Host Adaptation Through Hybridization: Genome Analysis of Triticale Powdery Mildew Reveals Unique Combination of Lineage-Specific Effectors

The emergence of new fungal pathogens through hybridization represents a serious challenge for agriculture. Hybridization between the wheat mildew (Blumeria graminis f. sp. tritici) and rye mildew (B. graminis f. sp. secalis) pathogens has led to the emergence of a new mildew form (B. graminis f. sp. triticale) growing on triticale, a man-made amphiploid crop derived from crossing rye and wheat, which was originally resistant to the powdery mildew disease. The identification of the genetic basis of host adaptation in triticale mildew has been hampered by the lack of a reference genome. Here, we report the 141.4-Mb reference assembly of triticale mildew isolate THUN-12 derived from long-read sequencing and genetic map-based scaffolding. All 11 triticale mildew chromosomes were assembled from telomere-to-telomere and revealed that 19.7% of the hybrid genome was inherited from the rye mildew parental lineage. We identified lineage-specific regions in the hybrid, inherited from the rye or wheat mildew parental lineages, that harbor numerous bona fide candidate effectors. We propose that the combination of lineage-specific effectors in the hybrid genome is crucial for host adaptation, allowing the fungus to simultaneously circumvent the immune systems contributed by wheat and rye in the triticale crop. In line with this, we demonstrate the functional transfer of the SvrPm3 effector from wheat to triticale mildew, a virulence effector that specifically suppresses resistance of the wheat Pm3 allelic series. This transfer is the likely underlying cause for the observed poor effectiveness of several Pm3 alleles against triticale mildew and exemplifies the negative implications of pathogen hybridizations on resistance breeding. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license

Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat

Introgressions of chromosomal segments from related species into wheat are important sources of resistance against fungal diseases. The durability and effectiveness of introgressed resistance genes upon agricultural deployment is highly variable-a phenomenon that remains poorly understood, as the corresponding fungal avirulence genes are largely unknown. Until its breakdown, the Pm17 resistance gene introgressed from rye to wheat provided broad resistance against powdery mildew (Blumeria graminis). Here, we used quantitative trait locus (QTL) mapping to identify the corresponding wheat mildew avirulence effector AvrPm17. It is encoded by two paralogous genes that exhibit signatures of reoccurring gene conversion events and are members of a mildew sublineage specific effector cluster. Extensive haplovariant mining in wheat mildew and related sublineages identified several ancient virulent AvrPm17 variants that were present as standing genetic variation in wheat powdery mildew prior to the Pm17 introgression, thereby paving the way for the rapid breakdown of the Pm17 resistance. QTL mapping in mildew identified a second genetic component likely corresponding to an additional resistance gene present on the 1AL.1RS translocation carrying Pm17. This gene remained previously undetected due to suppressed recombination within the introgressed rye chromosomal segment. We conclude that the initial effectiveness of 1AL.1RS was based on simultaneous introgression of two genetically linked resistance genes. Our results demonstrate the relevance of pathogen-based genetic approaches to disentangling complex resistance loci in wheat. We propose that identification and monitoring of avirulence gene diversity in pathogen populations become an integral part of introgression breeding to ensure effective and durable resistance in wheat

A chromosome-scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew

Blumeria graminis f. sp. tritici (B.g. tritici) is the causal agent of the wheat powdery mildew disease. The highly fragmented B.g. tritici genome available so far has prevented a systematic analysis of effector genes that are known to be involved in host adaptation. To study the diversity and evolution of effector genes we produced a chromosome‐scale assembly of the B.g. tritici genome. The genome assembly and annotation was achieved by combining long‐read sequencing with high‐density genetic mapping, bacterial artificial chromosome fingerprinting and transcriptomics. We found that the 166.6 Mb B.g. tritici genome encodes 844 candidate effector genes, over 40% more than previously reported. Candidate effector genes have characteristic local genomic organization such as gene clustering and enrichment for recombination‐active regions and certain transposable element families. A large group of 412 candidate effector genes shows high plasticity in terms of copy number variation in a global set of 36 isolates and of transcription levels. Our data suggest that copy number variation and transcriptional flexibility are the main drivers for adaptation in B.g. tritici. The high repeat content may play a role in providing a genomic environment that allows rapid evolution of effector genes with selection as the driving force

Developing of biophysical food for monitoring postharvest supply chains for avocado and potato and deploying of biophysical apple

