From Genetics to Functional Genomics: Improvement in Drought Signaling and Tolerance in Wheat

Biochemical and Proteomic Analyses in Drought-Tolerant Wheat Mutants Obtained by Gamma Irradiation

The bread wheat cultivar (Triticum aestivum L. cv. Sagittario) as a parental line and its mutant, drought-tolerant lines (Mutant lines 4 and 5) were subjected to polyethylene glycol (PEG)-induced drought. Drought stress resulted in decreased chlorophyll levels and the accumulation of proline and TBARS, despite increases in activities of catalase, peroxidase, and superoxide dismutase enzymes. Transcription of the genes encoding these enzymes and delta-1-pyrroline 5-carboxylase synthetase was induced by drought. 2-DE gel electrophoresis analysis identified differentially expressed proteins (DEPs) in the mutant lines, which are distinguished by "chloroplast", "mitochondrion", "pyruvate dehydrogenase complex", and "homeostatic process" terms. The drought tolerance of the mutant lines might be attributed to improved photosynthesis, efficient ATP synthesis, and modified antioxidant capacity. In addition to proteomics data, the drought tolerance of wheat genotypes might also be assessed by chlorophyll content and TaPOX gene expression. To our knowledge, this is the first proteomic analysis of gamma-induced mutants of bread wheat. These findings are expected to be utilized in plant breeding studies.

Rice Big Grain1 improves grain yield in ectopically expressing rice and heterologously expressing tobacco plants

Functional genomics through transgenesis has provided faster and more reliable methods for identifying, characterizing, and utilizing genes or quantitative trait loci linked to agronomic traits to target yield. The present study explored the role of Big Grain1 (BG1) gene of rice (Oryza sativa L.) in yield improvement of crop plants. We aimed to identify the genetic variation of OsBG1 in various indica rice cultivars by studying the allelic polymorphism of the gene, while also investigating the gene's potential to increase crop yield through the transgenic approach. Our study reports the presence of an extra 393 bp sequence having two 6 bp enhancer elements in the 3' regulatory sequence of OsBG1 in the large-grain cultivar IR64 but not in the small-grain cultivar Badshahbhog. A single copy of the OsBG1 gene in both the cultivars and a 4.1-fold higher expression of OsBG1 in IR64 than in Badshahbhog imply that the grain size is positively correlated with the level of OsBG1 expression in rice. The ectopic expression of OsBG1 under the endosperm-specific glutelin C promoter in Badshahbhog enhanced the flag leaf length, panicle weight, and panicle length by an average of 33.2%, 33.7%, and 30.5%, respectively. The length of anthers, spikelet fertility, and grain yield per plant increased in transgenic rice lines by an average of 27.5%, 8.3%, and 54.4%, respectively. Heterologous expression of OsBG1 under the constitutive 2xCaMV35S promoter improved the number of seed pods per plant and seed yield per plant in transgenic tobacco lines by an average of 2.2-fold and 2.6-fold, respectively. Improving crop yield is crucial to ensure food security and socio-economic stability, and identifying suitable genetic factor is the essential step towards this endeavor. Our findings suggest that the OsBG1 gene is a promising candidate for improving the grain yield of monocot and dicot plant systems by molecular breeding and genetic engineering.

The potential of genome editing to create novel alleles of resistance genes in rice

Rice, a staple food for a significant portion of the global population, faces persistent threats from various pathogens and pests, necessitating the development of resilient crop varieties. Deployment of resistance genes in rice is the best practice to manage diseases and reduce environmental damage by reducing the application of agro-chemicals. Genome editing technologies, such as CRISPR-Cas, have revolutionized the field of molecular biology, offering precise and efficient tools for targeted modifications within the rice genome. This study delves into the application of these tools to engineer novel alleles of resistance genes in rice, aiming to enhance the plant's innate ability to combat evolving threats. By harnessing the power of genome editing, researchers can introduce tailored genetic modifications that bolster the plant's defense mechanisms without compromising its essential characteristics. In this study, we synthesize recent advancements in genome editing methodologies applicable to rice and discuss the ethical considerations and regulatory frameworks surrounding the creation of genetically modified crops. Additionally, it explores potential challenges and future prospects for deploying edited rice varieties in agricultural landscapes. In summary, this study highlights the promise of genome editing in reshaping the genetic landscape of rice to confront emerging challenges, contributing to global food security and sustainable agriculture practices.

Genomics empowering conservation action and improvement of celery in the face of climate change

MAIN CONCLUSION

Integration of genomic approaches like whole genome sequencing, functional genomics, evolutionary genomics, and CRISPR/Cas9-based genome editing has accelerated the improvement of crop plants including leafy vegetables like celery in the face of climate change. The anthropogenic climate change is a real peril to the existence of life forms on our planet, including human and plant life. Climate change is predicted to be a significant threat to biodiversity and food security in the coming decades and is rapidly transforming global farming systems. To avoid the ghastly future in the face of climate change, the elucidation of shifts in the geographical range of plant species, species adaptation, and evolution is necessary for plant scientists to develop climate-resilient strategies. In the post-genomics era, the increasing availability of genomic resources and integration of multifaceted genomics elements is empowering biodiversity conservation action, restoration efforts, and identification of genomic regions adaptive to climate change. Genomics has accelerated the true characterization of crop wild relatives, genomic variations, and the development of climate-resilient varieties to ensure food security for 10 billion people by 2050. In this review, we have summarized the applications of multifaceted genomic tools, like conservation genomics, whole genome sequencing, functional genomics, genome editing, pangenomics, in the conservation and adaptation of plant species with a focus on celery, an aromatic and medicinal Apiaceae vegetable. We focus on how conservation scientists can utilize genomics and genomic data in conservation and improvement.

Potential role of the regulatory miR1119-MYC2 module in wheat (Triticum aestivum L.) drought tolerance

MicroRNA (miRNA)-target gene modules are essential components of plants' abiotic stress signalling pathways Little is known about the drought-responsive miRNA-target modules in wheat, but systems biology approaches have enabled the prediction of these regulatory modules and systematic study of their roles in responses to abiotic stresses. Using such an approach, we sought miRNA-target module(s) that may be differentially expressed under drought and non-stressed conditions by mining Expressed Sequence Tag (EST) libraries of wheat roots and identified a strong candidate (miR1119-MYC2). We then assessed molecular and physiochemical differences between two wheat genotypes with contrasting drought tolerance in a controlled drought experiment and assessed possible relationships between their tolerance and evaluated traits. We found that the miR1119-MYC2 module significantly responds to drought stress in wheat roots. It is differentially expressed between the contrasting wheat genotypes and under drought versus non-stressed conditions. We also found significant associations between the module's expression profiles and ABA hormone content, water relations, photosynthetic activities, H₂O₂ levels, plasma membrane damage, and antioxidant enzyme activities in wheat. Collectively, our results suggest that a regulatory module consisting of miR1119 and MYC2 may play an important role in wheat's drought tolerance.

Epigenetic Changes Occurring in Plant Inbreeding

Inbreeding is the crossing of closely related individuals in nature or a plantation or self-pollinating plants, which produces plants with high homozygosity. This process can reduce genetic diversity in the offspring and decrease heterozygosity, whereas inbred depression (ID) can often reduce viability. Inbred depression is common in plants and animals and has played a significant role in evolution. In the review, we aim to show that inbreeding can, through the action of epigenetic mechanisms, affect gene expression, resulting in changes in the metabolism and phenotype of organisms. This is particularly important in plant breeding because epigenetic profiles can be linked to the deterioration or improvement of agriculturally important characteristics.

Genome-wise association study identified genomic regions associated with drought tolerance in mungbean (Vigna radiata (L.) R. Wilczek)

A total of 282 mungbean accessions were resequenced to identify genome-wide variants and construct a highly precise variant map, and drought tolerance-related loci and superior alleles were identified by GWAS. Mungbean (Vigna radiata (L.) R. Wilczek) is an important food legume crop that is highly adapted to drought environments, but severe drought significantly curtails mungbean production. Here, we resequenced 282 mungbean accessions to identify genome-wide variants and constructed a highly precise map of mungbean variants. A genome-wide association study was performed to identify genomic regions for 14 drought tolerance-related traits in plants grown under stress and well-watered conditions over three years. One hundred forty-six SNPs associated with drought tolerance were detected, and 26 candidate loci associated with more than two traits were subsequently selected. Two hundred fifteen candidate genes were identified at these loci, including eleven transcription factor genes, seven protein kinase genes and other protein coding genes that may respond to drought stress. Furthermore, we identified superior alleles that were associated with drought tolerance and positively selected during the breeding process. These results provide valuable genomic resources for molecular breeding and will accelerate future efforts aimed at mungbean improvement.

