Gene expression analysis reveals important pathways for drought response in leaves and roots of a wheat cultivar adapted to rainfed cropping in the Cerrado biome

Accelerating wheat improvement through trait characterization: advances and perspectives

Wheat (Triticum spp.) is a primary dietary staple food for humanity. Many wheat genetic resources with variable genomes have a record of domestication history and are widespread throughout the world. To develop elite wheat varieties, agronomical and stress-responsive trait characterization is foremost for evaluating existing germplasm to promote breeding. However, genomic complexity is one of the primary impediments to trait mining and characterization. Multiple reference genomes and cutting-edge technologies like haplotype mapping, genomic selection, precise gene editing tools, high-throughput phenotyping platforms, high-efficiency genetic transformation systems, and speed-breeding facilities are transforming wheat functional genomics research to understand the genomic diversity of polyploidy. This review focuses on the research achievements in wheat genomics, the available omics approaches, and bioinformatic resources developed in the past decades. Advances in genomics and system biology approaches are highlighted to circumvent bottlenecks in genomic and phenotypic selection, as well as gene transfer. In addition, we propose conducting precise functional genomic studies and developing sustainable breeding strategies for wheat. These developments in understanding wheat traits have speed up the creation of high-yielding, stress-resistant, and nutritionally enhanced wheat varieties, which will help in addressing global food security and agricultural sustainability in the era of climate change.

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.

Variety-specific transcript accumulation during reproductive stage in drought-stressed rice

The divergence of natural stress tolerance mechanisms between species is an intriguing phenomenon. To study it in rice, a comparative transcriptome analysis was carried out in 'heading' stage tissue (flag leaf, panicles and roots) of Nagina 22 (N22; drought-tolerant) and IR64 (drought-sensitive) plants subjected to field drought. Interestingly, N22 showed almost double the number of differentially expressed genes (DEGs) than IR64. Many DEGs colocalized within drought-related QTLs responsible for grain yield and drought tolerance and also associated with drought tolerance and critical drought-related plant traits such as leaf rolling, trehalose content, sucrose and cellulose content. Besides, co-expression analysis of the DEGs revealed several 'hub' genes known to actively regulate drought stress response. Strikingly, 1366 DEGs, including 21 'hub' genes, showed a distinct opposite regulation in the two rice varieties under similar drought conditions. Annotation of these variety-specific DEGs (VS-DEGs) revealed that they are distributed in various biological pathways. Furthermore, 103 VS-DEGs were found to physically interact with over 1300 genes, including 32 that physically interact with other VS-DEGs as well. The promoter region of these genes has sequence variations among the two rice varieties, which might be in part responsible for their unique expression pattern.

Comparative transcriptome profiling of a resistant vs susceptible bread wheat (Triticum aestivum L.) cultivar in response to water deficit and cold stress

Bread wheat (Triticum aestivum L.) is one of the most important agricultural plants wearing abiotic stresses, such as water deficit and cold, that cause its productivity reduction. Since resistance to abiotic factors is a multigenic trait, therefore modern genome-wide approaches can help to involve various genetic material in breeding. One technique is full transcriptome analysis that reveals groups of stress response genes serving marker-assisted selection markers. Comparing transcriptome profiles of the same genetic material under several stresses is essential and makes the whole picture. Here, we addressed this by studying the transcriptomic response to water deficit and cold stress for two evolutionarily distant bread wheat varieties: stress-resistant cv. Saratovskaya 29 (S29) and stress-sensitive cv. Yanetzkis Probat (YP). For the first time, transcriptomes for these cultivars grown under abiotic stress conditions were obtained using Illumina based MACE technology. We identified groups of genes involved in response to cold and water deficiency stresses, including responses to each stress factor and both factors simultaneously that may be candidates for resistance genes. We discovered a core group of genes that have a similar pattern of stress-induced expression changes. The particular expression pattern was revealed not only for the studied varieties but also for the published transcriptomic data on cv. Jing 411 and cv. Fielder. Comparative transcriptome profiling of cv. S29 and cv. YP in response to water deficit and cold stress confirmed the hypothesis that stress-induced expression change is unequal within a homeologous gene group. As a rule, at least one changed significantly while the others had a relatively lower expression. Also, we found several SNPs distributed throughout the genomes of cv. S29 and cv. YP and distinguished the studied varieties from each other and the reference cv. Chinese Spring. Our results provide new data for genomics-assisted breeding of stress-tolerant wheat cultivars.

