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RNA-Seq Analysis of Developing Grains of Wheat to Intrigue Into the Complex Molecular Mechanism of the Heat Stress Response
... Sequence data can be aligned to a reference genome to build full-length transcripts. Transcriptome sequencing data can be used to define novel transcripts, leading to the discovery of neoantigens 15,16 In this assay, transcriptional changes were assessed in a limited number of genes during tissue culture (exvivo). Changes were mainly found in genes involved in molecular functions which affect the stability or regulation of cellular compartments. ...
This study compared the expression of TP53 in lymphocytes from malignant melanoma (MM) patients with positive sentinel nodes to healthy controls (HCs) following exposure to various doses of UVA radiation. The Lymphocyte Genome Sensitivity (LGS) assay indicated significant differences in DNA damage in lymphocytes between MM patients and HCs. qPCR data demonstrated an overall 3.4-fold increase in TP53 expression in lymphocytes from MM patients compared to healthy controls, following treatment with 0.5 mW/cm² UVA radiation. Western blotting confirmed that p53 expression was increased in MM lymphocytes following UVA exposure compared to healthy individuals. Genome transcriptome profiling data displayed differences in gene expression between UVA-treated lymphocytes from MM patients and HCs. Peripheral lymphocytes from MM patients are more susceptible to the genotoxic effects of UVA compared to healthy individuals. Our previous studies showed that UVA exposure of various intensities caused significant differences in the levels of DNA damage between lymphocytes from cancer patients compared to HCs through the LGS assay. The present study’s results provide further credibility to the LGS assay as a screening test for cancer detection. Peripheral lymphocytes could be a promising blood biopsy biomarker for staging of carcinomas and prevention of carcinoma progression at early stages.
Improving the baking quality is a primary challenge in the wheat flour production value chain, as baking quality represents a crucial factor in determining its overall value. In the present study, we conducted a comparative RNA-Seq analysis on the high baking quality mutant “O-64.1.10” genotype and its low baking quality wild type "Omid" cultivar to recognize potential genes associated with bread quality. The cDNA libraries were constructed from immature grains that were 15 days post-anthesis, with an average of 16.24 and 18.97 million paired-end short-read sequences in the mutant and wild-type, respectively. A total number of 733 transcripts with differential expression were identified, 585 genes up-regulated and 188 genes down-regulated in the “O-64.1.10” genotype compared to the “Omid”. In addition, the families of HSF, bZIP, C2C2-Dof, B3-ARF, BES1, C3H, GRF, HB-HD-ZIP, PLATZ, MADS-MIKC, GARP-G2-like, NAC, OFP and TUB were appeared as the key transcription factors with specific expression in the “O-64.1.10” genotype. At the same time, pathways related to baking quality were identified through Kyoto Encyclopedia of Genes and Genomes. Collectively, we found that the endoplasmic network, metabolic pathways, secondary metabolite biosynthesis, hormone signaling pathway, B group vitamins, protein pathways, pathways associated with carbohydrate and fat metabolism, as well as the biosynthesis and metabolism of various amino acids, have a great deal of potential to play a significant role in the baking quality. Ultimately, the RNA-seq results were confirmed using quantitative Reverse Transcription PCR for some hub genes such as alpha-gliadin, low molecular weight glutenin subunit and terpene synthase (gibberellin) and as a resource for future study, 127 EST-SSR primers were generated using RNA-seq data.
Increasing temperature is a key component of global climate change, affecting crop growth and productivity worldwide. Wheat is a major cereal crop grown in various parts of the globe, which is affected severely by heat stress. The morphological parameters affected include germination, seedling establishment, source-sink activity, leaf area, shoot and root growth. The physiological parameters such as photosynthesis, respiration, leaf senescence, water and nutrient relation are also affected by heat. At the cellular level, heat stress leads to the generation of reactive oxygen species that disrupt the membrane system of thylakoid, chloroplast and plasma membrane. The deactivation of the photosystem, reduction in photosynthesis and inactivation of rubisco affect the production of photoassimilates and their allocation. This ultimately affects anthesis, grain filling, size, number and maturity of wheat grains, which hamper crop productivity. The interplay of various systems comprising antioxidants and hormones plays a crucial role in imparting heat stress tolerance in wheat. Thus, implementation of various omics technologies could foster in-depth insights on heat stress effects, eventually devising heat stress mitigation strategies by conventional and modern breeding to develop heat-tolerant wheat varieties. This review provides an integrative view of heat stress responses in wheat and also discusses approaches to develop heat-tolerant wheat varieties.
Key message
Large-scale faba bean transcriptome data are available, and the first genotyping platform based on liquid-phase probe targeted capture technology was developed for genetic and molecular breeding studies.