Combined analysis of transcriptome and metabolome reveals the molecular mechanism and candidate genes of Haloxylon drought tolerance

Haloxylon ammodendron and Haloxylon persicum, as typical desert plants, show strong drought tolerance and environmental adaptability. They are ideal model plants for studying the molecular mechanisms of drought tolerance. Transcriptomic and metabolomic analyses were performed to reveal the response mechanisms of H. ammodendron and H. persicum to a drought environment at the levels of transcription and physiological metabolism. The results showed that the morphological structures of H. ammodendron and H. persicum showed adaptability to drought stress. Under drought conditions, the peroxidase activity, abscisic acid content, auxin content, and gibberellin content of H. ammodendron increased, while the contents of proline and malondialdehyde decreased. The amino acid content of H. persicum was increased, while the contents of proline, malondialdehyde, auxin, and gibberellin were decreased. Under drought conditions, 12,233 and 17,953 differentially expressed genes (DEGs) were identified in H. ammodendron and H. persicum , respectively, including members of multiple transcription factor families such as FAR1, AP2/ERF, C2H2, bHLH, MYB, C2C2, and WRKY that were significantly up-regulated under drought stress. In the positive ion mode, 296 and 452 differential metabolites (DEMs) were identified in H. ammodendron and H. persicum, respectively; in the negative ion mode, 252 and 354 DEMs were identified, primarily in carbohydrate and lipid metabolism. A combined transcriptome and metabolome analysis showed that drought stress promoted the glycolysis/gluconeogenesis pathways of H. ammodendron and H. persicum and increased the expression of amino acid synthesis pathways, consistent with the physiological results. In addition, transcriptome and metabolome were jointly used to analyze the expression changes of the genes/metabolites of H. ammodendron and H. persicum that were associated with drought tolerance but were regulated differently in the two plants. This study identified drought-tolerance genes and metabolites in H. ammodendron and H. persicum and has provided new ideas for studying the drought stress response of Haloxylon.

Different adaptive patterns of wheat with different drought tolerance under drought stresses and rehydration revealed by integrated metabolomic and transcriptomic analysis

Wheat as a staple food crop is enduring ever-frequent intermittent and changing drought with the climate change. It is of great significance to highlight the adaptive approaches under such variable conditions at multiple levels to provide a comprehensive understanding of drought tolerance and facilitate the genetic breeding of wheat. Therefore, three wheat lines with different drought tolerance (drought-tolerant mutant Mu > common wheat CK > drought susceptible mutant mu) were analyzed under moderate and severe drought stresses as well as rehydration. Samples were subjected to transcriptomic and metabolomic profiling in combination with physiological and biochemical determination. The moderate drought stress rendered 198 and 115 differentially expressed metabolites (DEMs) in CK and Mu, respectively. The severe drought stress rendered 166, 151 and 137 DEMs in CK, Mu and mu, respectively. The rehydration rendered 150 and 127 DEMs in CK and Mu. 12,557 and 10,402 differentially expressed genes (DEGs) were identified for CK and Mu under moderate drought stress, respectively. 9,893, 7,924, and 9,387 DEGs were identified for CK, Mu, and mu under severe drought stress, respectively. 13,874 and 14,839 were identified in CK and Mu under rehydration, respectively. Metabolomics results showed that amino acid was the most differentially expressed metabolites, followed by phenolic acids. Flavonoids played an important role in drought tolerance. Most enriched pathways under drought included biosynthesis of secondary metabolites, metabolic pathways and photosynthesis. Metabolites and genes involved in osmotic regulation, antioxidase activities, and ABA signaling were more enriched in Mu than in CK and mu. Various drought-responsive genes and metabolites in Mu showed different trends with those in CK and mu. Increased amino acids biosynthetic capability and ROS scavenging ability resulted from higher antioxidase activities and increased flavonoids may be the mechanisms underlying the drought tolerance characteristic of Mu. Recovery from reversible ROS damage and rapid amino acid biosynthesis may contribute to the rapid recovery of Mu. The present study provides new insights for mechanisms of wheat under complex drought conditions.

Multiplex CRISPR/Cas9-mediated genome editing to address drought tolerance in wheat

Genome editing tools have rapidly been adopted by plant scientists for crop improvement. Genome editing using a multiplex sgRNA-CRISPR/Cas9 genome editing system is a useful technique for crop improvement in monocot species. In this study, we utilized precise gene editing techniques to generate wheat 3'(2'), 5'-bisphosphate nucleotidase (TaSal1) mutants using a multiplex sgRNA-CRISPR/Cas9 genome editing system. Five active TaSal1 homologous genes were found in the genome of Giza168 in addition to another apparently inactive gene on chromosome 4A. Three gRNAs were designed and used to target exons 4, 5 and 7 of the five wheat TaSal1 genes. Among the 120 Giza168 transgenic plants, 41 lines exhibited mutations and produced heritable TaSal1 mutations in the M1 progeny and 5 lines were full 5 gene knock-outs. These mutant plants exhibit a rolled-leaf phenotype in young leaves and bended stems, but there were no significant changes in the internode length and width, leaf morphology, and stem shape. Anatomical and scanning electron microscope studies of the young leaves of mutated TaSal1 lines showed closed stomata, increased stomata width and increase in the size of the bulliform cells. Sal1 mutant seedlings germinated and grew better on media containing polyethylene glycol than wildtype seedlings. Our results indicate that the application of the multiplex sgRNA-CRISPR/Cas9 genome editing is efficient tool for mutating more multiple TaSal1 loci in hexaploid wheat.

CRISPR-Cas9 Gene Editing of the Sal1 Gene Family in Wheat

The highly conserved Sal1 encodes a bifunctional enzyme with inositol polyphosphate-1-phosphatase and 3′ (2′), 5′-bisphosphate nucleotidase activity and has been shown to alter abiotic stress tolerance in plants when disrupted. Precise gene editing techniques were used to generate Sal1 mutants in hexaploid bread wheat. The CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats) Cas9 system with three guide RNAs (gRNAs) was used to inactivate six Sal1 homologous genes within the Bobwhite wheat genome. The resulting mutant wheat plants with all their Sal1 genes disabled had slimmer stems, had a modest reduction in biomass and senesced more slowly in water limiting conditions, but did not exhibit improved yield under drought conditions. Our results show that multiplexed gRNAs enabled effective targeted gene editing of the Sal1 gene family in hexaploid wheat. These Sal1 mutant wheat plants will be a resource for further research studying the function of this gene family in wheat.

Capturing Wheat Phenotypes at the Genome Level

Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public-private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.

Crosstalk between H2 S and NO: an emerging signalling pathway during waterlogging stress in legume crops

In legumes, waterlogging is a major detrimental factor leading to huge yield losses. Generally, legumes lack tolerance to submergence, and conventional breeding to develop tolerant varieties are limited due to the lack of tolerant germplasm and potential target genes. Moreover, our understanding of the various signalling cascades, their interactions and key pathways induced during waterlogging is limited. Here, we focus on the role of two important plant signalling molecules, viz. hydrogen sulphide (H₂ S) and nitric oxide (NO), during waterlogging stress in legumes. Plants and soil microbes produce these signalling molecules both endogenously and exogenously under various stresses, including waterlogging. NO and H₂ S are known to regulate key physiological pathways, such as stomatal closure, leaf senescence and regulation of numerous stress signalling pathways, while NO plays a pivotal role in adventitious root formation during waterlogging. The crosstalk between H₂ S and NO is synergistic because of the resemblance of their physiological effects and proteomic functions, which mainly operate through cysteine-dependent post-translational modifications via S-nitrosation and persulfidation. Such knowledge has provided novel platforms for researchers to unravel the complexity associated with H₂ S-NO signalling and interactions with plant stress hormones. This review provides an overall summary on H₂ S and NO, including biosynthesis, biological importance, crosstalk, transporter regulation as well as understanding their role during waterlogging using 'multi-omics' approach. Understanding H₂ S and NO signalling will help in deciphering the metabolic interactions and identifying key regulatory genes that could be used for developing waterlogging tolerance in legumes.

