Designing future crops: challenges and strategies for sustainable agriculture

The molecular basis of cereal grain proteostasis

Storage proteins deposited in the endosperm of cereal grains are both a nitrogen reserve for seed germination and seedling growth and a primary protein source for human nutrition. Detailed surveys of the patterns of storage protein accumulation in cereal grains during grain development have been undertaken, but an in-depth understanding of the molecular mechanisms that regulate these patterns is still lacking. Accumulation of storage proteins in cereal grains involves a series of subcellular compartments, a set of energy-dependent events that compete with other cellular processes, and a balance of protein synthesis and protein degradation rates at different times during the developmental process. In this review, we focus on the importance of rates in cereal grain storage protein accumulation during grain development and outline the potential implications and applications of this information to accelerate modern agriculture breeding programmes and optimize energy use efficiency in proteostasis.

From data to knowledge - big data needs stewardship, a plant phenomics perspective

The research data life cycle from project planning to data publishing is an integral part of current research. Until the last decade, researchers were responsible for all associated phases in addition to the actual research and were assisted only at certain points by IT or bioinformaticians. Starting with advances in sequencing, the automation of analytical methods in all life science fields, including in plant phenotyping, has led to ever-increasing amounts of ever more complex data. The tasks associated with these challenges now often exceed the expertise of and infrastructure available to scientists, leading to an increased risk of data loss over time. The IPK Gatersleben has one of the world's largest germplasm collections and two decades of experience in crop plant research data management. In this article we show how challenges in modern, data-driven research can be addressed by data stewards. Based on concrete use cases, data management processes and best practices from plant phenotyping, we describe which expertise and skills are required and how data stewards as an integral actor can enhance the quality of a necessary digital transformation in progressive research.

Biostimulant Effects of Chaetomium globosum and Minimedusa polyspora Culture Filtrates on Cichorium intybus Plant: Growth Performance and Metabolomic Traits

In this study, we investigated the biostimulant effect of fungal culture filtrates obtained from Chaetomium globosum and Minimedusa polyspora on growth performance and metabolomic traits of chicory (Cichorium intybus) plants. For the first time, we showed that M. polyspora culture filtrate exerts a direct plant growth-promoting effect through an increase of biomass, both in shoots and roots, and of the leaf area. Conversely, no significant effect on morphological traits and biomass yield was observed in C. intybus plants treated with C. globosum culture filtrate. Based on ¹H-NMR metabolomics data, differential metabolites and their related metabolic pathways were highlighted. The treatment with C. globosum and M. polyspora culture filtrates stimulated a common response in C. intybus roots involving the synthesis of 3-OH-butyrate through the decrease in the synthesis of fatty acids and sterols, as a mechanism balancing the NADPH/NADP⁺ ratio. The fungal culture filtrates differently triggered the phenylpropanoid pathway in C. intybus plants: C. globosum culture filtrate increased phenylalanine and chicoric acid in the roots, whereas M. polyspora culture filtrate stimulated an increase of 4-OH-benzoate. Chicoric acid, whose biosynthetic pathway in the chicory plant is putative and still not well known, is a very promising natural compound playing an important role in plant defense. On the contrary, benzoic acids serve as precursors for a wide variety of essential compounds playing crucial roles in plant fitness and defense response activation. To the best of our knowledge, this is the first study that shows the biostimulant effect of C. globosum and M. polyspora culture filtrates on C. intybus growth and metabolome, increasing the knowledge on fungal bioresources for the development of biostimulants.

The Potential Role of RNA Structure in Crop Molecular Breeding

The continually growing human population creates a concomitantly increasing demand for nutritious crops with high yields. Advances in high throughput sequencing technologies have revealed the genetic architecture of major crops. This includes extensive information enabling comprehensive genetic markers for breeding selection, new gene discoveries, and novel gene regulatory strategies for crop editing. RNA structure is an important type of genetic feature, essential for post-transcriptional regulation of gene expression. Here, we summarize recent advances in genome-wide RNA structure studies in crops and review the associated RNA structure-mediated regulation of gene expression. We also discuss the functional importance of those single nucleotide variations that induce large RNA structure disparities. Lastly, we discuss the potential role of RNA structure in crop molecular breeding.

