and a short (< 30 min) exposure to 45 °C was lethal. Ochthebius species were the most heat tolerant and displayed increasing behavioural responses with increasing temperature. In the Nebrioporus and Ochthebius genera, the species occupying lotic, more environmentally stable habitats, showed greater mortality, and avoidance responses were higher or initiated at lower stress thresholds than lentic species. In contrast, both Enochrus species displayed a similar mortality, and the lentic species E. bicolor emerged and flew more than the lotic E. falcarius, in concordance with its higher dispersal capacity. 4. Avoidance responses could provide interesting information about species' physiological amplitudes as a complement to lethal responses. The lotic species here studied showed narrower physiological amplitude (i.e. N. baeticus and O. glaber) or lower dispersal ability (i.e. E. falcarius) than their lentic relatives; both traits could result in a higher vulnerability of lotic species to thermal habitat changes.     

Wool cortisol is a better indicator of stress than blood cortisol in ewes exposed to heat stress and water restriction

This study investigated the effect of water restriction on wool and blood cortisol concentrations and water consumption patterns in heat-stressed sheep. Nine Corriedale female sheep (average BW=43±6.5 kg) were individually fed diets based on maintenance requirement in metabolic crates. They were assigned to three treatments according to a Latin square design (3×3) for three periods with a 21-day duration for each period (nine sheep per treatment). Treatments included free access to water (FAW), 2 h water restriction (2hWR) and 3 h water restriction (3hWR) after feeding. Average temperature–humidity index in the experimental room was 27.9 throughout the experiment that defines heat stress conditions. Wool samples were taken at the end of each period on day 21. No differences were found in cortisol concentration in each fragment (dried, washed and residual extract) of wool (P<0.05). Total wool cortisol concentration was higher in the 3hWR group than the other treatments (P<0.05). Blood cortisol was not different among the treatments (P>0.05) and resulted in higher variable data compared with wool cortisol. Blood neutrophils and neutrophil/lymphocyte ratio suppressed in FAW and 3hWR groups compared with the 2hWR group (P<0.05). The duration of water consumption recorded after feeding in the 3hWR group was higher than in the 2hWR group when recorded in the afternoon (P<0.01). Water consumption rate was higher in the 3hWR group than in the 2hWR group (P<0.01). However, total water consumed was lower in the 3hWR group compared with other treatments (P>0.05). It can be concluded that wool cortisol provides more precise and accurate data than blood cortisol during heat stress conditions. Water restriction for 3 h after feeding can act as a stressor and is critical for sheep during heat stress as the consumption of water decreases with restriction.     

The combined effect of salinity and heat reveals a specific physiological,biochemical and molecular response in tomato plants

Many studies have described the response mechanisms of plants to salinity and heat applied individually; however, under field conditions some abiotic stresses often occur simultaneously. Recent studies revealed that the response of plants to a combination of two different stresses is specific and cannot be deduced from the stresses applied individually. Here, we report on the response of tomato plants to a combination of heat and salt stress. Interestingly, and in contrast to the expected negative effect of the stress combination on plant growth, our results show that the combination of heat and salinity provides a significant level of protection to tomato plants from the effects of salinity. We observed a specific response of plants to the stress combination that included accumulation of glycine betaine and trehalose. The accumulation of these compounds under the stress combination was linked to the maintenance of a high K⁺ concentration and thus a lower Na⁺/K⁺ ratio, with a better performance of the cell water status and photosynthesis as compared with salinity alone. Our findings unravel new and unexpected aspects of the response of plants to stress combination and provide a proposed list of enzymatic targets for improving crop tolerance to the abiotic field environment.     

冬小麦农田暂时水分胁迫状况下水、热通量日变化

以冬小麦农田尺度为研究对象,采用涡度相关技术测定农田能茸平衡各分量,研究暂时水分胁迫状况下农田蒸散通量和蒸发比值（evaporative fraction）日变化特征。结果表明,冬小麦在农田郁闭（LAI≥3）且土壤含水量为田间持水量的55％-65％时,晴天日农田潜热通量日变化在正午前后存在明显的“蒸散高地（evapotranspiration plateau）”现象,持续时间达2．5—4h,表现为蒸散通量增量日变化突然极显著降低,即蒸散通量呈相对稳定、甚至下降的变化趋势;反映在蒸发比值日变化过程方面,夜间和日出日落前后时刻蒸发比值变化较大,7：00-18：00时段内蒸发比值曲线近似呈倒“s”型,9：00～16：00时段内蒸发比值比较稳定,正午前后蒸散高地出现时,蒸发比值有所下降大约在0．5—0．65范围内,12：00—13：30时段内蒸发比值平均值接近9：00—16：00时段内蒸发比值平均值。     