Abstract
Faba bean (Vicia faba L., 2n = 12) is an important food legume crop that is widely grown for multiple uses worldwide. However, no reference genome is currently available due to its very large genome size (approximately 13 Gb) and limited single nucleotide polymorphism (SNP) markers as well as highly efficient genotyping tools have been reported for faba bean. In this study, 16.7 billion clean reads were obtained from transcriptome libraries of flowers and leaves of 102 global faba bean accessions. A total of 243,120 unigenes were de novo assembled and functionally annotated. Moreover, a total of 1,579,411 SNPs were identified and further filtered according to a selection pipeline to develop a high-throughput, flexible, low-cost Faba_bean_130K targeted next-generation sequencing (TNGS) genotyping platform. A set of 69 Chinese faba bean accessions were genotyped with the TNGS genotyping platform, and the average mapping rate of captured reads to reference transcripts was 93.14%, of which 53.23% were located in the targeted regions. The TNGS genotyping results were validated by Sanger sequencing and the average consistency rate reached 93.6%. Comprehensive population genetic analysis was performed on the 69 Chinese faba bean accessions and identified four genetic subgroups correlated with the geographic distribution. This study provides valuable genomic resources and a reliable genotyping tool that could be implemented in genetic and molecular breeding studies to accelerate new cultivar development and improvement in faba bean.
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. Drought (water deficit stress) is a major environmental stress threatening wheat (Triticum aestivum L.) productivity worldwide particularly under modeled global climate change scenarios. It is estimated that almost 50% of wheat cultivated in the developing world is sown under dryland cropping systems 1. Increasing resilience to abiotic stresses through genetic improvement thus become a critical component of wheat breeding. To identify genes related to drought tolerance and understand mechanisms of plant reaction to water deficit in this type of germplasm is crucial for developing cultivars with better water use efficiency. Drought can affect wheat growth during all phenological stages but heading and grain filling are two sensitive stages 2 since they involve processes such as fertilization, embryogenesis, photosynthesis and starch biosynthesis OPEN
Global warming has increased the frequency of extreme high temperature events. High temperature is a major abiotic stress that limits the growth and production of plants. Therefore, the plant response to heat stress (HS) has been a focus of research. However, the plant response to HS involves complex physiological traits and molecular or gene networks that are not fully understood. Here, we review recent progress in the physiological (photosynthesis, cell membrane thermostability, oxidative damage, and others), transcriptional, and post-transcriptional (noncoding RNAs) regulation of the plant response to HS. We also summarize advances in understanding of the epigenetic regulation (DNA methylation, histone modification, and chromatin remodeling) and epigenetic memory underlying plant–heat interactions. Finally, we discuss the challenges and opportunities of future research in the plant response to HS.
Faba bean (Vicia faba L.) is a pulse crop of high nutritional value and high importance for sustainable agriculture and soil protection. With the objective of identifying gene-based SNPs, transcriptome sequencing was performed in order to reduce faba bean genome complexity. A set of 1,819 gene-based Snp markers polymorphic in three recombinant line populations was selected to enable the construction of a high-density consensus genetic map encompassing 1,728 markers well distributed in six linkage groups and spanning 1,547.71 cM with an average inter-marker distance of 0.89 cM. orthology-based comparison of the faba bean consensus map with legume genome assemblies highlighted synteny patterns that partly reflected the phylogenetic relationships among species. Solid blocks of macrosynteny were observed between faba bean and the most closely-related sequenced legume species such as pea, barrel medic or chickpea. Numerous blocks could also be identified in more divergent species such as common bean or cowpea. the genetic tools developed in this work can be used in association mapping, genetic diversity, linkage disequilibrium or comparative genomics and provide a backbone for map-based cloning. This will make the identification of candidate genes of interest more efficient and will accelerate marker-assisted selection (MAS) and genomic-assisted breeding (GAB) in faba bean.
Background:
Wheat grain avenin-like proteins (ALPs) belong to a recently discovered class of wheat grain storage protein. ALPs in wheat grains not only have beneficial effects on dough quality but also display antifungal activities, which is a novel observation for wheat storage proteins. Previous studies have shown that ALPs are likely present in the albumin/globulin fractions of total protein extract from wheat flour. However, the accumulation characteristics of these ALPs in the mature wheat grain remains unknown.
Results:
In the present study, a total of 13 ALPs homologs were isolated and characterized in the albumin/globulin fractions of the wheat protein extract. A combination of multiple techniques including RP-HPLC, SDS-PAGE, MALDI-TOF and peptide sequencing were used for accurate separation and identification of individual ALP homolog. The C-terminal TaALP-by-4AL/7DS, TaALP-by-4AL/7AS/7DS, TaALP-bx/4AL/7AS/7DS, TaALP-ay-7DS, TaALP-ay-4AL, TaALP-ax-4AL, TaALP-ax-7AS, and TaALP-ax-7DS, were separated as individual protein bands from wheat flour for the first time. These unique ALPs peptides were mapped to the latest wheat genome assembly in the IWGSC database. The characteristic defence related proteins present in albumin and globulin fractions, such as protein disulfide-isomerase (PDI), grain softness protein (GSP), alpha-amylase inhibitors (AAIs) and endogenous alpha-amylase/subtilisin inhibitor were also found to co-segregate with these identified ALPs, avenin-3 and α-gliadins. The molecular weight range and the electrophoresis segregation properties of ALPs were characterised in comparison with the proteins containing the tryp_alpha_amyl domain (PF00234) and the gliadin domain (PF13016), which play a role in plant immunity and grain quality. We examined the phylogenetic relationships of the AAIs, GSP, avenin-3, α-gliadins and ALPs, based on the alignment of their functional domains. MALDI-TOF profiling indicated the occurrence of certain post-translations modifications (PTMs) in some ALP subunits.