Leveraging National Germplasm Collections to Determine Significantly Associated Categorical Traits in Crops: Upland and Pima Cotton as a Case Study

Observable qualitative traits are relatively stable across environments and are commonly used to evaluate crop genetic diversity. Recently, molecular markers have largely superseded describing phenotypes in diversity surveys. However, qualitative descriptors are useful in cataloging germplasm collections and for describing new germplasm in patents, publications, and/or the Plant Variety Protection (PVP) system. This research focused on the comparative analysis of standardized cotton traits as represented within the National Cotton Germplasm Collection (NCGC). The cotton traits are named by 'descriptors' that have non-numerical sub-categories (descriptor states) reflecting the details of how each trait manifests or is absent in the plant. We statistically assessed selected accessions from three major groups of Gossypium as defined by the NCGC curator: (1) "Stoneville accessions (SA)," containing mainly Upland cotton (Gossypium hirsutum) cultivars; (2) "Texas accessions (TEX)," containing mainly G. hirsutum landraces; and (3) Gossypium barbadense (Gb), containing cultivars or landraces of Pima cotton (Gossypium barbadense). For 33 cotton descriptors we: (a) revealed distributions of character states for each descriptor within each group; (b) analyzed bivariate associations between paired descriptors; and (c) clustered accessions based on their descriptors. The fewest significant associations between descriptors occurred in the SA dataset, likely reflecting extensive breeding for cultivar development. In contrast, the TEX and Gb datasets showed a higher number of significant associations between descriptors, likely correlating with less impact from breeding efforts. Three significant bivariate associations were identified for all three groups, bract nectaries:boll nectaries, leaf hair:stem hair, and lint color:seed fuzz color. Unsupervised clustering analysis recapitulated the species labels for about 97% of the accessions. Unexpected clustering results indicated accessions that may benefit from potential further investigation. In the future, the significant associations between standardized descriptors can be used by curators to determine whether new exotic/unusual accessions most closely resemble Upland or Pima cotton. In addition, the study shows how existing descriptors for large germplasm datasets can be useful to inform downstream goals in breeding and research, such as identifying rare individuals with specific trait combinations and targeting breakdown of remaining trait associations through breeding, thus demonstrating the utility of the analytical methods employed in categorizing germplasm diversity within the collection.

Unravelling resources use efficiency and its drivers for water transfer and grain production processes in pumping irrigation system

Improving the resource utilization efficiency in irrigation systems contributes to the sustainability of the regional water-energy-grain nexus. Based on the water, energy and grain relationships quantification, the comprehensive efficiency (CE) of water transfer and grain production processes and its driving mechanism were analyzed, considering a pumping irrigation system in the Lianshui irrigation district (LID) in eastern China, as a case study. The annual crop output, crop water footprint, and electric energy consumption were estimated as 905.3 M kg (1 M = 10⁶), 914.7 M m³ (50.7% blue water), and 3004.0 kWh, respectively, from 2005 to 2018; the corresponding crop water productivity (CWP), electricity energy productivity (EEP), water intake efficiency of electric energy (WIE) were 0.91 kg/m³, 80.39 kg/kJ, and 75.22 m³/kJ, respectively. CWP, EEP, and WIE varied among crops; however, none of the three indicators showed an obvious trend of change with time. The CE of integrated grain was 0.48 and showed an increase over time, indicating that the sustainability of the studied pumping irrigation system was improving. The driving effect of artificial factors (e. g. social development, agricultural input, and water management) on the CE was more obvious than that of natural conditions (e. g. climate). Increasing agricultural machinery and urbanization rates and reducing the agricultural water rate are conducive to improving the resource utilization efficiency in pumping irrigation systems. The analysis framework coupling water footprint and traditional paradigms proposed in this paper provides a feasible approach for the stability and sustainability of irrigated agricultural systems observation.

Omics-based interdisciplinarity is accelerating plant breeding

Plant breeding is one of the oldest and most important activities accompanying human civilization. During the past thousand years, plant breeding has achieved three significant innovations, each of which derives from introgression of new theories or technologies. These innovations have significantly increased the food supply and allowed for population development. However, with population increases and resource shortages, the world is continuously facing the challenge of food security, which calls for next innovation in plant breeding. Recent technological advances in multiple disciplines have boosted the development of omics, which is accelerating plant breeding. Here, we review the recent advances in omics and discuss our understanding of how interdisciplinary researches will prompt new innovations in plant breeding.