Genetic Improvement of Wheat for Drought Tolerance: Progress, Challenges and Opportunities

Wheat production and productivity are challenged by recurrent droughts associated with climate change globally. Drought and heat stress resilient cultivars can alleviate yield loss in marginal production agro-ecologies. The ability of some crop genotypes to thrive and yield in drought conditions is attributable to the inherent genetic variation and environmental adaptation, presenting opportunities to develop drought-tolerant varieties. Understanding the underlying genetic, physiological, biochemical, and environmental mechanisms and their interactions is key critical opportunity for drought tolerance improvement. Therefore, the objective of this review is to document the progress, challenges, and opportunities in breeding for drought tolerance in wheat. The paper outlines the following key aspects: (1) challenges associated with breeding for adaptation to drought-prone environments, (2) opportunities such as genetic variation in wheat for drought tolerance, selection methods, the interplay between above-ground phenotypic traits and root attributes in drought adaptation and drought-responsive attributes and (3) approaches, technologies and innovations in drought tolerance breeding. In the end, the paper summarises genetic gains and perspectives in drought tolerance breeding in wheat. The review will serve as baseline information for wheat breeders and agronomists to guide the development and deployment of drought-adapted and high-performing new-generation wheat varieties.

Characterization of the Gene Expression Profile Response to Drought Stress in Populus ussuriensis Using PacBio SMRT and Illumina Sequencing

In this study, we characterized the gene expression profile in the roots of Populus ussuriensis at 0, 6, 12, 24, 48 and 120 h after the start of polyethylene glycol (PEG)-induced drought stress using PacBio single-molecule real-time sequencing (SMRT-seq) and Illumina RNA sequencing. Compared to the control, 2244 differentially expressed genes (DEGs) were identified, and many of these DEGs were associated with the signal transduction, antioxidant system, ion accumulation and drought-inducing proteins. Changes in certain physiological and biochemical indexes, such as antioxidant activity and the contents of Ca²⁺, proline, and total soluble sugars, were further confirmed in P. ussuriensis roots. Furthermore, most of the differentially expressed transcription factors were members of the AP2/ERF, C2H2, MYB, NAC, C2C2 and WRKY families. Additionally, based on PacBio SMRT-seq results, 5955 long non-coding RNAs and 700 alternative splicing events were identified. Our results provide a global view of the gene expression profile that contributes to drought resistance in P. ussuriensis and meaningful information for genetic engineering research in the future.

Molecular Insights into Freezing Stress in Peach Based on Multi-Omics and Biotechnology: An Overview

In nature or field conditions, plants are frequently exposed to diverse environmental stressors. Among abiotic stresses, the low temperature of freezing conditions is a critical factor that influences plants, including horticultural crops, decreasing their growth, development, and eventually quality and productivity. Fortunately, plants have developed a mechanism to improve the tolerance to freezing during exposure to a range of low temperatures. In this present review, current findings on freezing stress physiology and genetics in peach (Prunus persica) were refined with an emphasis on adaptive mechanisms for cold acclimation, deacclimation, and reacclimation. In addition, advancements using multi-omics and genetic engineering approaches unravel the molecular physiological mechanisms, including hormonal regulations and their general perceptions of freezing tolerance in peach were comprehensively described. This review might pave the way for future research to the horticulturalists and research scientists to overcome the challenges of freezing temperature and improvement of crop management in these conditions.

Identification and mapping of QTL associated with some traits related for drought tolerance in wheat using SSR markers

Background

Wheat is the most important crop around the world. Drought stresses affect wheat production and their characterization. Most of the traits that are affected by drought are quantitative traits, so detection of the quantitative trait’s loci (QTLs) related to these traits is very important for breeder and wheat producers. In this trend, 285 F2 individuals from crosses between four bread wheat genotypes (Triticum aestivum L.), i.e., Sakha93, Sids1, Sakha94, and Gemmiza9, were used for identified QTLs associated with plant height (PH) and leaf wilting (LW). Single marker analysis and composite interval mapping (CIM) were used.

Results

A total of 116 QTLs loci were detected which covered 19 chromosomes out of the 21 chromosomes of wheat. PH and LW had 74 and 42 QTLs loci, respectively. On the other hand, chromosome 7A showed to bear the highest number of QTLs loci (15 loci). While chromosome 1A beard the highest number of QTLs loci related to PH (10 loci), chromosome 2B and 7A beard the highest number of QTLs related LW. We highly recommend our finding to help breeders in wheat breeding programs to improve plant height and leaf wilting.

Conclusion

Our investigation concluded that SSR markers have high efficiency in the identification of QTLs related to abiotic stress; also the CIM method had more advanced priority for QTLs mapping.

Genome Wide Association Study Uncovers the QTLome for Osmotic Adjustment and Related Drought Adaptive Traits in Durum Wheat

Osmotic adjustment (OA) is a major component of drought resistance in crops. The genetic basis of OA in wheat and other crops remains largely unknown. In this study, 248 field-grown durum wheat elite accessions grown under well-watered conditions, underwent a progressively severe drought treatment started at heading. Leaf samples were collected at heading and 17 days later. The following traits were considered: flowering time (FT), leaf relative water content (RWC), osmotic potential (ψs), OA, chlorophyll content (SPAD), and leaf rolling (LR). The high variability (3.89-fold) in OA among drought-stressed accessions resulted in high repeatability of the trait (h² = 72.3%). Notably, a high positive correlation (r = 0.78) between OA and RWC was found under severe drought conditions. A genome-wide association study (GWAS) revealed 15 significant QTLs (Quantitative Trait Loci) for OA (global R² = 63.6%), as well as eight major QTL hotspots/clusters on chromosome arms 1BL, 2BL, 4AL, 5AL, 6AL, 6BL, and 7BS, where a higher OA capacity was positively associated with RWC and/or SPAD, and negatively with LR, indicating a beneficial effect of OA on the water status of the plant. The comparative analysis with the results of 15 previous field trials conducted under varying water regimes showed concurrent effects of five OA QTL cluster hotspots on normalized difference vegetation index (NDVI), thousand-kernel weight (TKW), and/or grain yield (GY). Gene content analysis of the cluster regions revealed the presence of several candidate genes, including bidirectional sugar transporter SWEET, rhomboid-like protein, and S-adenosyl-L-methionine-dependent methyltransferases superfamily protein, as well as DREB1. Our results support OA as a valuable proxy for marker-assisted selection (MAS) aimed at enhancing drought resistance in wheat.

Water stress resilient cereal crops: Lessons from wild relatives

Cereal crops are significant contributors to global diets. As climate change disrupts weather patterns and wreaks havoc on crops, the need for generating stress-resilient, high-yielding varieties is more urgent than ever. One extremely promising avenue in this regard is to exploit the tremendous genetic diversity expressed by the wild ancestors of current day crop species. These crop wild relatives thrive in a range of environments and accordingly often harbor an array of traits that allow them to do so. The identification and introgression of these traits into our staple cereal crops can lessen yield losses in stressful environments. In the last decades, a surge in extreme drought and flooding events have severely impacted cereal crop production. Climate models predict a persistence of this trend, thus reinforcing the need for research on water stress resilience. Here we review: (i) how water stress (drought and flooding) impacts crop performance; and (ii) how identification of tolerance traits and mechanisms from wild relatives of the main cereal crops, that is, rice, maize, wheat, and barley, can lead to improved survival and sustained yields in these crops under water stress conditions.