Horticultural products are prone to high postharvest losses due to their perishability and susceptibility to drivers for food decay, including temperature. A narrow temperature window must typically be maintained to prevent accelerated decay and, at the same time, thermal damage, such as chilling injury. Food simulators or so-called biophysical food help monitor temperature anomalies in the postharvest cold chain, and optimize refrigerated transport and storage. This biophysical food for fruit and vegetables needs to be tailored for each commodity or cultivar to consider different physical properties influencing their thermal response. We developed new biophysical food for two sizes of both avocado (cv. ‘Hass') and potato (cv. ‘Kufir Jyoti’ and ‘Agria’). The shell design and filling were adapted to mimic the specific characteristics of the real products. Integrated sensors logged core and surface temperature. Furthermore, we optimized the production steps of our existing biophysical food prototype for apples (cv. ‘Braeburn’) and deployed them in a cold storage facility in India. Thereby our biophysical apple was used to map the thermal distribution inside a cooling unit. By mimicking the real commodities' thermal response via biophysical food, we gain complementary insights compared to only monitoring air temperature. Our plug-and-play biophysical food can be stored with real food, particularly to sense conditions in hard-to-reach locations. These biophysical food temperature data will help improve cold chain operations to achieve optimal and homogenous cooling and decrease postharvest losses.ISSN:0260-8774ISSN:1873-577

Comparison of freezing and convective dehydrofreezing of vegetables for reducing cell damage

Freezing is a standard method to preserve perishable agricultural products such as fruits and vegetables, which increases off-season availability. Nevertheless, freezing of plant tissue with high water content causes cellular damage by the formation of ice crystals. This damage leads to drip loss and decreased firmness, which then reduces the quality of the thawed product. To maximize cell survival for industrial freezing processes, a promising freezing method, namely convective dehydrofreezing, was benchmarked against conventional freezing methods for different fruit and vegetables. We analyzed the final quality of thawed carrot, bell pepper, and cucumber cuts by quantifying drip loss and tissue firmness. The tissue microstructure was investigated by X-ray computed tomography after slow and fast freezing. We found that convective dehydrofreezing of bell pepper leads on average to a 52% firmer product in comparison with conventional freezing at −20 °C. For dehydrofrozen carrot, the firmness was similarly increased by 35%. Together with the significantly reduced drip loss for all tested species, these results are indicative of lower cell damage in dehydrofrozen samples. We found that dehydrofreezing of bell pepper, using different pre-drying times with resulting moisture content between 818% and 1303% dry basis, did not lead to a significant difference in drip loss or product firmness. Additionally, it was shown that freezing at an ultra-low temperature of −196 °C reduced product quality as the cucumber firmness decreased by 34% compared to conventional freezing. Freezing at low temperatures by convective freezing at −80 °C improved quality for bell pepper by producing 67% firmer products than conventional freezing.ISSN:0260-8774ISSN:1873-577

Digital twins enable the quantification of the trade-offs in maintaining citrus quality and marketability in the refrigerated supply chain.

Supply chains of fresh fruit must maintain a very narrow window of hygrothermal conditions after harvest. Any excursions outside this range can markedly lower the consumer acceptability of the fruit. However, the loss in fruit quality and marketability largely remains invisible to stakeholders throughout the supply chain. Here we developed a physics-based digital twin of citrus fruit to pinpoint when, why and to what extent fruit quality and marketability are reduced. Sensor data on 47 commercial shipments are thereby translated into actionable metrics for supply chain stakeholders by mapping the variability using principal component analysis. We unveiled a large spread (between 3% and 60%) in the shipments for different metrics of quality and marketability. Half of the shipments currently lie outside the ideal trade-off range between maintaining quality, killing fruit fly larvae and avoiding chilling injury. The digital twin technology opens the possibility to obtain the real-time coupling with sensor data to monitor food quality and marketability

How much do process parameters affect the residual quality attributes of dried fruits and vegetables for convective drying?

Drying processes reduce the amount of available essential nutrients in dried plant-based foods to a large extent compared to fresh produce. This reduction is much larger than the differences in the final quality of products dried using various processing parameters and, in most cases, different drying methods. This aspect is, however, rarely highlighted. Here, the extent to which different convective drying methods reduce the nutritional content, namely vitamin C, carotenoids and phenolic content of dried fruits and vegetables, compared to fresh produce was quantified using literature data. The impact of different drying process parameters, such as air temperature, airspeed and relative humidity on the nutritional content of fruits and vegetables were compared. Results revealed that convective drying reduced the amount of vitamin C, carotenoids and the phenolic content of dried fruits and vegetables by up to 70%. The reduction in the residual vitamin C and carotenoid content of dried fruits and vegetables due to differences in air temperature (∼40%), airspeed (∼20%), and relative humidity (∼20%) is much less than the nutritional quality losses due to the drying process. The residual vitamin C, carotenoids and phenolic contents in convective-dried fruits and vegetables are ∼30% less than those in freeze-dried products. This study confirms that little absolute gains in nutritional quality can be achieved by opting for either an alternative drying method or optimizing processing parameters since the drying process already results in a low nutritional quality of dried products. As such, the remaining micronutrient concentration of dried products should not necessarily be a decisive criterion in selecting the most appropriate drying method or processing parameters for fruits and vegetables. Instead, other key performance indicators such as the drying time, energy consumption, or sensory properties such as color, texture, and rehydration capacity could eventually have a greater influence on the decision-making process.ISSN:0960-3085ISSN:1744-357

To Wrap Or to Not Wrap Cucumbers?

