Identification of drought responsive proteins and related proteomic QTLs in barley

Jasmonic acid improves barley photosynthetic efficiency through a possible regulatory module, MYC2-RcaA, under combined drought and salinity stress

The combined stress of drought and salinity is prevalent in various regions of the world, affects several physiological and biochemical processes in crops, and causes their yield to decrease. Photosynthesis is one of the main processes that are disturbed by combined stress. Therefore, improving the photosynthetic efficiency of crops is one of the most promising strategies to overcome environmental stresses, making studying the molecular basis of regulation of photosynthesis a necessity. In this study, we sought a potential mechanism that regulated a major component of the combined stress response in the important crop barley (Hordeum vulgare L.), namely the Rubisco activase A (RcaA) gene. Promoter analysis of the RcaA gene led to identifying Jasmonic acid (JA)-responsive elements with a high occurrence. Specifically, a Myelocytomatosis oncogenes 2 (MYC2) transcription factor binding site was highlighted as a plausible functional promoter motif. We conducted a controlled greenhouse experiment with an abiotic stress-susceptible barley genotype and evaluated expression profiling of the RcaA and MYC2 genes, photosynthetic parameters, plant water status, and cell membrane damages under JA, combined drought and salinity stress (CS) and JA + CS treatments. Our results showed that applying JA enhances barley's photosynthetic efficiency and water relations and considerably compensates for the adverse effects of combined stress. Significant association was observed among gene expression profiles and evaluated physiochemical characteristics. The results showed a plausible regulatory route through the JA-dependent MYC2-RcaA module involved in photosynthesis regulation and combined stress tolerance. These findings provide valuable knowledge for further functional studies of the regulation of photosynthesis under abiotic stresses toward the development of multiple-stress-tolerant crops.

Global Proteome Profiling Revealed the Adaptive Reprogramming of Barley Flag Leaf to Drought and Elevated Temperature

Plants, as sessile organisms, have developed sophisticated mechanisms to survive in changing environments. Recent advances in omics approaches have facilitated the exploration of plant genomes; however, the molecular mechanisms underlying the responses of barley and other cereals to multiple abiotic stresses remain largely unclear. Exposure to stress stimuli affects many proteins with regulatory and protective functions. In the present study, we employed liquid chromatography coupled with high-resolution mass spectrometry to identify stress-responsive proteins on the genome-wide scale of barley flag leaves exposed to drought, heat, or both. Profound alterations in the proteome of genotypes with different flag leaf sizes were found. The role of stress-inducible proteins was discussed and candidates underlying the universal stress response were proposed, including dehydrins. Moreover, the putative functions of several unknown proteins that can mediate responses to stress stimuli were explored using Pfam annotation, including calmodulin-like proteins. Finally, the confrontation of protein and mRNA abundances was performed. A correlation network between transcripts and proteins performance revealed several components of the stress-adaptive pathways in barley flag leaf. Taking the findings together, promising candidates for improving the tolerance of barley and other cereals to multivariate stresses were uncovered. The presented proteomic landscape and its relationship to transcriptomic remodeling provide novel insights for understanding the molecular responses of plants to environmental cues.

Plant Tolerance to Drought Stress with Emphasis on Wheat

Environmental stresses, such as drought, have negative effects on crop yield. Drought is a stress whose impact tends to increase in some critical regions. However, the worldwide population is continuously increasing and climate change may affect its food supply in the upcoming years. Therefore, there is an ongoing effort to understand the molecular processes that may contribute to improving drought tolerance of strategic crops. These investigations should contribute to delivering drought-tolerant cultivars by selective breeding. For this reason, it is worthwhile to review regularly the literature concerning the molecular mechanisms and technologies that could facilitate gene pyramiding for drought tolerance. This review summarizes achievements obtained using QTL mapping, genomics, synteny, epigenetics, and transgenics for the selective breeding of drought-tolerant wheat cultivars. Synthetic apomixis combined with the msh1 mutation opens the way to induce and stabilize epigenomes in crops, which offers the potential of accelerating selective breeding for drought tolerance in arid and semi-arid regions.