Regulation of Calvin-Benson cycle enzymes under high temperature stress

The Calvin-Benson cycle (CBC) consists of three critical processes, including fixation of CO₂ by Rubisco, reduction of 3-phosphoglycerate (3PGA) to triose phosphate (triose-P) with NADPH and ATP generated by the light reactions, and regeneration of ribulose 1,5-bisphosphate (RuBP) from triose-P. The activities of photosynthesis-related proteins, mainly from the CBC, were found more significantly affected and regulated in plants challenged with high temperature stress, including Rubisco, Rubisco activase (RCA) and the enzymes involved in RuBP regeneration, such as sedoheptulose-1,7-bisphosphatase (SBPase). Over the past years, the regulatory mechanism of CBC, especially for redox-regulation, has attracted major interest, because balancing flux at the various enzymatic reactions and maintaining metabolite levels in a range are of critical importance for the optimal operation of CBC under high temperature stress, providing insights into the genetic manipulation of photosynthesis. Here, we summarize recent progress regarding the identification of various layers of regulation point to the key enzymes of CBC for acclimation to environmental temperature changes along with open questions are also discussed.

Progress in soybean functional genomics over the past decade

Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.

Significance of the Diversification of Wheat Species for the Assembly and Functioning of the Root-Associated Microbiome

Wheat, one of the major crops in the world, has had a complex history that includes genomic hybridizations between Triticum and Aegilops species and several domestication events, which resulted in various wild and domesticated species (especially Triticum aestivum and Triticum durum), many of them still existing today. The large body of information available on wheat-microbe interactions, however, was mostly obtained without considering the importance of wheat evolutionary history and its consequences for wheat microbial ecology. This review addresses our current understanding of the microbiome of wheat root and rhizosphere in light of the information available on pre- and post-domestication wheat history, including differences between wild and domesticated wheats, ancient and modern types of cultivars as well as individual cultivars within a given wheat species. This analysis highlighted two major trends. First, most data deal with the taxonomic diversity rather than the microbial functioning of root-associated wheat microbiota, with so far a bias toward bacteria and mycorrhizal fungi that will progressively attenuate thanks to the inclusion of markers encompassing other micro-eukaryotes and archaea. Second, the comparison of wheat genotypes has mostly focused on the comparison of T. aestivum cultivars, sometimes with little consideration for their particular genetic and physiological traits. It is expected that the development of current sequencing technologies will enable to revisit the diversity of the wheat microbiome. This will provide a renewed opportunity to better understand the significance of wheat evolutionary history, and also to obtain the baseline information needed to develop microbiome-based breeding strategies for sustainable wheat farming.

Recent advances in E-monitoring of plant diseases

Infectious plant diseases are caused by pathogenic microorganisms, such as fungi, oomycetes, bacteria, viruses, phytoplasma, and nematodes. Plant diseases have a significant effect on the plant quality and yield and they can destroy the entire plant if they are not controlled in time. To minimize disease-related losses, it is essential to identify and control pathogens in the early stages. Plant disease control is thus a fundamental challenge both for global food security and sustainable agriculture. Conventional methods for plant diseases control have given place to electronic control (E-monitoring) due to their lack of portability, being time consuming, need for a specialized user, etc. E-monitoring using electronic nose (e-nose), biosensors, wearable sensors, and 'electronic eyes' has attracted increasing attention in recent years. Detection, identification, and quantification of pathogens based on electronic sensors (E-sensors) are both convenient and practical and may be used in combination with conventional methods. This paper discusses recent advances made in E-sensors as component parts in combination with wearable sensors, in electronic sensing systems to control and detect viruses, bacteria, pathogens and fungi. In addition, future challenges using sensors to manage plant diseases are investigated.

Combining novel technologies with interdisciplinary basic research to enhance horticultural crops

Horticultural crops mainly include fruits, vegetables, ornamental trees and flowers, and tea trees (Melaleuca alternifolia). They produce a variety of nutrients for the daily human diet in addition to the nutrition provided by staple crops, and some of them additionally possess ornamental and medicinal features. As such, horticultural crops make unique and important contributions to both food security and a colorful lifestyle. Under the current climate change scenario, the growing population and limited arable land means that agriculture, and especially horticulture, has been facing unprecedented challenges to meet the diverse demands of human daily life. Breeding horticultural crops with high quality and adaptability and establishing an effective system that combines cultivation, post-harvest handling, and sales becomes increasingly imperative for horticultural production. This review discusses characteristic and recent research highlights in horticultural crops, focusing on the breeding of quality traits and the mechanisms that underpin them. It additionally addresses challenges and potential solutions in horticultural production and post-harvest practices. Finally, we provide a prospective as to how emerging technologies can be implemented alongside interdisciplinary basic research to enhance our understanding and exploitation of horticultural crops.