RNA-seq analysis reveals different drought tolerance mechanisms in two broadly adapted wheat cultivars 'TAM 111' and 'TAM 112'

Wheat cultivars 'TAM 111' and 'TAM 112' have been dominantly grown in the Southern U.S. Great Plains for many years due to their high yield and drought tolerance. To identify the molecular basis and genetic control of drought tolerance in these two landmark cultivars, RNA-seq analysis was conducted to compare gene expression difference in flag leaves under fully irrigated (wet) and water deficient (dry) conditions. A total of 2254 genes showed significantly altered expression patterns under dry and wet conditions in the two cultivars. TAM 111 had 593 and 1532 dry-wet differentially expressed genes (DEGs), and TAM 112 had 777 and 1670 at heading and grain-filling stages, respectively. The two cultivars have 1214 (53.9%) dry-wet DEGs in common, which agreed with their excellent adaption to drought, but 438 and 602 dry-wet DEGs were respectively shown only in TAM 111 and TAM 112 suggested that each has a specific mechanism to cope with drought. Annotations of all 2254 genes showed 1855 have functions related to biosynthesis, stress responses, defense responses, transcription factors and cellular components related to ion or protein transportation and signal transduction. Comparing hierarchical structure of biological processes, molecule functions and cellular components revealed the significant regulation differences between TAM 111 and TAM 112, particularly for genes of phosphorylation and adenyl ribonucleotide binding, and proteins located in nucleus and plasma membrane. TAM 112 showed more active than TAM 111 in response to drought and carried more specific genes with most of them were up-regulated in responses to stresses of water deprivation, heat and oxidative, ABA-induced signal pathway and transcription regulation. In addition, 258 genes encoding predicted uncharacterized proteins and 141 unannotated genes with no similar sequences identified in the databases may represent novel genes related to drought response in TAM 111 or TAM 112. This research thus revealed different drought-tolerance mechanisms in TAM 111 and TAM 112 and identified useful drought tolerance genes for wheat adaption. Data of gene sequence and expression regulation from this study also provided useful information of annotating novel genes associated with drought tolerance in the wheat genome.

Genetic Characterization of a Wheat Association Mapping Panel Relevant to Brazilian Breeding Using a High-Density Single Nucleotide Polymorphism Array

Bread wheat (Triticum aestivum L.) is one of the world’s most important crops. Maintaining wheat yield gains across all of its major production areas is a key target toward underpinning global food security. Brazil is a major wheat producer in South America, generating grain yields of around 6.8 million tons per year. Here, we establish and genotype a wheat association mapping resource relevant to contemporary Brazilian wheat breeding programs. The panel of 558 wheat accessions was genotyped using an Illumina iSelect 90,000 single nucleotide polymorphism array. Following quality control, the final data matrix consisted of 470 accessions and 22,475 polymorphic genetic markers (minor allele frequency ≥5%, missing data <5%). Principal component analysis identified distinct differences between materials bred predominantly for the northern Cerrado region, compared to those bred for southern Brazilian agricultural areas. We augmented the genotypic data with 26 functional Kompetitive Allele-Specific PCR (KASP) markers to identify the allelic combinations at genes with previously known effects on agronomically important traits in the panel. This highlighted breeding targets for immediate consideration – notably, increased Fusarium head blight resistance via the Fhb1 locus. To demonstrate the panel’s likely future utility, genome-wide association scans for several phenotypic traits were undertaken. Significant (Bonferroni corrected P < 0.05) marker-trait associations were detected for Fusarium kernel damage (a proxy for type 2 Fusarium resistance), identifying previously known quantitative trait loci in the panel. This association mapping panel represents an important resource for Brazilian wheat breeding, allowing future genetic studies to analyze multiple agronomic traits within a single genetically diverse population.