Genome-Wide Diversity of MADS-Box Genes in Bread Wheat is Associated with its Rapid Global Adaptability

MADS-box gene family members play multifarious roles in regulating the growth and development of crop plants and hold enormous promise for bolstering grain yield potential under changing global environments. Bread wheat (Triticum aestivum L.) is a key stable food crop around the globe. Until now, the available information concerning MADS-box genes in the wheat genome has been insufficient. Here, a comprehensive genome-wide analysis identified 300 high confidence MADS-box genes from the publicly available reference genome of wheat. Comparative phylogenetic analyses with Arabidopsis and rice MADS-box genes classified the wheat genes into 16 distinct subfamilies. Gene duplications were mainly identified in subfamilies containing unbalanced homeologs, pointing towards a potential mechanism for gene family expansion. Moreover, a more rapid evolution was inferred for M-type genes, as compared with MIKC-type genes, indicating their significance in understanding the evolutionary history of the wheat genome. We speculate that subfamily-specific distal telomeric duplications in unbalanced homeologs facilitate the rapid adaptation of wheat to changing environments. Furthermore, our in-silico expression data strongly proposed MADS-box genes as active guardians of plants against pathogen insurgency and harsh environmental conditions. In conclusion, we provide an entire complement of MADS-box genes identified in the wheat genome that could accelerate functional genomics efforts and possibly facilitate bridging gaps between genotype-to-phenotype relationships through fine-tuning of agronomically important traits.

Recent Advances for Drought Stress Tolerance in Maize (Zea mays L.): Present Status and Future Prospects

Drought stress has severely hampered maize production, affecting the livelihood and economics of millions of people worldwide. In the future, as a result of climate change, unpredictable weather events will become more frequent hence the implementation of adaptive strategies will be inevitable. Through utilizing different genetic and breeding approaches, efforts are in progress to develop the drought tolerance in maize. The recent approaches of genomics-assisted breeding, transcriptomics, proteomics, transgenics, and genome editing have fast-tracked enhancement for drought stress tolerance under laboratory and field conditions. Drought stress tolerance in maize could be considerably improved by combining omics technologies with novel breeding methods and high-throughput phenotyping (HTP). This review focuses on maize responses against drought, as well as novel breeding and system biology approaches applied to better understand drought tolerance mechanisms and the development of drought-tolerant maize cultivars. Researchers must disentangle the molecular and physiological bases of drought tolerance features in order to increase maize yield. Therefore, the integrated investments in field-based HTP, system biology, and sophisticated breeding methodologies are expected to help increase and stabilize maize production in the face of climate change.

Comparative Molecular and Metabolic Profiling of Two Contrasting Wheat Cultivars under Drought Stress

Drought is one of the most important threats to plants and agriculture; therefore, understanding of the mechanisms of drought tolerance is crucial for breeding of new tolerant varieties. Here, we assessed the effects of a long-term water deficit stress simulated on a precision phenotyping system on some morphological criteria and metabolite traits, as well as the expression of drought associated transcriptional factors of two contrasting drought-responsive African wheat cultivars, Condor and Wadielniel. The current study showed that under drought stress Wadielniel exhibits significant higher tillering and height compared to Condor. Further, we used gas chromatography and ultra-high performance liquid chromatography mass-spectrometry to identify compounds that change between the two cultivars upon drought. Partial least square discriminant analysis (PLS-DA) revealed that 50 metabolites with a possible role in drought stress regulation were significantly changed in both cultivars under water deficit stress. These metabolites included several amino acids, most notably proline, some organic acids, and lipid classes PC 36:3 and TAG 56:9, which were significantly altered under drought stress. Here, the results discussed in the context of understanding the mechanisms involved in the drought response of wheat cultivars, as the phenotype parameters, metabolite content and expression of drought associated transcriptional factors could also be used for potential crop improvement under drought stress.

Genetically Modified Sugarcane Intercropping Soybean Impact on Rhizosphere Bacterial Communities and Co-occurrence Patterns

Strategies involving genes in the dehydration-responsive element binding (DREB) family, which participates in drought stress regulation, and intercropping with legumes are becoming prominent options in promoting sustainable sugarcane cultivation. An increasing number of studies focusing on root interactions in intercropping systems, particularly involving transgenic crops, are being conducted to better understand and thus, harness beneficial soil microbes to enhance plant growth. We designed experiments to investigate the characteristics of two intercropping patterns, soybean with wild-type (WT) sugarcane and soybean with genetically modified (GM) Ea-DREB2B-overexpressing sugarcane, to assess the response of the rhizosphere microbiota to the different cropping patterns. Bacterial diversity in the rhizosphere microbial community differed between the two intercropping pattens. In addition, the biomass of GM sugarcane that intercropped with soybean was significantly improved compared with WT sugarcane, and the aboveground biomass and root biomass of GM soybean intercropping sugarcane increased by 49.15 and 46.03% compared with monoculture. Furthermore, a beneficial rhizosphere environment for the growth of Actinobacteria was established in the systems intercropped with GM sugarcane. Improving the production mode of crops by genetic modification is a key strategy to improving crop yields and provides new opportunities to further investigate the effects of intercropping on plant roots and soil microbiota. Thus, this study provides a basis for selecting suitable sugarcane-soybean intercropping patterns and a theoretical foundation for a sustainable sugarcane production.

Survey of Drought-Associated TAWRKY2-D1 Gene Diversity in Bread Wheat and Wheat Relatives

Recent advances in plant genomics revealed numerous factors related to drought tolerance, including a family of WRKY transcription factors. The aim of this study was to evaluate polymorphism of the TaWRKY2-D1 across a range of bread wheat cultivars, interspecific hybrids, and wild wheat relatives within the Triticum genus as a potential molecular target for marker-assistant selection. The initial sequencing of the TaWRKY2-D1 gene in six Ukrainian commercial cultivars detected some sequence variations along the ~ 1.8 kb of gene promoter and the followed coding region composed of four exons and three introns. Based on the gained sequence information, five sets of primers covering different gene regions were designed to annotate theTaWRKY2-D1 genetic diversity in 202 wheat cultivars, including 77 accessions from the CIMMYT collection, 72 commercial varieties cultivated in Ukraine, and 53 hybrids and wild wheat species. The combination of developed DNA markers enabled effective and reproducible annotation of cultivars genetic diversity. The primers set targeting introns adjusted to the gene's exon 3, turned out to be the most informative for screening heterogeneity of the TaWRKY2-D1. The developed molecular markers represent effective, informative means for selecting drought tolerance germplasm donors to promote wheat breeding programs.

Genetic Improvement in Sunflower Breeding—Integrated Omics Approach

Foresight in climate change and the challenges ahead requires a systematic approach to sunflower breeding that will encompass all available technologies. There is a great scarcity of desirable genetic variation, which is in fact undiscovered because it has not been sufficiently researched as detection and designing favorable genetic variation largely depends on thorough genome sequencing through broad and deep resequencing. Basic exploration of genomes is insufficient to find insight about important physiological and molecular mechanisms unique to crops. That is why integrating information from genomics, epigenomics, transcriptomics, proteomics, metabolomics and phenomics enables a comprehensive understanding of the molecular mechanisms in the background of architecture of many important quantitative traits. Omics technologies offer novel possibilities for deciphering the complex pathways and molecular profiling through the level of systems biology and can provide important answers that can be utilized for more efficient breeding of sunflower. In this review, we present omics profiling approaches in order to address their possibilities and usefulness as a potential breeding tools in sunflower genetic improvement.

Transcriptome and Co-expression Network Analyses Reveal Differential Gene Expression and Pathways in Response to Severe Drought Stress in Peanut (Arachis hypogaea L.)

Drought is one of the major abiotic stress factors limiting peanut production. It causes the loss of pod yield during the pod formation stage. Here, one previously identified drought-tolerant cultivar, "L422" of peanut, was stressed by drought (35 ± 5%) at pod formation stage for 5, 7, and 9 days. To analyze the drought effects on peanut, we conducted physiological and transcriptome analysis in leaves under well-watered (CK1, CK2, and CK3) and drought-stress conditions (T1, T2, and T3). By transcriptome analysis, 3,586, 6,730, and 8,054 differentially expressed genes (DEGs) were identified in "L422" at 5 days (CK1 vs T1), 7 days (CK2 vs T2), and 9 days (CK3 vs T3) of drought stress, respectively, and 2,846 genes were common DEGs among the three-time points. Furthermore, the result of weighted gene co-expression network analysis (WGCNA) revealed one significant module that was closely correlated between drought stress and physiological data. A total of 1,313 significantly up-/down-regulated genes, including 61 transcription factors, were identified in the module at three-time points throughout the drought stress stage. Additionally, six vital metabolic pathways, namely, "MAPK signaling pathway-plant," "flavonoid biosynthesis," "starch and sucrose metabolism," "phenylpropanoid biosynthesis," "glutathione metabolism," and "plant hormone signal transduction" were enriched in "L422" under severe drought stress. Nine genes responding to drought tolerance were selected for quantitative real-time PCR (qRT-PCR) verification and the results agreed with transcriptional profile data, which reveals the reliability and accuracy of transcriptome data. Taken together, these findings could lead to a better understanding of drought tolerance and facilitate the breeding of drought-resistant peanut cultivars.