The combined effects of a long‐term experimental drought and an extreme drought on the use of plant‐water sources in a Mediterranean forest

Vegetation in water‐limited ecosystems relies strongly on access to deep water reserves to withstand dry periods. Most of these ecosystems have shallow soils over deep groundwater reserves. Understanding the functioning and functional plasticity of species‐specific root systems and the patterns of or differences in the use of water sources under more frequent or intense droughts is therefore necessary to properly predict the responses of seasonally dry ecosystems to future climate. We used stable isotopes to investigate the seasonal patterns of water uptake by a sclerophyll forest on sloped terrain with shallow soils. We assessed the effect of a long‐term experimental drought (12 years) and the added impact of an extreme natural drought that produced widespread tree mortality and crown defoliation. The dominant species, Quercus ilex, Arbutus unedo and Phillyrea latifolia, all have dimorphic root systems enabling them to access different water sources in space and time. The plants extracted water mainly from the soil in the cold and wet seasons but increased their use of groundwater during the summer drought. Interestingly, the plants subjected to the long‐term experimental drought shifted water uptake toward deeper (10–35 cm) soil layers during the wet season and reduced groundwater uptake in summer, indicating plasticity in the functional distribution of fine roots that dampened the effect of our experimental drought over the long term. An extreme drought in 2011, however, further reduced the contribution of deep soil layers and groundwater to transpiration, which resulted in greater crown defoliation in the drought‐affected plants. This study suggests that extreme droughts aggravate moderate but persistent drier conditions (simulated by our manipulation) and may lead to the depletion of water from groundwater reservoirs and weathered bedrock, threatening the preservation of these Mediterranean ecosystems in their current structures and compositions.     

The temporal response to drought in a Mediterranean evergreen tree: comparing a regional precipitation gradient and a throughfall exclusion experiment

Like many midlatitude ecosystems, Mediterranean forests will suffer longer and more intense droughts with the ongoing climate change. The responses to drought in long‐lived trees differ depending on the time scale considered, and short‐term responses are currently better understood than longer term acclimation. We assessed the temporal changes in trees facing a chronic reduction in water availability by comparing leaf‐scale physiological traits, branch‐scale hydraulic traits, and stand‐scale biomass partitioning in the evergreen Quercus ilex across a regional precipitation gradient (long‐term changes) and in a partial throughfall exclusion experiment (TEE, medium term changes). At the leaf scale, gas exchange, mass per unit area and nitrogen concentration showed homeostatic responses to drought as they did not change among the sites of the precipitation gradient or in the experimental treatments of the TEE. A similar homeostatic response was observed for the xylem vulnerability to cavitation at the branch scale. In contrast, the ratio of leaf area over sapwood area (LA/SA) in young branches exhibited a transient response to drought because it decreased in response to the TEE the first 4 years of treatment, but did not change among the sites of the gradient. At the stand scale, leaf area index (LAI) decreased, and the ratios of stem SA to LAI and of fine root area to LAI both increased in trees subjected to throughfall exclusion and from the wettest to the driest site of the gradient. Taken together, these results suggest that acclimation to chronic drought in long‐lived Q. ilex is mediated by changes in hydraulic allometry that shift progressively from low (branch) to high (stand) organizational levels, and act to maintain the leaf water potential within the range of xylem hydraulic function and leaf photosynthetic assimilation.     