In light of increasing public pressure, retailers strive to remove plastic packaging as much as possible from fresh fruits and vegetables to reduce the environmental impacts along their supply chains. Plastic packaging, however, also has an important protective function, similar to the fruit's peel. For cucumbers transported from Spain and sold in Switzerland, our investigations in the form of a life cycle assessment study showed that the plastic wrapping has a rather low environmental impact (only about 1%) in comparison to the total environmental impacts of the fruit from grower to grocer. Hence, each cucumber that has to be thrown away has the equivalent environmental impact of 93 plastic cucumber wraps. We found that plastic wrapping protects the environment more by saving more cucumbers from spoilage than it harms the environment by the additional use of plastic. If, by using the plastic wrap, we reduce cucumber losses at retail only by 1.1%, its use already has a net environmental benefit. Currently, in the cucumber import supply chain from Spain to Switzerland, the use of plastic wrapping lowers the cucumber losses at retail by an estimated 4.8%; therefore, it makes sense to use it from an environmental perspective. The environmental benefit of food waste reduction due to plastic wrapping the cucumbers was found to be 4.9 times higher than the negative environmental impact due to the packaging itself. Alternative strategies to preserve fresh cucumbers without using plastic wrapping will have to compete with this challenging limit

How long and effective does a mask protect you from an infected person who emits virus-laden particles: By implementing one-dimensional physics-based modeling

SARS-CoV-2 spreads via droplets, aerosols, and smear infection. From the beginning of the COVID-19 pandemic, using a facemask in different locations was recommended to slow down the spread of the virus. To evaluate facemasks' performance, masks' filtration efficiency is tested for a range of particle sizes. Although such tests quantify the blockage of the mask for a range of particle sizes, the test does not quantify the cumulative amount of virus-laden particles inhaled or exhaled by its wearer. In this study, we quantify the accumulated viruses that the healthy person inhales as a function of time, activity level, type of mask, and room condition using a physics-based model. We considered different types of masks, such as surgical masks and filtering facepieces (FFPs), and different characteristics of public places such as office rooms, buses, trains, and airplanes. To do such quantification, we implemented a physics-based model of the mask. Our results confirm the importance of both people wearing a mask compared to when only one wears the mask. The protection time for light activity in an office room decreases from 7.8 to 1.4 h with surgical mask IIR. The protection time is further reduced by 85 and 99% if the infected person starts to cough or increases the activity level, respectively. Results show the leakage of the mask can considerably affect the performance of the mask. For the surgical mask, the apparent filtration efficiency reduces by 75% with such a leakage, which cannot provide sufficient protection despite the high filtration efficiency of the mask. The facemask model presented provides key input in order to evaluate the protection of masks for different conditions in public places. The physics-based model of the facemask is provided as an online application.ISSN:2296-256

Digital twins for selecting the optimal ventilated strawberry packaging based on the unique hygrothermal conditions of a shipment from farm to retailer

Berries are one of the most challenging products to preserve after harvest due to their high perishability and short shelf life. Ventilated packaging plays a key role in maintaining fruit quality along the supply chain. However, every supply chain is composed of different unit operations, and every shipment encounters unique hygrothermal conditions such as air temperature fluctuations over time, sub-optimal humidity conditions, and the risk of condensation. Therefore, every supply chain has an optimal packaging that provides the best hygrothermal climate and ventilation to the fruit. Given the vast space of potential supply chain scenarios and packaging configurations, in-silico studies are an attractive alternative for selecting this optimal packaging. In this study, we developed physics-based digital twins for ventilated packaging of strawberries. We utilized measured air temperature and humidity data from an actual supply chain from the farm to the retail store. With these digital twins, we mimicked in-silico how the strawberries evolve hygrothermally, physiologically, and microbiologically along the supply chain inside 21 different types of ventilated packaging. We predicted actionable metrics of fruit quality and shelf life for these 21 packages. These metrics include total mass loss, risk of putative mold infection due to Botrytis cinerea, retention time of condensate, and remaining shelf life based on respiration, transpiration, and mold growth. In addition, we analyzed the impact of package-related metrics, such as total vent area, degree of filling, pressure drop across the package, and seven-eighths cooling time, on fruit quality metrics. With this approach, we pinpointed the critical quality loss points in the supply chain for every package. We identified the package that performs best in balancing the three-way trade-off between the respiration-driven biochemical shelf life, transpiration-driven physical shelf life, and mold growth-driven microbial shelf life of fruit. Our findings showed that the performance of open trays is comparable to ventilated clamshells, as long as a high humidity is maintained along the supply chain. Flow-wrapped packages presented the highest risk of condensation and microbial growth. We also quantified the spatial heterogeneity in fruit quality within the packages and highlighted the most vulnerable locations for quality loss inside each packaging type. Our study presents a novel, holistic approach to select the optimal ventilated packaging of strawberries from farm to retailer based on its measured hygrothermal fingerprint. This approach can help reduce food loss and contribute towards making supply chains smart and efficient