Factors affecting the rapid changes of protein under short-term heat stress

BACKGROUND

Protein content determines the state of cells. The variation in protein abundance is crucial when organisms are in the early stages of heat stress, but the reasons affecting their changes are largely unknown.

RESULTS

We quantified 47,535 mRNAs and 3742 proteins in the filling grains of wheat in two different thermal environments. The impact of mRNA abundance and sequence features involved in protein translation and degradation on protein expression was evaluated by regression analysis. Transcription, codon usage and amino acid frequency were the main drivers of changes in protein expression under heat stress, and their combined contribution explains 58.2 and 66.4% of the protein variation at 30 and 40 °C (20 °C as control), respectively. Transcription contributes more to alterations in protein content at 40 °C (31%) than at 30 °C (6%). Furthermore, the usage of codon AAG may be closely related to the rapid alteration of proteins under heat stress. The contributions of AAG were 24 and 13% at 30 and 40 °C, respectively.

CONCLUSION

In this study, we analyzed the factors affecting the changes in protein expression in the early stage of heat stress and evaluated their influence.

Salinity Duration Differently Modulates Physiological Parameters and Metabolites Profile in Roots of Two Contrasting Barley Genotypes

Hordeum maritimum With. is a wild salt tolerant cereal present in the saline depressions of the Eastern Tunisia, where it significantly contributes to the annual biomass production. In a previous study on shoot tissues it was shown that this species withstands with high salinity at the seedling stage restricting the sodium entry into shoot and modulating over time the leaf synthesis of organic osmolytes for osmotic adjustment. However, the tolerance strategy mechanisms of this plant at root level have not yet been investigated. The current research aimed at elucidating the morphological, physiological and biochemical changes occurring at root level in H. maritimum and in the salt sensitive cultivar Hordeum vulgare L. cv. Lamsi during five-weeks extended salinity (200 mM NaCl), salt removal after two weeks of salinity and non-salt control. H. maritimum since the first phases of salinity was able to compartmentalize higher amounts of sodium in the roots compared to the other cultivar, avoiding transferring it to shoot and impairing photosynthetic metabolism. This allowed the roots of wild plants to receive recent photosynthates from leaves, gaining from them energy and carbon skeletons to compartmentalize toxic ions in the vacuoles, synthesize and accumulate organic osmolytes, control ion and water homeostasis and re-establish the ability of root to grow. H. vulgare was also able to accumulate compatible osmolytes but only in the first weeks of salinity, while soon after the roots stopped up taking potassium and growing. In the last week of salinity stress, the wild species further increased the root to shoot ratio to enhance the root retention of toxic ions and consequently delaying the damages both to shoot and root. This delay of few weeks in showing the symptoms of stress may be pivotal for enabling the survival of the wild species when soil salinity is transient and not permanent.

Comparing transcriptional responses to Fusarium crown rot in wheat and barley identified an important relationship between disease resistance and drought tolerance

BACKGROUND

Fusarium crown rot (FCR) is a chronic disease in cereal production worldwide. The impact of this disease is highly environmentally dependant and significant yield losses occur mainly in drought-affected crops.

RESULTS

In the study reported here, we evaluated possible relationships between genes conferring FCR resistance and drought tolerance using two approaches. The first approach studied FCR induced differentially expressed genes (DEGs) targeting two barley and one wheat loci against a panel of genes curated from the literature based on known functions in drought tolerance. Of the 149 curated genes, 61.0% were responsive to FCR infection across the three loci. The second approach was a comparison of the global DEGs induced by FCR infection with the global transcriptomic responses under drought in wheat. This analysis found that approximately 48.0% of the DEGs detected one week following drought treatment and 74.4% of the DEGs detected three weeks following drought treatment were also differentially expressed between the susceptible and resistant isolines under FCR infection at one or more timepoints. As for the results from the first approach, the vast majority of common DEGs were downregulated under drought and expressed more highly in the resistant isoline than the sensitive isoline under FCR infection.

CONCLUSIONS

Results from this study suggest that the resistant isoline in wheat was experiencing less drought stress, which could contribute to the stronger defence response than the sensitive isoline. However, most of the genes induced by drought stress in barley were more highly expressed in the susceptible isolines than the resistant isolines under infection, indicating that genes conferring drought tolerance and FCR resistance may interact differently between these two crop species. Nevertheless, the strong relationship between FCR resistance and drought responsiveness provides further evidence indicating the possibility to enhance FCR resistance by manipulating genes conferring drought tolerance.

Comparative physiological and proteomic analysis of cultivated and wild safflower response to drought stress and re-watering

Drought is one of the major environmental stress that adversely affect the growth and development of oil seed plant, safflower. There is a limited knowledge on proteomic responses to support physiological, biochemical changes in how safflowers can regulate growth and metabolism under drought conditions and followed by re-watering. The changes in morphological, physiological, biochemical and proteomics of safflower genotypes (Carthamus tinctorius L.; Remzibey-05 and Linas, tolerant and sensitive cultivars, respectively, and C. oxyacantha M. Bieb., wild type) after exposure to drought and followed by re-watering have been examined. Drought negatively affected the shoot weight, water content, chlorophyll fluorescence, and biochemical parameters, including photosynthetic pigment, proline, MDA, and H₂O₂ contents and antioxidant enzyme activities in all genotypes, while the re-watering period allowed Remzibey-05 to recover, and it even provided the wild type completely recovered (approximately 100%). A total of 72 protein spots were observed as differently accumulated under treatments. The identified proteins were mainly involved in photosynthesis and carbohydrate, protein, defense, and energy metabolisms. Protein accumulation related to these metabolisms in Remzibey-05 were decreased under drought, while increased following re-watering. However, sensitive cultivar, Linas, could not exhibit an effective performance under drought and recovery when compared with other safflower genotypes.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at (10.1007/s12298-021-00934-2).

Auxin-salicylic acid cross-talk ameliorates OsMYB-R1 mediated defense towards heavy metal, drought and fungal stress

The MYB TF family is an immensely large and functionally diverse class of proteins involved in the regulation of cell cycle, cell morphogenesis to stress signaling mechanism. The present study deciphered the hormonal cross-talk of wound inducible and stress-responsive OsMYB-R1 transcription factor in combating abiotic [Cr(VI) and drought/PEG] as well as biotic (Rhizoctonia solani) stress. OsMYB-R1 over-expressing rice transgenics exhibit a significant increase in lateral roots, which may be associated with increased tolerance under Cr(VI) and drought exposure. In contrast, its loss-of-function reduces stress tolerance. Higher auxin accumulation in the OsMYB-R1 over-expressed lines further strengthens the protective role of lateral roots under stress conditions. RNA-seq. data reveals over-representation of salicylic acid signaling molecule calcium-dependent protein kinases, which probably activate the stress-responsive downstream genes (Peroxidases, Glutathione S-transferases, Osmotins, Heat Shock Proteins, Pathogenesis Related-Proteins). Enzymatic studies further confirm OsMYB-R1 mediated robust antioxidant system as catalase, guaiacol peroxidase and superoxide dismutase activities were found to be increased in the over-expressed lines. Our results suggest that OsMYB-R1 is part of a complex network of transcription factors controlling the cross-talk of auxin and salicylic acid signaling and other genes in response to multiple stresses by modifying molecular signaling, internal cellular homeostasis and root morphology.