Novel Single-Nucleotide Variants for Morpho-Physiological Traits Involved in Enhancing Drought Stress Tolerance in Barley

Barley (Hordeum vulgare L.) thrives in the arid and semi-arid regions of the world; nevertheless, it suffers large grain yield losses due to drought stress. A panel of 426 lines of barley was evaluated in Egypt under deficit (DI) and full irrigation (FI) during the 2019 and 2020 growing seasons. Observations were recorded on the number of days to flowering (NDF), total chlorophyll content (CH), canopy temperature (CAN), grain filling duration (GFD), plant height (PH), and grain yield (Yield) under DI and FI. The lines were genotyped using the 9K Infinium iSelect single nucleotide polymorphisms (SNP) genotyping platform, which resulted in 6913 high-quality SNPs. In conjunction with the SNP markers, the phenotypic data were subjected to a genome-wide association scan (GWAS) using Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK). The GWAS results indicated that 36 SNPs were significantly associated with the studied traits under DI and FI. Furthermore, eight markers were significant and common across DI and FI water regimes, while 14 markers were uniquely associated with the studied traits under DI. Under DI and FI, three (11_10326, 11_20042, and 11_20170) and five (11_20099, 11_10326, 11_20840, 12_30298, and 11_20605) markers, respectively, had pleiotropic effect on at least two traits. Among the significant markers, 24 were annotated to known barley genes. Most of these genes were involved in plant responses to environmental stimuli such as drought. Overall, nine of the significant markers were previously reported, and 27 markers might be considered novel. Several markers identified in this study could enable the prediction of barley accessions with optimal agronomic performance under DI and FI.

Pleiotropic effects of recombinant protease inhibitors in plants

Recombinant gene encoded protease inhibitors have been identified as some of the most effective antidigestive molecules to guard against proteolysis of essential proteins and plant attacking proteases from herbivorous pests and pathogenic microorganisms. Protease inhibitors (PIs) can be over expressed in transgenic plants to complement internal host defense systems, Bt toxins in genetically modified pest resistance and abiotic stress tolerance achieved through cystatins expression. Although the understanding of the role of proteolytic enzymes and their inhibitors encoded by both endogenous and transgenes expressed in crop plants has significantly advanced, their implication in biological systems still requires further elucidations. This paper, therefore, succinctly reviewed most recently published literature on recombinant proteases inhibitors (RPIs), focusing mainly on their unintended consequences in plants, other living organisms, and the environment. The review discusses major negative and unintended effects of RPIs involving the inhibitors' non-specificity on protease enzymes, non-target organisms and ubiquitous versatility in their mechanism of inhibition. The paper also discusses some direct and indirect effects of RPIs such as degradation by distinct classes of proteases, reduced functionality due to plant exposure to severe environmental stress and any other potential negative influences exerted on both the host plant as well as the environment. These pleiotropic effects must be decisively monitored to eliminate and prevent any potential adverse effects that transgenic plants carrying recombinant inhibitor genes may have on non-target organisms and biodiversity.

Preparation and Curation of Omics Data for Genome-Wide Association Studies

With the development of large-scale molecular phenotyping platforms, genome-wide association studies have greatly developed, being no longer limited to the analysis of classical agronomic traits, such as yield or flowering time, but also embracing the dissection of the genetic basis of molecular traits. Data generated by omics platforms, however, pose some technical and statistical challenges to the classical methodology and assumptions of an association study. Although genotyping data are subject to strict filtering procedures, and several advanced statistical approaches are now available to adjust for population structure, less attention has been instead devoted to the preparation of omics data prior to GWAS. In the present chapter, we briefly present the methods to acquire profiling data from transcripts, proteins, and small molecules, and discuss the tools and possibilities to clean, normalize, and remove the unwanted variation from large datasets of molecular phenotypic traits prior to their use in GWAS.

Application of Mass Spectrometry-Based Proteomics to Barley Research

Barley (Hordeum vulgare) is the fourth most cultivated crop in the world in terms of production volume, and it is also the most important raw material of the malting and brewing industries. Barley belongs to the grass (Poaceae) family and plays an important role in food security and food safety for both humans and livestock. With the global population set to reach 9.7 billion by 2050, but with less available and/or suitable land for agriculture, the use of biotechnology tools in breeding programs are of considerable importance in the quest to meet the growing food gap. Proteomics as a member of the "omics" technologies has become popular for the investigation of proteins in cereal crops and particularly barley and its related products such as malt and beer. This technology has been applied to study how proteins in barley respond to adverse environmental conditions including abiotic and/or biotic stresses, how they are impacted during food processing including malting and brewing, and the presence of proteins implicated in celiac disease. Moreover, proteomics can be used in the future to inform breeding programs that aim to enhance the nutritional value and broaden the application of this crop in new food and beverage products. Mass spectrometry analysis is a valuable tool that, along with genomics and transcriptomics, can inform plant breeding strategies that aim to produce superior barley varieties. In this review, recent studies employing both qualitative and quantitative mass spectrometry approaches are explored with a focus on their application in cultivation, manufacturing, processing, quality, and the safety of barley and its related products.