Enhancing crop diversity for food security in the face of climate uncertainty

Global agriculture is dominated by a handful of species that currently supply a huge proportion of our food and feed. It additionally faces the massive challenge of providing food for 10 billion people by 2050, despite increasing environmental deterioration. One way to better plan production in the face of current and continuing climate change is to better understand how our domestication of these crops included their adaptation to environments that were highly distinct from those of their centre of origin. There are many prominent examples of this, including the development of temperate Zea mays (maize) and the alteration of day-length requirements in Solanum tuberosum (potato). Despite the pre-eminence of some 15 crops, more than 50 000 species are edible, with 7000 of these considered semi-cultivated. Opportunities afforded by next-generation sequencing technologies alongside other methods, including metabolomics and high-throughput phenotyping, are starting to contribute to a better characterization of a handful of these species. Moreover, the first examples of de novo domestication have appeared, whereby key target genes are modified in a wild species in order to confer predictable traits of agronomic value. Here, we review the scale of the challenge, drawing extensively on the characterization of past agriculture to suggest informed strategies upon which the breeding of future climate-resilient crops can be based.

Rice functional genomics: decades' efforts and roads ahead

Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.

Glyphosate-Eating Fungi: Study on Fungal Saprotrophic Strains' Ability to Tolerate and Utilise Glyphosate as a Nutritional Source and on the Ability of Purpureocillium lilacinum to Degrade It

Glyphosate is the most commonly used herbicide worldwide. Its improper use during recent decades has resulted in glyphosate contamination of soils and waters. Fungal bioremediation is an environmentally friendly, cost effective, and feasible solution to glyphosate contamination in soils. In this study, several saprotrophic fungi isolated from agricultural environments were screened for their ability to tolerate and utilise Roundup in different cultural conditions as a nutritional source. Purpureocillium lilacinum was further screened to evaluate the ability to break down and utilise glyphosate as a P source in a liquid medium. The dose-response effect for Roundup, and the difference in toxicity between pure glyphosate and Roundup were also studied. This study reports the ability of several strains to tolerate 1 mM and 10 mM Roundup and to utilise it as nutritional source. P. lilacinum was reported for the first time for its ability to degrade glyphosate to a considerable extent (80%) and to utilise it as a P source, without showing dose-dependent negative effects on growth. Pure glyphosate was found to be more toxic than Roundup for P. lilacinum. Our results showed that pure glyphosate toxicity can be only partially addressed by the pH decrease determined in the culture medium. In conclusion, our study emphasises the noteworthy potential of P. lilacinum in glyphosate degradation.

Rewilding crops for climate resilience: economic analysis and de novo domestication strategies

To match predicted population growth, annual food production should be doubled by 2050. This is not achievable by current agronomical and breeding practices, due to the impact of climate changes and associated abiotic stresses on agricultural production systems. Here, we analyze the impact of global climate trends on crop productivity and show that the overall loss in crop production from climate-driven abiotic stresses may exceed US$170 billion year-1 and represents a major threat to global food security. We also show that abiotic stress tolerance had been present in wild progenitors of modern crops but was lost during their domestication. We argue for a major shift in our paradigm of crop breeding, focusing on climate resilience, and call for a broader use of wild relatives as a major tool in this process. We argue that, while molecular tools are currently in place to harness the potential of climate-resilient genes present in wild relatives, the complex polygenic nature of tolerance traits remains a major bottleneck in this process. Future research efforts should be focused not only on finding appropriate wild relatives but also on development of efficient cell-based high-throughput phenotyping platforms allowing assessment of the in planta operation of key genes.