Conclusions:
We reported for the first time the complete profiling of ALPs present in the albumin/globulin fractions of wheat grain protein extracts. We concluded that majority of the ALPs homologs are expressed in wheat grains. We found clear evidence of PTMs in several ALPs peptides. The identification of both gliadin domain (PF13016) and Tryp_alpha_amyl domain (PF00234) in the mature forms of ALPs highlighted the multiple functional properties of ALPs in grain quality and disease resistance.
Peppers (Capsicum annuum L.), belonging to the Solanaceae family, are one of the most economically important crops globally. Like other crops, peppers are threatened by diverse environmental conditions due to different pathogens and abiotic stresses. High-quality reference genomes with massive datasets of transcriptomes from various conditions can provide clues to preferred agronomic traits for breeding. However, few global gene expression profiling datasets have been published to examine the environmental stress-resistant mechanisms in peppers. In this study, we report the RNA-seq analyses of peppers treated with heat, cold, salinity, and osmotic stress at six different time points. RNA-seq libraries from 78 RNA samples containing three biological replicates per time point for each of the abiotic stresses and a mock control were constructed. A total of 204.68 Gb of transcriptome data were verified by differentially expressed genes and gene ontology enrichment analysis. Analyses of the transcriptome data in this study will provide useful information for basic studies of various stimuli to facilitate the development of stress-resistant pepper cultivars.
Climate change exerts adverse effects on crop production. Plant researchers have therefore focused on the identification of solutions that minimize the negative impacts of climate change on crops. This Special Issue comprises 23 articles that celebrate the 2020 International Year of Plant Health, highlighting the processes, mechanisms, and traits that will underpin future sustainability of crop quality and yield. These articles critically evaluate recent advances in our understanding of climate change impacts on plants, within the context of climate-smart agriculture. © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Experimental Biology.
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.
Coincidence of high temperature with terminal reproductive pheno-stages of cotton is chief constraint to achieve yield potential. This high temperature interfere plant defensive system, physiological process, water relations and lint yield production. In this study, we modulated the detrimental outcomes of heat stress on cotton through the foliar spray of nutrients. Cotton crop was exposed to sub-optimal and supra-optimal thermal regimes for a period of one week at squaring, flowering and boll formation stages under glass house and field conditions. Foliar spray of potassium (K-1.5%), zinc (Zn-0.2%) and boron (B-0.1%) were applied at three reproductive stages one day prior to expose high temperature regimes. High temperature increased lipid membrane damage through increased malondialdehyde (MDA) contents in cotton leaves. High temperature stress also reduced leaf chlorophyll contents, net photosynthetic rate, stomatal conductance, water potential, averaged boll weight (g) and seed cotton yield per plant. Various nutrients variably influenced growth and physiology of heat-stressed cotton plants. Zinc outclassed all other nutrients in increasing leaf SOD, CAT, POX, AsA, TPC activity, chlorophyll contents, net photosynthetic rate, stomatal conductance, water potential, boll weight and seed cotton yield per plant. For example, zinc improved seed cotton yield under supra-optimal thermal regime by 17% and under sub-optimal thermal regime by 12% of glasshouse study while 19% under high temperature sowing dates of field study than the water treated plants under the same temperatures. Conclusively, increasing intensities of temperature adversely affected the recorded responses of cotton and exogenous application of Zn efficaciously alleviated heat induced perturbations. Moreover, exogenous nutrients mediated upregulations in physiochemical attributes induced heat tolerance at morphological level.
Various attempts have been made to understand the traits and genes associated with heat stress tolerance in wheat (Triticum aestivum L.) in the field and under controlled conditions. Attempts made under controlled conditions have not been conclusive, mainly through a lack of sufficient precision in simulating the ambient temperature dynamics and microenvironments prevalent in the field. In addition, inconsistency in field phenotyping is a major concern. Hence, we attempted to develop a method for phenotyping wheat for heat stress tolerance through a novel temperature‐controlled phenotyping facility (TCPF), along with an inexpensive tool to ensure uniform crop establishment. The objective was to improve the precision of assessing plants' responses to elevated temperatures, particularly when these experiments are challenged by a large number of genotypes to be screened that show significant variations in their phenology. The study involved 75 genotypes from a recombinant inbred line population with differing responses to heat stress under three conditions: in the TCPF and in the field [regular field season and late sown (LS)] across two consecutive years. The results revealed that the yield components were different under LS and TCPF conditions. These differences reflected the plants' responses to morphophenological adaptations arising from the late planting time and were not really reflective of the heat stress response. However, greater precision in differentiating high‐temperature responses in the TCPF was evident from the repeatability in terms of growth, physiology, and productivity. This could be attributed to uniform crop establishment and improved capacity to maintain the desired temperature for phenotyping.