Field-grown transgenic wheat expressing the sunflower gene HaHB4 significantly outyields the wild type

HaHB4 is a sunflower transcription factor belonging to the homeodomain-leucine zipper I family whose ectopic expression in Arabidopsis triggers drought tolerance. The use of PCR to clone the HaHB4 coding sequence for wheat transformation caused unprogrammed mutations producing subtle differences in its activation ability in yeast. Transgenic wheat plants carrying a mutated version of HaHB4 were tested in 37 field experiments. A selected transgenic line yielded 6% more (P<0.001) and had 9.4% larger water use efficiency (P<0.02) than its control across the evaluated environments. Differences in grain yield between cultivars were explained by the 8% improvement in grain number per square meter (P<0.0001), and were more pronounced in stress (16% benefit) than in non-stress conditions (3% benefit), reaching a maximum of 97% in one of the driest environments. Increased grain number per square meter of transgenic plants was accompanied by positive trends in spikelet numbers per spike, tillers per plant, and fertile florets per plant. The gene transcripts associated with abiotic stress showed that HaHB4's action was not dependent on the response triggered either by RD19 or by DREB1a, traditional candidates related to water deficit responses. HaHB4 enabled wheat to show some of the benefits of a species highly adapted to water scarcity, especially in marginal regions characterized by frequent droughts.

Analysis of transcriptional responses in root tissue of bread wheat landrace (Triticum aestivum L.) reveals drought avoidance mechanisms under water scarcity

In this study, high-throughput sequencing (RNA-Seq) was utilized to evaluate differential expression of transcripts and their related genes involved in response to terminal drought in root tissues of bread wheat landrace (L-82) and drought-sensitive genotype (Marvdasht). Subsets of 460 differentially expressed genes (DEGs) in drought-tolerant genotype and 236 in drought-sensitive genotype were distinguished and functionally annotated with 105 gene ontology (GO) terms and 77 metabolic pathways. Transcriptome profiling of drought-resistant genotype “L-82” showed up-regulation of genes mostly involved in Oxidation-reduction process, secondary metabolite biosynthesis, abiotic stress response, transferase activity and heat shock proteins. On the other hand, down-regulated genes mostly involved in signaling, oxidation-reduction process, secondary metabolite biosynthesis, auxin-responsive protein and lipid metabolism. We hypothesized that the drought tolerance in “L-82” was a result of avoidance strategies. Up-regulation of genes related to the deeper root system and adequate hydraulic characteristics to allow water uptake under water scarcity confirms our hypothesis. The transcriptomic sequences generated in this study provide information about mechanisms of acclimation to drought in the selected bread wheat landrace, “L-82”, and will help us to unravel the mechanisms underlying the ability of crops to reproduce and keep its productivity even under drought stress.

Omics Approaches for Engineering Wheat Production under Abiotic Stresses

Abiotic stresses greatly influenced wheat productivity executed by environmental factors such as drought, salt, water submergence and heavy metals. The effective management at the molecular level is mandatory for a thorough understanding of plant response to abiotic stress. Understanding the molecular mechanism of stress tolerance is complex and requires information at the omic level. In the areas of genomics, transcriptomics and proteomics enormous progress has been made in the omics field. The rising field of ionomics is also being utilized for examining abiotic stress resilience in wheat. Omic approaches produce a huge amount of data and sufficient developments in computational tools have been accomplished for efficient analysis. However, the integration of omic-scale information to address complex genetics and physiological questions is still a challenge. Though, the incorporation of omic-scale data to address complex genetic qualities and physiological inquiries is as yet a challenge. In this review, we have reported advances in omic tools in the perspective of conventional and present day approaches being utilized to dismember abiotic stress tolerance in wheat. Attention was given to methodologies, for example, quantitative trait loci (QTL), genome-wide association studies (GWAS) and genomic selection (GS). Comparative genomics and candidate genes methodologies are additionally talked about considering the identification of potential genomic loci, genes and biochemical pathways engaged with stress resilience in wheat. This review additionally gives an extensive list of accessible online omic assets for wheat and its effective use. We have additionally addressed the significance of genomics in the integrated approach and perceived high-throughput multi-dimensional phenotyping as a significant restricting component for the enhancement of abiotic stress resistance in wheat.