Genome-wide small RNA profiling reveals tiller development in tall fescue (Festuca arundinacea Schreb)

Background

Tall fescue (Festuca arundinacea Schreb.) is a major cool-season forage and turfgrass species. The low tiller density and size dramatically limits its turf performance and forage yield. MicroRNAs (miRNA)-genes modules play critical roles in tiller development in plants. In this study, a genome-wide small RNA profiling was carried out in two tall fescue genotypes contrasting for tillering production (‘Ch-3’, high tiller production rate and ‘Ch-5’, low tiller production rate) and two types of tissue samples at different tillering development stage (Pre-tillering, grass before tillering; Tillering, grass after tillering). ‘Ch-3’, ‘Ch-5’, Pre-tillering, and Tillering samples were analyzed using high-throughput RNA sequencing.

Results

A total of 222 million high-quality clean reads were generated and 208 miRNAs were discovered, including 148 known miRNAs belonging to 70 families and 60 novel ones. Furthermore, 18 miRNAs were involved in tall fescue tiller development process. Among them, 14 miRNAs displayed increased abundance in both Ch-3 and Tillering plants compared with that in Ch-5 and Pre-tillering plants and were positive with tillering, while another four miRNAs were negative with tiller development. Out of the three miRNAs osa-miR156a, zma-miR528a-3p and osa-miR444b.2, the rest of 15 miRNAs were newfound and associated with tiller development in plants. Based on our previous full-length transcriptome analysis in tall fescue, 28,927 potential target genes were discovered for all identified miRNAs. Most of the 212 target genes of the 18 miRNAs were dominantly enriched into “ubiquitin-mediated proteolysis”, “phagosome”, “fatty acid biosynthesis”, “oxidative phosphorylation”, and “biosynthesis of unsaturated fatty acids” KEGG pathways. In addition, bdi-miR167e-3p targets two kinase proteins EIF2AK4 and IRAK4, and osa-miR397a targets auxin response factor 5, which may be the significant miRNA-genes controllers in tillering development.

Conclusions

This is the first genome-wide miRNA profiles analysis to identify regulators involved in tiller development in cool-season turfgrass. Tillering related 18 miRNAs and their 212 target genes provide novel information for the understanding of the molecular mechanisms of miRNA-genes mediated tiller development in cool-season turfgrass.

Overexpression of wheat transcription factor (TaHsfA6b) provides thermotolerance in barley

Overexpressing a heat shock factor gene (TaHsfA6bT) from wheat provides thermotolerance in barley by constitutive expression of heat and other abiotic stress-response genes. Temperature is one of the most crucial abiotic factors defining the yield potential of temperate cereal crops, such as barley. The regulators of heat shock response (HSR), heat stress transcription factors (Hsfs), modulate the transcription level of heat-responsive genes to protect the plants from heat stress. In this study, an Hsf from wheat (TaHsfA6b) is overexpressed in barley for providing thermotolerance. Transgenic barley lines overexpressing TaHsfA6b showed improvement in thermotolerance. The constitutive overexpression of a TaHsfA6b gene upregulated the expression of major heat shock proteins and other abiotic stress-responsive genes. RNA-seq and qRT-PCR analysis confirmed the upregulation of Hsps, chaperonins, DNAJ, LEA protein genes, and genes related to anti-oxidative enzymes in transgenic lines. Excessive generation and accumulation of reactive oxygen species (ROS) occurred in wild-type (WT) plants during heat stress; however, the transgenic lines reflected improved ROS homeostasis mechanisms, showing lesser ROS accumulation under high temperature. No negative phenotypic changes were observed in overexpression lines. These results suggest that TaHsfA6b is a regulator of HSR and its overexpression altered the expression patterns of some main stress-related genes and enhanced the thermotolerance of this cereal crop.

Epigenetics: possible applications in climate-smart crop breeding

To better adapt transiently or lastingly to stimuli from the surrounding environment, the chromatin states in plant cells vary to allow the cells to fine-tune their transcriptional profiles. Modifications of chromatin states involve a wide range of post-transcriptional histone modifications, histone variants, DNA methylation, and activity of non-coding RNAs, which can epigenetically determine specific transcriptional outputs. Recent advances in the area of '-omics' of major crops have facilitated identification of epigenetic marks and their effect on plant response to environmental stresses. As most epigenetic mechanisms are known from studies in model plants, we summarize in this review recent epigenetic studies that may be important for improvement of crop adaptation and resilience to environmental changes, ultimately leading to the generation of stable climate-smart crops. This has paved the way for exploitation of epigenetic variation in crop breeding.

Recent Progress in Germplasm Evaluation and Gene Mapping to Enable Breeding of Drought-Tolerant Wheat

There is a need to increase wheat productivity to meet the food demands of the ever-growing human population. However, accelerated development of high yielding varieties is hindered by drought, which is worsening due to climate change. In this context, germplasm diversity is central to the development of drought-tolerant wheat. Extensive collections of these genetic resources are conserved in national and international genebanks. In addition to phenotypic assessments, the use of advanced molecular techniques (e.g., genotype by sequencing) to identify quantitative trait loci (QTLs) for drought tolerance related traits is useful for genome- and marker-assisted selection based approaches. Therefore, to assist wheat breeders at a critical time, we searched the recent peer-reviewed literature (2011-current), first, to identify wheat germplasm observed to be useful genetic sources for drought tolerance, and second, to report QTLs associated with drought tolerance. Though many breeders limit the parents used in breeding programs to a familiar core collection, the results of this review show that larger germplasm collections have been sources of useful genes for drought tolerance in wheat. The review also demonstrates that QTLs for drought tolerance in wheat are associated with diverse physio-morphological traits, at different growth stages. Here, we also briefly discuss the potential of genome engineering/editing to improve drought tolerance in wheat. The use of CRISPR-Cas9 and other gene-editing technologies can be used to fine-tune the expression of genes controlling drought adaptive traits, while high throughput phenotyping (HTP) techniques can potentially accelerate the selection process. These efforts are empowered by wheat researcher consortia.

Identification and expression analysis of WRKY gene family under drought stress in peanut (Arachis hypogaea L.)

WRKY transcription factors play crucial roles in regulation mechanism leading to the adaption of plants to the complex environment. In this study, AhWRKY family was comprehensively analyzed using bioinformatic approaches in combination with transcriptome sequencing data of the drought-tolerant peanut variety ‘L422’. A total of 158 AhWRKY genes were identified and named according to their distribution on the chromosomes. Based on the structural features and phylogenetic analysis of AhWRKY proteins, the AhWRKY family members were classified into three (3) groups, of which group II included five (5) subgroups. Results of structure and conserved motifs analysis for the AhWRKY genes confirmed the accuracy of the clustering analysis. In addition, 12 tandem and 136 segmental duplication genes were identified. The results indicated that segmental duplication events were the main driving force in the evolution of AhWRKY family. Collinearity analysis found that 32 gene pairs existed between Arachis hypogaea and two diploid wild ancestors (Arachis duranensis and Arachis ipaensis), which provided valuable clues for phylogenetic characteristics of AhWRKY family. Furthermore, 19 stress-related cis-acting elements were found in the promoter regions. During the study of gene expression level of AhWRKY family members in response to drought stress, 73 differentially expressed AhWRKY genes were obtained to have been influenced by drought stress. These results provide fundamental insights for further study of WRKY genes in peanut drought resistance.

iTRAQ-Based Proteomic Analysis Reveals Several Strategies to Cope with Drought Stress in Maize Seedlings

Drought stress, especially during the seedling stage, seriously limits the growth of maize and reduces production in the northeast of China. To investigate the molecular mechanisms of drought response in maize seedlings, proteome changes were analyzed. Using an isotopic tagging relative quantitation (iTRAQ) based method, a total of 207 differentially accumulated protein species (DAPS) were identified under drought stress in maize seedlings. The DAPS were classified into ten essential groups and analyzed thoroughly, which involved in signaling, osmotic regulation, protein synthesis and turnover, reactive oxygen species (ROS) scavenging, membrane trafficking, transcription related, cell structure and cell cycle, fatty acid metabolism, carbohydrate and energy metabolism, as well as photosynthesis and photorespiration. The enhancements of ROS scavenging, osmotic regulation, protein turnover, membrane trafficking, and photosynthesis may play important roles in improving drought tolerance of maize seedlings. Besides, the inhibitions of some protein synthesis and slowdown of cell division could reduce the growth rate and avoid excessive water loss, which is possible to be the main reasons for enhancing drought avoidance of maize seedlings. The incongruence between protein and transcript levels was expectedly observed in the process of confirming iTRAQ data by quantitative real-time polymerase chain reaction (qRT-PCR) analysis, which further indicated that the multiplex post-transcriptional regulation and post-translational modification occurred in drought-stressed maize seedlings. Finally, a hypothetical strategy was proposed that maize seedlings coped with drought stress by improving drought tolerance (via. promoting osmotic adjustment and antioxidant capacity) and enhancing drought avoidance (via. reducing water loss). Our study provides valuable insight to mechanisms underlying drought response in maize seedlings.