Wheat genetic improvement by integration of advanced genomic technologies is one way of improving productivity. To facilitate the breeding of economically important traits in wheat, SNP loci and underlying candidate genes associated with the 36 agro-morphological traits were studied in a diverse panel of 404 genotypes. By using Breeders’ 35K Axiom array in a comprehensive genome-wide association study covering 4364.79 cM of the wheat genome and applying a compressed mixed linear model, a total of 146 SNPs (-log10 P ≥ 4) were found associated with 23 traits out of 36 traits studied explaining 3.7–47.0% of phenotypic variance. To reveal this a subset of 260 genotypes was characterized phenotypically for six quantitative traits [days to heading (DTH), days to maturity (DTM), plant height (PH), spike length (SL), awn length (Awn_L), and leaf length (Leaf_L)] under five environments. Gene annotations mined ∼38 putative candidate genes which were confirmed using tissue and stage specific gene expression data from RNA Seq. We observed strong co-localized loci for four traits (glume pubescence, SL, PH, and awn color) on chromosome 1B (24.64 cM) annotated five putative candidate genes. This study led to the discovery of hitherto unreported loci for some less explored traits (such as leaf sheath wax, awn attitude, and glume pubescence) besides the refined chromosomal regions of known loci associated with the traits. This study provides valuable information of the genetic loci and their potential genes underlying the traits such as awn characters which are being considered as important contributors toward yield enhancement.
Environmental stresses greatly limit crop yield. With the increase in extreme weather events due to climate change and the constant pressure of diseases and pests, there is an urgent need to develop crop varieties that can tolerate multiple stresses. However, our knowledge of how plants broadly respond to stress is limited. Here, we explore the rice core stress response via meta-analysis of publicly available rice transcriptome data. Our results confirm that rice universally down-regulates photosynthesis in response to both abiotic and biotic stress. Rice also generally up-regulates hormone-responsive genes during stress response, most notably genes in the abscisic acid, jasmonic acid and salicylic acid pathways. We identified several promoter motifs that are likely involved in stress-responsive regulatory mechanisms in rice. With this work, we provide a list of candidate genes to study for improving rice stress tolerance in light of environmental stresses. This work also serves as a proof of concept to show that meta-analysis of diverse transcriptome data is a valid approach to develop robust hypotheses for how plants respond to stress.
Crop varieties or genotypes of a given species are pivotal for agricultural production and ownership, management and improvement of their germplasm is a great challenge. Its morphological identification requires time, cost and descriptors are often compromised statistically due to phenotypic plasticity. Development of DNA based signature of varieties can overcome these limitations. There is a global need to implement world trade organization (WTO) and intellectual property rights (IPR) guidelines of Plant Breeders Rights (PBR) where DUS (distinctness, uniformity and stability) testing can be supplemented by DNA profile. Universalization and minimization of SNP number without compromising identification accuracy is the major challenge in development of varietal profile by rapid genotype assay. Besides this, there is no server-based approach reducing computational skill with global accessibility of referral phenotypic and genotypic data. We report world’s first model web server for crop variety identification using >350 Indian wheat varieties and Axiom 35 K SNP chip data. Standard filtering and linkage disequilibrium approach were used to develop varietal signature in Linux using HTML, Java, PHP and MySQL with provision of QR code generator to facilitate bar-coding. Phylogenetic tree constructed by selected SNPs confirms six major trait based clusters of varieties and their pedigree. Our user friendly server based tool, VISTa (Variety Identification System of Triticum aestivum) (http://webtom.cabgrid.res.in/vista) can be used in DUS testing having dispute resolution of sovereignty and access benefit sharing (ABS) issues. This model approach can be used in other crops with pan-global level management of crop germplasm in endeavour of crop productivity.
Fifteen full-length wheat grain avenin-like protein coding genes ( TaALP ) were identified on chromosome arms 7AS, 4AL, and 7DS of bread wheat with each containing five genes. Besides the a- and b-type ALPs, a c type was identified in the current paper. Both a and b types have two subunits, named x and y types. The five genes on each of the three chromosome arms consisted of two x-type genes, two y-type genes, and one c-type gene. The a-type genes were typically of 520 bp in length, whereas the b types were of 850 bp in length, and the c type was of 470 bp in length. The ALP gene transcript levels were significantly up-regulated in Blumeria graminis f. sp. tritici (Bgt) -infected wheat grain caryopsis at early grain filling. Wild emmer wheat [(WEW), Triticum dicoccoides ] populations were focused on in our paper to identify allelic variations of ALP genes and to study the influence of natural selection on certain alleles. Consequently, 25 alleles were identified for TdALP-bx-7AS , 13 alleles were identified for TdALP-ax-7AS , 7 alleles were identified for TdALP-ay-7AS , and 4 alleles were identified for TdALP-ax-4AL . Correlation studies on TdALP gene diversity and ecological stresses suggested that environmental factors contribute to the ALP polymorphism formation in WEW. Many allelic variants of ALPs in the endosperm of WEW are not present in bread wheat and therefore could be utilized in breeding bread wheat varieties for better quality and elite plant defense characteristics.