Combined Proteomic and Physiological Analysis of Chloroplasts Reveals Drought and Recovery Response Mechanisms in Nicotiana benthamiana

Chloroplasts play essential roles in plant metabolic processes and stress responses by functioning as environmental sensors. Understanding chloroplast responses to drought stress and subsequent recovery will help the ability to improve stress tolerance in plants. Here, a combined proteomic and physiological approach was used to investigate the response mechanisms of Nicotiana benthamiana chloroplasts to drought stress and subsequent recovery. Early in the stress response, changes in stomatal movement were accompanied by immediate changes in protein synthesis to sustain the photosynthetic process. Thereafter, increasing drought stress seriously affected photosynthetic efficiency and led to altered expression of photosynthesis- and carbon-fixation-related proteins to protect the plants against photo-oxidative damage. Additional repair mechanisms were activated at the early stage of recovery to restore physiological functions and repair drought-induced damages, even while the negative effects of drought stress were still ongoing. Prolonging the re-watering period led to the gradual recovery of photosynthesis at both physiological and protein levels, indicating that a long repair process is required to restore plant function. Our findings provide a precise view of drought and recovery response mechanisms in N. benthamiana and serve as a reference for further investigation into the physiological and molecular mechanisms underlying plant drought tolerance.

Changes in the Flower and Leaf Proteome of Common Buckwheat (Fagopyrum esculentum Moench) under High Temperature

Common buckwheat (Fagopyrum esculentum Moench), a pseudocereal crop, produces a large number of flowers, but this does not guarantee high seed yields. This species demonstrates strong abortion of flowers and embryos. High temperatures during the generative growth phase result in an increase in the degeneration of embryo sacs. The aim of this study was to investigate proteomic changes in flowers and leaves of two common buckwheat accessions with different degrees of heat tolerance, Panda and PA15. Two-dimensional gel electrophoresis and mass spectrometry techniques were used to analyze the proteome profiles. Analyses were conducted for flower buds, open flowers capable of fertilization, and wilted flowers, as well as donor leaves, i.e., those growing closest to the inflorescences. High temperature up-regulated the expression of 182 proteins. The proteomic response to heat stress differed between the accessions and among their organs. In the Panda accession, we observed a change in abundance of 17, 13, 28, and 11 proteins, in buds, open and wilted flowers, and leaves, respectively. However, in the PA15 accession there were 34, 21, 63, and 21 such proteins, respectively. Fifteen heat-affected proteins were common to both accessions. The indole-3-glycerol phosphate synthase chloroplastic-like isoform X2 accumulated in the open flowers of the heat-sensitive cultivar Panda in response to high temperature, and may be a candidate protein as a marker of heat sensitivity in buckwheat plants.

Physiological and Proteomic Signatures Reveal Mechanisms of Superior Drought Resilience in Pearl Millet Compared to Wheat

Presently, pearl millet and wheat are belonging to highly important cereal crops. Pearl millet, however, is an under-utilized crop, despite its superior resilience to drought and heat stress in contrast to wheat. To investigate this in more detail, we performed comparative physiological screening and large scale proteomics of drought stress responses in drought-tolerant and susceptible genotypes of pearl millet and wheat. These chosen genotypes are widely used in breeding and farming practices. The physiological responses demonstrated large differences in the regulation of root morphology and photosynthetic machinery, revealing a stay-green phenotype in pearl millet. Subsequent tissue-specific proteome analysis of leaves, roots and seeds led to the identification of 12,558 proteins in pearl millet and wheat under well-watered and stress conditions. To allow for this comparative proteome analysis and to provide a platform for future functional proteomics studies we performed a systematic phylogenetic analysis of all orthologues in pearl millet, wheat, foxtail millet, sorghum, barley, brachypodium, rice, maize, Arabidopsis, and soybean. In summary, we define (i) a stay-green proteome signature in the drought-tolerant pearl millet phenotype and (ii) differential senescence proteome signatures in contrasting wheat phenotypes not capable of coping with similar drought stress. These different responses have a significant effect on yield and grain filling processes reflected by the harvest index. Proteome signatures related to root morphology and seed yield demonstrated the unexpected intra- and interspecies-specific biochemical plasticity for stress adaptation for both pearl millet and wheat genotypes. These quantitative reference data provide tissue- and phenotype-specific marker proteins of stress defense mechanisms which are not predictable from the genome sequence itself and have potential value for marker-assisted breeding beyond genome assisted breeding.