Transcriptomic and evolutionary analysis of the mechanisms by which P. argentatum, a rubber producing perennial, responds to drought

BACKGROUND

Guayule (Parthenium argentatum Gray) is a drought tolerant, rubber producing perennial shrub native to northern Mexico and the US Southwest. Hevea brasiliensis, currently the world's only source of natural rubber, is grown as a monoculture, leaving it vulnerable to both biotic and abiotic stressors. Isolation of rubber from guayule occurs by mechanical harvesting of the entire plant. It has been reported that environmental conditions leading up to harvest have a profound impact on rubber yield. The link between rubber biosynthesis and drought, a common environmental condition in guayule's native habitat, is currently unclear.

RESULTS

We took a transcriptomic and comparative genomic approach to determine how drought impacts rubber biosynthesis in guayule. We compared transcriptional profiles of stem tissue, the location of guayule rubber biosynthesis, collected from field-grown plants subjected to water-deficit (drought) and well-watered (control) conditions. Plants subjected to the imposed drought conditions displayed an increase in production of transcripts associated with defense responses and water homeostasis, and a decrease in transcripts associated with rubber biosynthesis. An evolutionary and comparative analysis of stress-response transcripts suggests that more anciently duplicated transcripts shared among the Asteraceae, rather than recently derived duplicates, are contributing to the drought response observed in guayule. In addition, we identified several deeply conserved long non-coding RNAs (lncRNAs) containing microRNA binding motifs. One lncRNA in particular, with origins at the base of Asteraceae, may be regulating the vegetative to reproductive transition observed in water-stressed guayule by acting as a miRNA sponge for miR166.

CONCLUSIONS

These data represent the first genomic analyses of how guayule responds to drought like conditions in agricultural production settings. We identified an inverse relationship between stress-responsive transcripts and those associated with precursor pathways to rubber biosynthesis suggesting a physiological trade-off between maintaining homeostasis and plant productivity. We also identify a number of regulators of abiotic responses, including transcription factors and lncRNAs, that are strong candidates for future projects aimed at modulating rubber biosynthesis under water-limiting conditions common to guayules' native production environment.

Using environmental clustering to identify specific drought tolerance QTLs in bread wheat (T. aestivum L.)

Environmental clustering helps to identify QTLs associated with grain yield in different water stress scenarios. These QTLs could be useful for breeders to improve grain yields and increase genetic resilience in marginal environments. Drought is one of the main abiotic stresses limiting winter bread wheat growth and productivity around the world. The acquisition of new high-yielding and stress-tolerant varieties is therefore necessary and requires improved understanding of the physiological and genetic bases of drought resistance. A panel of 210 elite European varieties was evaluated in 35 field trials. Grain yield and its components were scored in each trial. A crop model was then run with detailed climatic data and soil water status to assess the dynamics of water stress in each environment. Varieties were registered from 1992 to 2011, allowing us to test timewise genetic progress. Finally, a genome-wide association study (GWAS) was carried out using genotyping data from a 280 K SNP chip. The crop model simulation allowed us to group the environments into four water stress scenarios: an optimal condition with no water stress, a post-anthesis water stress, a moderate-anthesis water stress and a high pre-anthesis water stress. Compared to the optimal water condition, grain yield losses in the stressed conditions were 3.3%, 12.4% and 31.2%, respectively. This environmental clustering improved understanding of the effect of drought on grain yields and explained 20% of the G × E interaction. The greatest genetic progress was obtained in the optimal condition, mostly represented in France. The GWAS identified several QTLs, some of which were specific of the different water stress patterns. Our results make breeding for improved drought resistance to specific environmental scenarios easier and will facilitate genetic progress in future environments, i.e., water stress environments.

Comparative metabolite profiling of two switchgrass ecotypes reveals differences in drought stress responses and rhizosheath weight

Rhizosheath comprises soil that adheres firmly to roots. In this study, two ecotypes of switchgrass with different rhizosheath sizes after drought stress were analyzed which showed metabolic differences under drought conditions. The rhizosheath comprises soil that adheres firmly to roots by a combination of root hairs and mucilage and may aid in root growth under soil drying. The aim of this work is to reveal the potential metabolites involved in rhizosheath formation under drought stress conditions. Panicum virgatum L. (switchgrass), which belongs to the Poaceae family, is an important biofuel and fodder crop in drought areas. Five switchgrass ecotypes (cv. Alamo, cv. Blackwake, cv. Summer, cv. Cave-in-Rock and cv. Kanlow) have a broad range of rhizosheath weight under drought conditions. For two selected ecotypes with contrast rhizosheath weight (cv. Alamo and cv. Kanlow), root hair length and density, lateral root number, root morphological parameters were measured, and real-time qRT-PCR was performed. Gas chromatography mass spectrophotometry (GC-MS) was used to determine the primary metabolites in the shoots and roots of selected ecotypes under drought stress conditions. The change trends of root hair length and density, lateral root number and related gene expression were consistent with rhizosheath weight in Alamo and Kanlow under drought and watered conditions. For root morphological parameters, Alamo grew deeper than Kanlow, while Kanlow exhibited higher values for other parameters. In this study, the levels of amino acids, sugars and organic acids were significantly changed in response to drought stress in two switchgrass ecotypes. Several metabolites including amino acids (arginine, isoleucine, methionine and cysteine) and sugars (kestose, raffinose, fructose, fucose, sorbose and xylose) in the large soil-sheathed roots of Alamo and Kanlow were significantly increased compared to small or no soil-sheathed roots of Alamo and Kanlow. Difference in rhizosheath size is reflected in the plant internal metabolites under drought stress conditions. Additionally, our results highlight the importance of using metabolite profiling and provide a better understanding of rhizosheath formation at the cellular level.

RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat

Drought is one of the major impediments in wheat productivity. Traditional breeding and marker assisted QTL introgression had limited success. Available wheat genomic and RNA-seq data can decipher novel drought tolerance mechanisms with putative candidate gene and marker discovery. Drought is first sensed by root tissue but limited information is available about how roots respond to drought stress. In this view, two contrasting genotypes, namely, NI5439 41 (drought tolerant) and WL711 (drought susceptible) were used to generate ~78.2 GB data for the responses of wheat roots to drought. A total of 45139 DEGs, 13820 TF, 288 miRNAs, 640 pathways and 435829 putative markers were obtained. Study reveals use of such data in QTL to QTN refinement by analysis on two model drought-responsive QTLs on chromosome 3B in wheat roots possessing 18 differentially regulated genes with 190 sequence variants (173 SNPs and 17 InDels). Gene regulatory networks showed 69 hub-genes integrating ABA dependent and independent pathways controlling sensing of drought, root growth, uptake regulation, purine metabolism, thiamine metabolism and antibiotics pathways, stomatal closure and senescence. Eleven SSR markers were validated in a panel of 18 diverse wheat varieties. For effective future use of findings, web genomic resources were developed. We report RNA-Seq approach on wheat roots describing the drought response mechanisms under field drought conditions along with genomic resources, warranted in endeavour of wheat productivity.

CRISPR/Cas9 in plants: at play in the genome and at work for crop improvement

The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system uses single-guide RNAs for genome editing, making it a simple, robust, powerful tool for targeted gene mutagenesis, knockout and knock-in/replacement, as well as transcriptional regulation. Here, we review the working principles, components and potential modifications of CRISPR/Cas9 for efficient single and multiplex gene editing in plants. We also describe recent work that has used CRISPR/Cas9 to improve economically important traits in crop plants. Although the apparent ease of CRISPR/Cas9-mediated editing may make it appear as though scientists are merely playing with plant genomes, the combined power of CRISPR/Cas9 has enabled vital research to be completed in the battle toward optimization and adaptation of crop species, permitting crucial advances to be achieved in crop improvement.