Receptor-like proteins (RLPs) are involved in plant development and disease resistance. Only some of the RLPs in tomato (Solanum lycopersicum L.) have been functionally characterized though 176 genes encoding RLPs, which have been identified in the tomato genome. To further understand the role of RLPs in tomato, we performed genome-guided classification and transcriptome analysis of these genes. Phylogenic comparisons revealed that the tomato RLP members could be divided into eight subgroups and that the genes evolved independently compared to similar genes in Arabidopsis. Based on location and physical clustering analyses, we conclude that tomato RLPs likely expanded primarily through tandem duplication events. According to tissue specific RNA-seq data, 71 RLPs were expressed in at least one of the following tissues: root, leaf, bud, flower, or fruit. Several genes had expression patterns that were tissue specific. In addition, tomato RLP expression profiles after infection with different pathogens showed distinguish gene regulations according to disease induction and resistance response as well as infection by bacteria and virus. Notably, Some RLPs were highly and/or unique expressed in susceptible tomato to pathogen, suggesting that the RLP could be involved in disease response, possibly as a host-susceptibility factor. Our study could provide an important clues for further investigations into the function of tomato RLPs involved in developmental and response to pathogens.
Predictions of global increased temperature are for 1.8-4 °C by 2100. Increased temperature as an abiotic stress may exert a considerable influence on the levels of secondary metabolites in plants. These secondary metabolites may possibly exert biological activities beneficial in prevention or treatment of disorders linked to oxidative stress in human. Wheat secondary compounds in three Canadian and three Australian genotypes grown under controlled environments, in which the only changing parameter was temperature, were investigated. Kennedy and AC Navigator contained the highest amount of total phenolic acids among Australian and Canadian wheat genotypes, respectively. The total phenolic acids and total flavonoid contents of wheat genotypes increased following the increase of the growing temperature. In all the wheat genotypes, regardless of their growing temperatures, linoleic acid (C18:2n6) was measured as the main fatty acid. Significant increases in palmitic acid (C16:0) and oleic acid (C18:1n9) and significant decreases in linoleic acid (C18:2n6) and linolenic acid (C18:3n3) were observed at increased of growing temperature for all wheat genotypes. Growing temperature decreased campesterol content of wheat genotypes. Genotype and growing temperature significantly shifted the production of wheat secondary metabolites. This information might be used as a guide for breeding wheat varieties with higher antioxidant properties.
Abiotic stresses are one of the major constraints to crop production and food security worldwide. The situation has aggravated due to the drastic and rapid changes in global climate. Heat and drought are undoubtedly the two most important stresses having huge impact on growth and productivity of the crops. It is very important to understand the physiological, biochemical, and ecological interventions related to these stresses for better management. A wide range of plant responses to these stresses could be generalized into morphological, physiological, and biochemical responses. Interestingly, this review provides a detailed account of plant responses to heat and drought stresses with special focus on highlighting the commonalities and differences. Crop growth and yields are negatively affected by sub-optimal water supply and abnormal temperatures due to physical damages, physiological disruptions, and biochemical changes. Both these stresses have multi-lateral impacts and therefore, complex in mechanistic action. A better understanding of plant responses to these stresses has pragmatic implication for remedies and management. A comprehensive account of conventional as well as modern approaches to deal with heat and drought stresses have also been presented here. A side-by-side critical discussion on salient responses and management strategies for these two important abiotic stresses provides a unique insight into the phenomena. A holistic approach taking into account the different management options to deal with heat and drought stress simultaneously could be a win-win approach in future.
With the goal of providing a comprehensive, high-quality resource for both plant transcription factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF database PlantTFDB to version 4.0 (http://planttfdb.cbi.pku.edu.cn/). In the new version, we identified 320 370 TFs from 165 species, presenting a more comprehensive genomic TF repertoires of green plants. Besides updating the pre-existing abundant functional and evolutionary annotation for identified TFs, we generated three new types of annotation which provide more directly clues to investigate functional mechanisms underlying: (i) a set of high-quality, non-redundant TF binding motifs derived from experiments; (ii) multiple types of regulatory elements identified from high-throughput sequencing data; (iii) regulatory interactions curated from literature and inferred by combining TF binding motifs and regulatory elements. In addition, we upgraded previous TF prediction server, and set up four novel tools for regulation prediction and functional enrichment analyses. Finally, we set up a novel companion portal PlantRegMap (http://plantregmap.cbi.pku.edu.cn) for users to access the regulation resource and analysis tools conveniently.