De-novo Domestication for Improving Salt Tolerance in Crops

Global agriculture production is under serious threat from rapidly increasing population and adverse climate changes. Food security is currently a huge challenge to feed 10 billion people by 2050. Crop domestication through conventional approaches is not good enough to meet the food demands and unable to fast-track the crop yields. Also, intensive breeding and rigorous selection of superior traits causes genetic erosion and eliminates stress-responsive genes, which makes crops more prone to abiotic stresses. Salt stress is one of the most prevailing abiotic stresses that poses severe damages to crop yield around the globe. Recent innovations in state-of-the-art genomics and transcriptomics technologies have paved the way to develop salinity tolerant crops. De novo domestication is one of the promising strategies to produce superior new crop genotypes through exploiting the genetic diversity of crop wild relatives (CWRs). Next-generation sequencing (NGS) technologies open new avenues to identifying the unique salt-tolerant genes from the CWRs. It has also led to the assembly of highly annotated crop pan-genomes to snapshot the full landscape of genetic diversity and recapture the huge gene repertoire of a species. The identification of novel genes alongside the emergence of cutting-edge genome editing tools for targeted manipulation renders de novo domestication a way forward for developing salt-tolerance crops. However, some risk associated with gene-edited crops causes hurdles for its adoption worldwide. Halophytes-led breeding for salinity tolerance provides an alternative strategy to identify extremely salt tolerant varieties that can be used to develop new crops to mitigate salinity stress.

CRISPR/Cas systems: opportunities and challenges for crop breeding

Increasing crop production to meet the demands of a growing population depends largely on crop improvement through new plant-breeding techniques (NPBT) such as genome editing. CRISPR/Cas systems are NPBTs that enable efficient target-specific gene editing in crops, which is supposed to accelerate crop breeding in a way that is different from genetically modified (GM) technology. Herein, we review the applications of CRISPR/Cas systems in crop breeding focusing on crop domestication, heterosis, haploid induction, and synthetic biology, and summarize the screening methods of CRISPR/Cas-induced mutations in crops. We highlight the importance of molecular characterization of CRISPR/Cas-edited crops, and pay special attentions to emerging highly specific genome-editing tools such as base editors and prime editors. We also discuss future improvements of CRISPR/Cas systems for crop improvement.

Metabolic Alterations in Pisum sativum Roots during Plant Growth and Arbuscular Mycorrhiza Development

Intensive exchange of nutrients is a crucial part of the complex interaction between a host plant and fungi within arbuscular mycorrhizal (AM) symbiosis. For the first time, the present study demonstrates how inoculation with AMF Rhizophagus irregularis affects the pea (Pisum sativum L.) root metabolism at key stages of plant development. These correspond to days 21 (vegetation), 42 (flowering initiation), and 56 (fruiting-green pod). Metabolome profiling was carried out by means of a state-of-the-art GC-MS technique. The content shifts revealed include lipophilic compounds, sugars, carboxylates, and amino acids. The metabolic alterations were principally dependent on the stage of plant development but were also affected by the development of AM fungi, a fact which highlights interaction between symbiotic partners. The comparison of the present data with the results of leaf metabolome profiling earlier obtained did not reveal common signatures of metabolic response to mycorrhization in leaves and roots. We supposed that the feedback for the development and symbiotic interaction on the part of the supraorganismic system (root + AM fungi) was the cause of the difference between the metabolic profile shift in leaf and root cells that our examination revealed. New investigations are required to expand our knowledge of metabolome plasticity of the whole organism and/or system of organisms, and such results might be put to use for the intensification of sustainable agriculture.

Molecular Insights into Inflorescence Meristem Specification for Yield Potential in Cereal Crops

Flowering plants develop new organs throughout their life cycle. The vegetative shoot apical meristem (SAM) generates leaf whorls, branches and stems, whereas the reproductive SAM, called the inflorescence meristem (IM), forms florets arranged on a stem or an axis. In cereal crops, the inflorescence producing grains from fertilized florets makes the major yield contribution, which is determined by the numbers and structures of branches, spikelets and florets within the inflorescence. The developmental progression largely depends on the activity of IM. The proper regulations of IM size, specification and termination are outcomes of complex interactions between promoting and restricting factors/signals. Here, we focus on recent advances in molecular mechanisms underlying potential pathways of IM identification, maintenance and differentiation in cereal crops, including rice (Oryza sativa), maize (Zea mays), wheat (Triticum aestivum), and barley (Hordeum vulgare), highlighting the researches that have facilitated grain yield by, for example, modifying the number of inflorescence branches. Combinatorial functions of key regulators and crosstalk in IM determinacy and specification are summarized. This review delivers the knowledge to crop breeding applications aiming to the improvements in yield performance and productivity.