Transcriptional reference map of hormone responses in wheat spikes

Background

Phytohormones are key regulators of plant growth, development, and signalling networks involved in responses to diverse biotic and abiotic stresses. Transcriptional reference maps of hormone responses have been reported for several model plant species such as Arabidopsis thaliana, Oryza sativa, and Brachypodium distachyon. However, because of species differences and the complexity of the wheat genome, these transcriptome data are not appropriate reference material for wheat studies.

Results

We comprehensively analysed the transcriptomic responses in wheat spikes to seven phytohormones, including indole acetic acid (IAA), gibberellic acid (GA), abscisic acid (ABA), ethylene (ET), cytokinin (CK), salicylic acid (SA), and methyl jasmonic acid (MeJA). A total of 3386 genes were differentially expressed at 24 h after the hormone treatments. Furthermore, 22.7% of these genes exhibited overlapping transcriptional responses for at least two hormones, implying there is crosstalk among phytohormones. We subsequently identified genes with expression levels that were significantly and differentially induced by a specific phytohormone (i.e., hormone-specific responses). The data for these hormone-responsive genes were then compared with the transcriptome data for wheat spikes exposed to biotic (Fusarium head blight) and abiotic (water deficit) stresses.

Conclusion

Our data were used to develop a transcriptional reference map of hormone responses in wheat spikes.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5726-x) contains supplementary material, which is available to authorized users.

Stress-responsive miRNAome of Glycine max (L.) Merrill: molecular insights and way forward

MAIN CONCLUSION

Analysis of stress-associated miRNAs of Glycine max (L.) Merrill reveals wider ramifications of small RNA-mediated (conserved and legume-specific miRNAs) gene regulatory foot prints in molecular adaptive responses. MicroRNAs (miRNAs) are indispensable components of gene regulatory mechanism of plants. Soybean is a crop of immense commercial potential grown worldwide for its edible oil and soy meal. Intensive research efforts, using the next generation sequencing and bioinformatics techniques, have led to the identification and characterization of numerous small RNAs, especially microRNAs (miRNAs), in soybean. Furthermore, studies have unequivocally demonstrated the significance of miRNAs during the developmental processes and various stresses in soybean. In this review, we summarize the current state of understanding of miRNA-based abiotic and biotic stress responses in soybean. In addition, the molecular insights gained from the stress-related soybean miRNAs have been compared to the miRNAs of other crops, especially legumes, and the core commonalities have been highlighted, though differences among them were not ignored. Nature of response of soybean-derived conserved miRNAs during various stresses was also analyzed to gain deeper insights regarding sRNAome-based defense responses. This review further provides way forward in legume small RNA transcriptomics based on the adaptive responses of soybean and other legume-derived miRNAs.

Functional characterization of HSFs from wheat in response to heat and other abiotic stress conditions

High temperature stress is known to be one of the major limiting factors for wheat productivity worldwide. HSFs are known to play a central role in heat stress response in plants. Hence, the current study is an attempt to explore an in-depth involvement of TaHSFs in stress responses mainly in heat and other abiotic responses like salinity, drought, and cold stress. Effort was made to understand as how the expression of HSF is able to define the differential robustness of wheat varieties. Subsequent studies were done to establish the involvement of any temporal or spatial cue on the behavior of these TaHSFs under heat stress conditions. A total of 53 HSFs have been reported until date and out of these, few TaHSFs including one identified in our library, i.e., TaHsfA2d (Traes_4AS_52EB860E7.2), were selected for the expression analysis studies. The expressions of these HSFs were found to differ in both magnitude and sensitivity to the heat as well as other abiotic stresses. Moreover, these TaHSFs displayed wide range of expression in different tissues like anther, ovary, lemma, palea, awn, glume, and different stages of seed development. Thus, TaHSFs appear to be under dynamic expression as they respond in a unique manner to spatial, temporal, and environmental cues. Therefore, these HSFs can be used as candidate genes for understanding the molecular mechanism under heat stress and can be utilized for improving crop yield by enhancing the tolerance and survival of the crop plants under adverse environment conditions.

Genetic Modification for Wheat Improvement: From Transgenesis to Genome Editing

To feed the growing human population, global wheat yields should increase to approximately 5 tonnes per ha from the current 3.3 tonnes by 2050. To reach this goal, existing breeding practices must be complemented with new techniques built upon recent gains from wheat genome sequencing, and the accumulated knowledge of genetic determinants underlying the agricultural traits responsible for crop yield and quality. In this review we primarily focus on the tools and techniques available for accessing gene functions which lead to clear phenotypes in wheat. We provide a view of the development of wheat transformation techniques from a historical perspective, and summarize how techniques have been adapted to obtain gain-of-function phenotypes by gene overexpression, loss-of-function phenotypes by expressing antisense RNAs (RNA interference or RNAi), and most recently the manipulation of gene structure and expression using site-specific nucleases, such as CRISPR/Cas9, for genome editing. The review summarizes recent successes in the application of wheat genetic manipulation to increase yield, improve nutritional and health-promoting qualities in wheat, and enhance the crop's resistance to various biotic and abiotic stresses.

Compositional equivalence of event IND-ØØ412-7 to non-transgenic wheat

Wheat is the most widely grown cereal grain, occupying a significant portion of the total cultivated land. As drought is the major environmental stressor affecting crop production, yield maintenance under water deficit conditions appears as a highly desirable phenotype for crop improvement. The HaHB4 (Helianthus annuus homeobox 4) gene from sunflower encodes for a transcription factor involved in tolerance to environmental stress. The introduction of HaHB4 in wheat led to the development of event IND-ØØ412-7 (HB4^® wheat), which displayed higher yield in production environments of low productivity potential. Compositional analysis of IND-ØØ412-7 wheat, including 41 nutrients and 2 anti-nutrients for grain and 10 nutrients in forage, was performed. Results of these studies indicated that IND-ØØ412-7 is compositionally equivalent to non-transgenic wheat.

Multiple Near-Isogenic Lines Targeting a QTL Hotspot of Drought Tolerance Showed Contrasting Performance Under Post-anthesis Water Stress

The complex quantitative nature of drought-related traits is a major constraint to breed tolerant wheat varieties. Pairs of near-isogenic lines (NILs) with a common genetic background but differing in a particular locus could turn quantitative traits into a Mendelian factor facilitating our understanding of genotype and phenotype interactions. In this study, we report our fast track development and evaluation of NILs from C306 × Dharwar Dry targeting a wheat 4BS QTL hotspot in C306, which confers drought tolerance following the heterogeneous inbreed family (HIF) analysis coupled with immature embryo culture-based fast generation technique. Molecular marker screening and phenotyping for grain yield and related traits under post-anthesis water stress (WS) confirmed four isoline pairs, viz., qDSI.4B.1-2, qDSI.4B.1-3, qDSI.4B.1-6, and qDSI.4B.1-8. There were significant contrasts of responses between the NILs with C306 QTL (+NILs) and the NILs without C306 QTL (-NILs). Among the four confirmed NIL pairs, mean grain yield per plant of the +NILs and -NILs showed significant differences ranging from 9.61 to 10.81 and 6.30 to 7.56 g, respectively, under WS condition, whereas a similar grain yield was recorded between the +NILs and -NILs under well-watered condition. Isolines of +NIL and -NIL pairs showed similar chlorophyll content (SPAD), assimilation rate (A), and transpiration rate (Tr) at the beginning of the stress. However, the +NILs showed significantly higher SPAD (12%), A (66%), stomatal conductance (75%), and Tr (97%) than the -NILs at the seventh day of stress. Quantitative RT-PCR analysis targeting the MYB transcription factor gene Triticum aestivum MYB 82 (TaMYB82), within this genomic region which was retrieved from the wheat reference genome TGACv1, also revealed differential expression in +NILs and -NILs under stress. These results confirmed that the NILs can be invaluable resources for fine mapping of this QTL, and also for cloning and functional characterization of the gene(s) responsible for drought tolerance in wheat.