Aegilops speltoides is an important genetic resource for wheat improvement and has high levels of heat tolerance. A heat-tolerant accession of Ae. speltoides pau3809 was crossed with Triticum durum cv. PDW274, and BC2F4-6 backcross introgression lines (BILs) were developed, phenotyped for important physiological traits, genotyped using SSR markers and used for mapping the QTL governing heat tolerance component traits. A set of 90 BILs was selected from preliminary evaluation of a broader set of 262 BILs under heat stress. Phenotyping was conducted for physiological traits such as cell membrane thermostability, chlorophyll content, acquired thermotolerance, canopy temperature and stay green. Much variation for these traits was observed in random as well as selected sets of BILs, and comparison of the BILs with the recurrent parent showed improvement for these traits under normal as well as heat stress conditions, indicating that introgressions from Ae. speltoides might have led to the improvement in the heat tolerance potential of the BILs. Introgression profiling of the 90 BILs using SSR markers identified Ae. speltoides introgression on all the 14 chromosomes with introgressions observed on A as well as B genome chromosomes. QTL mapping identified loci for various heat tolerance component traits on chromosomes 2B, 3A, 3B, 5A, 5B and 7A at significant LOD scores and with phenotypic contributions varying from 11.1 to 28.7 % for different traits. The heat-tolerant BILs and QTL reported in the present study form a potential resource that can be used for wheat germplasm enhancement for heat stress tolerance.
In nature, plants have to cope with a wide range of stress conditions that often occur simultaneously or in sequence. To investigate how plants cope with multi-stress conditions, we analyzed the dynamics of whole-transcriptome profiles of Arabidopsis thaliana exposed to six sequential double stresses inflicted by combinations of (1) infection by the fungus Botrytis cinerea, (2) herbivory by Pieris rapae, and (3) drought stress. Each of these stresses induced specific expression profiles over time, in which one third of all differentially expressed genes was shared by at least two single stresses. Of these, 394 genes were differentially expressed during all three stress conditions, albeit often in opposite directions. When two stresses were applied in sequence, plants displayed transcriptome profiles that were very similar to the second stress, irrespective of the nature of the first stress. Nevertheless, significant first-stress-signatures could be identified in the sequential stress profiles. Bioinformatic analysis of the dynamics of co-expressed gene clusters highlighted specific clusters and biological processes of which the timing of activation or repression was altered by a prior stress. The first-stress-signatures in second stress transcriptional profiles were remarkably often related to responses to phytohormones, strengthening the notion that hormones are global modulators of interactions between different types of stress. Because prior stresses can affect the level of tolerance against a subsequent stress (e.g. prior herbivory strongly affected B. cinerea resistance), the first-stress-signatures can provide important leads for the identification of molecular players that are decisive in the interactions between stress response pathways. This article is protected by copyright. All rights reserved.
Non-model plants i.e., the species which have one or all of the characters such as long life cycle, difficulty to grow in the laboratory or poor fecundity, have been schemed out of sequencing projects earlier, due to high running cost of Sanger sequencing. Consequently, the information about their genomics and key biological processes are inadequate. However, the advent of fast and cost effective next generation sequencing (NGS) platforms in the recent past has enabled the unearthing of certain characteristic gene structures unique to these species. It has also aided in gaining insight about mechanisms underlying processes of gene expression and secondary metabolism as well as facilitated development of genomic resources for diversity characterization, evolutionary analysis and marker assisted breeding even without prior availability of genomic sequence information. In this review we explore how different Next Gen Sequencing platforms, as well as recent advances in NGS based high throughput genotyping technologies are rewarding efforts on de-novo whole genome/transcriptome sequencing, development of genome wide sequence based markers resources for improvement of non-model crops that are less costly than phenotyping.
During the last decade, we have witnessed globally a decline in annual growth rate in wheat production associated with an unprecedented increase in the price of food grain, making wheat grain availability difficult for the poor. Thishas been attributed partly to the difficulties in further improvement in genetic potential for wheat productivity through the use of current conventional methods ofwheat breeding, and partly to the impact of a variety of abiotic stresses (including drought and heat) due to increasingly variable climate. In this article, after a brief introduction about the problem and about the environments targeted for drought and heat tolerance, we briefly review the work being done to deal with this major problem, which the wheat breeders are facing globally. Since a variety of parameters have been used for estimating the level of drought and heat tolerance, we first discuss in detail the traits and the parameters usedto estimate drought and heat tolerance, outlining the known genetic architecture (including QTL mapping work, wherever available) of drought and heat tolerance using each of these traits. A brief description of the possibility of synergy among stress adaptive traits for providing tolerance against drought and heat stress is also given. Crop modeling and high-throughput phenotyping (using phenomics platforms) that became possible recently have also been discussed briefly. This is followed by an account of the strategies that have already been used and need to be used in future for developing wheat genotypes, which should be suitable for growing in drought and heat-prone areas. Both conventional methods of wheat breeding and molecular wheat breeding have been discussed, the latter including both marker-assisted selection (MAS) and transgenic approach. It has been shown that some significant progress has already been made using these approaches and that with the substantial growth in the area of genomics research; molecular breeding should become an important component of conventional wheat breeding research. © 2012 Wiley-Blackwell. Published 2012 by John Wiley and Sons, Inc.