Transcriptional regulation of osmotic stress tolerance in wheat (Triticum aestivum L.)

The current review provides an updated, new insights into the regulation of transcription mediated underlying mechanisms of wheat plants to osmotic stress perturbations. Osmotic stress tolerance mechanisms being complex are governed by multiple factors at physiological, biochemical and at the molecular level, hence approaches like "OMICS" that can underpin mechanisms behind osmotic tolerance in wheat is of paramount importance. The transcription factors (TFs) are a class of molecular proteins, which are involved in regulation, modulation and orchestrating the responses of plants to a variety of environmental stresses. Recent reports have provided novel insights on the role of TFs in osmotic stress tolerance via direct molecular links. However, our knowledge on the regulatory role TFs during osmotic stress tolerance in wheat remains limited. The present review in its first part sheds light on the importance of studying the role of osmotic stress tolerance in wheat plants and second aims to decipher molecular mechanisms of TFs belonging to several classes, including DREB, NAC, MYB, WRKY and bHLH, which have been reported to engage in osmotic stress mediated gene expression in wheat and third part covers the systems biology approaches to understand the transcriptional regulation of osmotic stress and the role of long non-coding RNAs in response to osmotic stress with special emphasis on wheat. The current concept may lead to an understanding in molecular regulation and signalling interaction of TFs under osmotic stress to clarify challenges and problems for devising potential strategies to improve complex regulatory events involved in plant tolerance to osmotic stress adaptive pathways in wheat.

Td4IN2: A drought-responsive durum wheat (Triticum durum Desf.) gene coding for a resistance like protein with serine/threonine protein kinase, nucleotide binding site and leucine rich domains

Wheat, the main food source for a third of world population, appears strongly under threat because of predicted increasing temperatures coupled to drought. Plant complex molecular response to drought stress relies on the gene network controlling cell reactions to abiotic stress. In the natural environment, plants are subjected to the combination of abiotic and biotic stresses. Also the response of plants to biotic stress, to cope with pathogens, involves the activation of a molecular network. Investigations on combination of abiotic and biotic stresses indicate the existence of cross-talk between the two networks and a kind of overlapping can be hypothesized. In this work we describe the isolation and characterization of a drought-related durum wheat (Triticum durum Desf.) gene, identified in a previous study, coding for a protein combining features of NBS-LRR type resistance protein with a S/TPK domain, involved in drought stress response. This is one of the few examples reported where all three domains are present in a single protein and, to our knowledge, it is the first report on a gene specifically induced by drought stress and drought-related conditions, with this particular structure.

Alternative splicing complexity contributes to genetic improvement of drought resistance in the rice maintainer HuHan2B

Water-saving and drought-resistantce rice (WDR) breeding practices have greatly increased grain yield and drought resistance. To study the genetic basis of adaptation to drought, transcriptome sequences from the WDR maintainer line HuHan2B and the recurrent parent HanFengB were analyzed for alternative splicing (AS) complexity. Intron retention, the dominant AS type, accounted for 42% of the observed AS events. Differential expression analysis revealed transcripts were preferentially expressed in different varieties and conditions. Based on gene ontology predictions, the biological functions of drought-induced transcripts were significantly enriched in genes involved in transcription regulation, chloroplast components and response to abiotic stimulus in HuHan2B, whereas developmental processes for reproduction were primarily enriched in HanFengB. The regulatory network of transcription factors was driven by cohorts of transcript splicing targets, resulting in more diversified regulatory relationships due to AS complexity than in our previous findings. Moreover, several genes were validated to accumulate novel splicing transcripts in a drought-induced manner. Together, these results suggest that HuHan2B and HanFengB share similar AS features but that a subset of genes with increased levels of AS involved in transcription regulatory networks may contribute an additional level of control for genetic improvement of drought resistance in rice maintainer HuHan2B through breeding.