Proteome-wide Systems Genetics to Identify Functional Regulators of Complex Traits

Proteomic technologies now enable the rapid quantification of thousands of proteins across genetically diverse samples. Integration of these data with systems-genetics analyses is a powerful approach to identify new regulators of economically important or disease-relevant phenotypes in various populations. In this review, we summarize the latest proteomic technologies and discuss technical challenges for their use in population studies. We demonstrate how the analysis of correlation structure and loci mapping can be used to identify genetic factors regulating functional protein networks and complex traits. Finally, we provide an extensive summary of the use of proteome-wide systems genetics throughout fungi, plant, and animal kingdoms and discuss the power of this approach to identify candidate regulators and drug targets in large human consortium studies.

Breeding and biotechnological interventions for trait improvement: status and prospects

Present review describes the molecular tools and strategies deployed in the trait discovery and improvement of major crops. The prospects and challenges associated with these approaches are discussed. Crop improvement relies on modulating the genes and genomic regions underlying key traits, either directly or indirectly. Direct approaches include overexpression, RNA interference, genome editing, etc., while breeding majorly constitutes the indirect approach. With the advent of latest tools and technologies, these strategies could hasten the improvement of crop species. Next-generation sequencing, high-throughput genotyping, precision editing, use of space technology for accelerated growth, etc. had provided a new dimension to crop improvement programmes that work towards delivering better varieties to cope up with the challenges. Also, studies have widened from understanding the response of plants to single stress to combined stress, which provides insights into the molecular mechanisms regulating tolerance to more than one stress at a given point of time. Altogether, next-generation genetics and genomics had made tremendous progress in delivering improved varieties; however, the scope still exists to expand its horizon to other species that remain underutilized. In this context, the present review systematically analyses the different genomics approaches that are deployed for trait discovery and improvement in major species that could serve as a roadmap for executing similar strategies in other crop species. The application, pros, and cons, and scope for improvement of each approach have been discussed with examples, and altogether, the review provides comprehensive coverage on the advances in genomics to meet the ever-growing demands for agricultural produce.

Physiological and Proteomic Signatures Reveal Mechanisms of Superior Drought Resilience in Pearl Millet Compared to Wheat

Presently, pearl millet and wheat are belonging to highly important cereal crops. Pearl millet, however, is an under-utilized crop, despite its superior resilience to drought and heat stress in contrast to wheat. To investigate this in more detail, we performed comparative physiological screening and large scale proteomics of drought stress responses in drought-tolerant and susceptible genotypes of pearl millet and wheat. These chosen genotypes are widely used in breeding and farming practices. The physiological responses demonstrated large differences in the regulation of root morphology and photosynthetic machinery, revealing a stay-green phenotype in pearl millet. Subsequent tissue-specific proteome analysis of leaves, roots and seeds led to the identification of 12,558 proteins in pearl millet and wheat under well-watered and stress conditions. To allow for this comparative proteome analysis and to provide a platform for future functional proteomics studies we performed a systematic phylogenetic analysis of all orthologues in pearl millet, wheat, foxtail millet, sorghum, barley, brachypodium, rice, maize, Arabidopsis, and soybean. In summary, we define (i) a stay-green proteome signature in the drought-tolerant pearl millet phenotype and (ii) differential senescence proteome signatures in contrasting wheat phenotypes not capable of coping with similar drought stress. These different responses have a significant effect on yield and grain filling processes reflected by the harvest index. Proteome signatures related to root morphology and seed yield demonstrated the unexpected intra- and interspecies-specific biochemical plasticity for stress adaptation for both pearl millet and wheat genotypes. These quantitative reference data provide tissue- and phenotype-specific marker proteins of stress defense mechanisms which are not predictable from the genome sequence itself and have potential value for marker-assisted breeding beyond genome assisted breeding.