The effect of nitrogen availability and water conditions on competition between a facultative CAM plant and an invasive grass

Abstract Plants with crassulacean acid metabolism (CAM) are increasing their abundance in drylands worldwide. The drivers and mechanisms underlying the increased dominance of CAM plants and CAM expression (i.e., nocturnal carboxylation) in facultative CAM plants, however, remain poorly understood. We investigated how nutrient and water availability affected competition between Mesembryanthemum crystallinum (a model facultative CAM species) and the invasive C₃ grass Bromus mollis that co‐occur in California's coastal grasslands. Specifically we investigated the extent to which water stress, nutrients, and competition affect nocturnal carboxylation in M. crystallinum. High nutrient and low water conditions favored M. crystallinum over B. mollis, in contrast to high water conditions. While low water conditions induced nocturnal carboxylation in 9‐week‐old individuals of M. crystallinum, in these low water treatments, a 66% reduction in nutrient applied over the entire experiment did not further enhance nocturnal carboxylation. In high water conditions M. crystallinum both alone and in association with B. mollis did not perform nocturnal carboxylation, regardless of the nutrient levels. Thus, nocturnal carboxylation in M. crystallinum was restricted by strong competition with B. mollis in high water conditions. This study provides empirical evidence of the competitive advantage of facultative CAM plants over grasses in drought conditions and of the restricted ability of M. crystallinum to use their photosynthetic plasticity (i.e., ability to switch to CAM behavior) to compete with grasses in well‐watered conditions. We suggest that a high drought tolerance could explain the increased dominance of facultative CAM plants in a future environment with increased drought and nitrogen deposition, while the potential of facultative CAM plants such as M. crystallinum to expand to wet environments is expected to be limited.     

The apparent viscosity of the protoplasm of subepidermal stem basis cells of Pisum sativum. Relation to aging, drought tolerance and water stress

Plants of Pisum sativum L. cv. Alaska wilt resistant were subjected to two different water stress regimes under controlled environment conditions: watering was stopped either on the 7th day (early stress) or on the 21st day (late stress) after planting. Plants under the early stress regime developed drought tolerance (adapted), while those under late stress did not. The apparent viscosity of the protoplasm of subepidermal stem basis cells was analyzed by the centrifugation and plasmolysis form method during the entire growth period.
The apparent viscosity of the subepidermal stem basis cells changed with plant age and was highest in 3-week-old plants. In controls the relation of apparent viscosity to age was the same when measured under full turgor and in relaxed state. Under early stress condition, however, the pattern of the viscosity changes with plant age was significantly different for turgescent and relaxed cells. In four week old plants, a higher apparent viscosity was measured in relaxed adapted cells than in relaxed control cells. It is suggested that the higher apparent viscosity is the result of a delayed cell aging.
Apparent viscosity was inversely proportional to soil moisture content and the osmotic potential of the cell sap for the cells of late stress plants, whereas no clear relation was found for the cells of early stress plants. This difference may indicate two mechanisms of viscosity changes: 1) osmotic dehydration of the protoplasm under water stress (passive viscosity change), 2) changes in the amount, hydration or architecture of macromolecules present in the cytoplasm (active viscosity change). Whereas differences in the apparent viscosity between control and stressed cells may not be the cause of drought tolerance, they seem to indicate the development of drought tolerance. Water stress history and plant age were the most critical factors controlling the apparent viscosity changes observed.     

The metabolic flux phenotype of heterotrophic Arabidopsis cells reveals a flexible balance between the cytosolic and plastidic contributions to carbohydrate oxidation in response to phosphate limitation

Understanding the mechanisms that allow plants to respond to variable and reduced availability of inorganic phosphate is of increasing agricultural importance because of the continuing depletion of the rock phosphate reserves that are used to combat inadequate phosphate levels in the soil. Changes in gene expression, protein levels, enzyme activities and metabolite levels all point to a reconfiguration of the central metabolic network in response to reduced availability of inorganic phosphate, but the metabolic significance of these changes can only be assessed in terms of the fluxes supported by the network. Steady‐state metabolic flux analysis was used to define the metabolic phenotype of a heterotrophic Arabidopsis thaliana cell culture grown on a Murashige and Skoog medium containing 0, 1.25 or 5 mm inorganic phosphate. Fluxes through the central metabolic network were deduced from the redistribution of ¹³C into metabolic intermediates and end products when cells were labelled with [1‐¹³C], [2‐¹³C], or [¹³C₆]glucose, in combination with ¹⁴C measurements of the rates of biomass accumulation. Analysis of the flux maps showed that reduced levels of phosphate in the growth medium stimulated flux through phosphoenolpyruvate carboxylase and malic enzyme, altered the balance between cytosolic and plastidic carbohydrate oxidation in favour of the plastid, and increased cell maintenance costs. We argue that plant cells respond to phosphate deprivation by reconfiguring the flux distribution through the pathways of carbohydrate oxidation to take advantage of better phosphate homeostasis in the plastid.