Heat-responsive miRNAs regulate the expression of the transcription factors (HSFs) and majority of the heat stress-associated genes (HSPs). Here we report identification of few heats - responsive miRNAs in wheat (Triticum aestivum L.)through de novo sequencing on Illumina Hiseq 2000. Validation of identified miRNAs in endospermic tissues of thermotolerant (HD2985) and thermosusceptible (NIAW-34-34) wheat cultivars using real time PCR showed up-regulation of 4 micro RNAs (tae-miR156, tae-miR167, tae-miR395b and tae-miR398) and down-regulation of 6 micro RNAs (tae-miR159a, tae-miR159b, tae-miR160, tae- miR171a, tae-miR319, and tae-miR1117) in response to the heat stress. Target analysis of identified miRNAs showed HSF3, HSFA4a, HSP17, HSP70 and superoxide dismutase (SOD) as most probable target genes. Expression profiling of identified target genes under heat stress (42°C, 2 h) showed 2.34, 1.33 fold (HSF3), 2.45, 1.44 fold (HSFA4a), 3.9, 1.9 fold (HSP17), 5.6, 2.4 fold (HSP70), 1.9, 1.2 fold (SOD) and 2.7, 1.6 fold (catalase) increase in the expression in HD2985 and NIAW-34-34 cultivars of wheat compared to control. A defragmented, small and pleated starch granule structure was observed in sample with low expression of target genes (NIAW-34-34) compared to intact, robust and globular starch granules in samples with high expression of target genes (HD2985). Transcript profiling and activity assay of soluble starch synthase (SSS) showed less transcript accumulation and activity in heat shock treated samples compared to control sample in both the cultivars.
Wheat is a staple food worldwide and provides 40% of the calories in the diet. Climate change and global warming pose a threat to wheat production, however, and demand a deeper understanding of how heat stress might impact wheat production and wheat biology. However, it is difficult to identify novel heat stress associated genes when the genomic information is not available. Wheat has a very large and complex genome that is about 37 times the size of the rice genome. The present study sequenced the whole transcriptome of the wheat cv. HD2329 at the flowering stage, under control (22° ± 3°C) and heat stress (42°C, 2 h) conditions using Illumina HiSeq and Roche GS-FLX 454 platforms. We assembled more than 26.3 and 25.6 million high-quality reads from the control and HS-treated tissues transcriptome sequences respectively. About 76,556 (control) and 54,033 (HS-treated) contigs were assembled and annotated de novo using different assemblers and a total of 21,529 unigenes were obtained. Gene expression profile showed significant differential expression of 1525 transcripts under heat stress, of which 27 transcripts showed very high (>10) fold upregulation. Cellular processes such as metabolic processes, protein phosphorylation, oxidations-reductions, among others were highly influenced by heat stress. In summary, these observations significantly enrich the transcript dataset of wheat available on public domain and show a de novo approach to discover the heat-responsive transcripts of wheat, which can accelerate the progress of wheat stress-genomics as well as the course of wheat breeding programs in the era of climate change.
Recurrent drought associated with climate change is among the principal constraints to global productivity of wheat (Triticum aestivum (L.) and T. turgidum (L.)). Numerous efforts to mitigate drought through breeding resilient varieties are underway across the world. Progress is, however, hampered because drought tolerance is a complex trait that is controlled by many genes and its full expression is affected by the environment. Furthermore, wheat has a structurally intricate and large genome. Consequently, breeding for drought tolerance requires the integration of various knowledge systems and methodologies from multiple disciplines in plant sciences. This review summarizes the progress made in dry land wheat improvement, advances in knowledge, complementary methodologies, and perspectives towards breeding for drought tolerance in the crop to create a coherent overview. Phenotypic, biochemical and genomics-assisted selection methodologies are discussed as leading research components used to exploit genetic variation. Advances in phenomic and genomic technologies are highlighted as options to circumvent existing bottlenecks in phenotypic and genomic selection, and gene transfer. The prospects of further integration of these technologies with other ‘omics’ technologies is also provided.
Aspartic protease (APs) plays important roles in plant growth, development and biotic and abiotic stresses. We previously reported that the expression of a rice AP gene (OsAP77, Os10g0537800) was induced by probenazole (PBZ), a chemical inducer of disease resistance. In this study we examined some characteristics of this gene in response to fungal, bacterial and viral pathogens.
To elucidate the spatial and temporal expression of OsAP77, the chimeric gene was constructed carrying the structural gene encoding β-glucuronidase (GUS) driven by the OsAP77 promoter. This construct was introduced into rice and the transgenic lines were tested to analyze gene expression by fungal, bacterial and viral infections. Inoculation with Magnaporthe oryzae or Xanthomonas oryzae pv. oryzae revealed the enhanced GUS activities in vascular tissues surrounding the symptom sites by each pathogen. Moreover, GUS activity also increased after inoculation with Cucumber mosaic virus (CMV). Transgenic plants immersed in a solution containing salicylic acid (SA), isonicotinic acid (INA), hydrogen peroxide (H2O2) or abscisic acid (ABA) showed an increased level of GUS activity exclusively in vascular tissues. RT-PCR analysis showed that OsAP77 was induced not only by infection with these pathogens, but also after treatment with SA, INA, H2O2 or ABA. A knockout mutant line of OsAP77 by the insertion of Tos17 after inoculation with M. oryzae, X. oryzae pv. oryzae or CMV showed an enhanced susceptibility compared to wild type.
These results suggest that the expression of OsAP77 is induced by pathogen infection and defense related signaling molecules in a vascular tissue specific manner and that this gene has a positive role of defense response against fungal, bacterial and viral infections.
The mechanism(s) by which Zn alleviates NaCl stress was investigated in Pistacia vera L. 'Badami'. Pistachio seedlings were treated with 0, 800, 1600, 2400, and 3200 mg of NaCl kg-1 of soil, along with Zn (0, 5, 10, and 20 mg kg-1 of soil). NaCl stress induced high oxidative stress, increasing lipid peroxidation, electrolyte leakage, and lipoxygenase (LOX, E.C. 1.13.11.12) activity to high levels. Zn supplement efficiently reduced all these adverse effects of salt stress. However, there were no significant differences among the above parameters in plants treated with Zn only. NaCl stress significantly increased the activity of antioxidant enzymes. The activity of antioxidant enzymes (superoxide dismutase [SOD, E.C. 1.15.1.1], catalase [CAT, E.C. 1.11.1.6]. and ascorbate peroxidase [APX, E.C. 1.11.1.11]) increased significantly in NaCl + Zn-treated plants, as compared with those treated with either NaCl or Zn alone. These results support the positive effects of Zn on antioxidant enzyme activity scavenging the reactive oxygen species produced in response to salt stress. Zinc treatment caused a significant increase in the amount of phenolics and in ascorbic acid content, as compared with salt treatment alone. Zinc treatment alone did not result in very high antioxidant enzyme activity in non-stressed plants.
Background
High density genotyping data are indispensable for genomic analyses of complex traits in animal and crop species. Maize is one of the most important crop plants worldwide, however a high density SNP genotyping array for analysis of its large and highly dynamic genome was not available so far.
Results
We developed a high density maize SNP array composed of 616,201 variants (SNPs and small indels). Initially, 57 M variants were discovered by sequencing 30 representative temperate maize lines and then stringently filtered for sequence quality scores and predicted conversion performance on the array resulting in the selection of 1.2 M polymorphic variants assayed on two screening arrays. To identify high-confidence variants, 285 DNA samples from a broad genetic diversity panel of worldwide maize lines including the samples used for sequencing, important founder lines for European maize breeding, hybrids, and proprietary samples with European, US, semi-tropical, and tropical origin were used for experimental validation. We selected 616 k variants according to their performance during validation, support of genotype calls through sequencing data, and physical distribution for further analysis and for the design of the commercially available Affymetrix® Axiom® Maize Genotyping Array. This array is composed of 609,442 SNPs and 6,759 indels. Among these are 116,224 variants in coding regions and 45,655 SNPs of the Illumina® MaizeSNP50 BeadChip for study comparison. In a subset of 45,974 variants, apart from the target SNP additional off-target variants are detected, which show only a minor bias towards intermediate allele frequencies. We performed principal coordinate and admixture analyses to determine the ability of the array to detect and resolve population structure and investigated the extent of LD within a worldwide validation panel.
Conclusions
The high density Affymetrix® Axiom® Maize Genotyping Array is optimized for European and American temperate maize and was developed based on a diverse sample panel by applying stringent quality filter criteria to ensure its suitability for a broad range of applications. With 600 k variants it is the largest currently publically available genotyping array in crop species.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-823) contains supplementary material, which is available to authorized users.
In this study, TaTEF-7A, a member of the transcript elongation factor gene family, and its flanking sequences were isolated. TaTEF-7A was located on chromosome 7A and was flanked by markers Xwmc83 and XP3156.3. Subcellular localization revealed that TaTEF-7A protein was localized in the nucleus. This gene was expressed in all organs,
but the highest expression occurred in young spikes and developing seeds. Overexpression of TaTEF-7A in Arabidopsis thaliana produced pleiotropic effects on vegetative and reproductive development that enhanced grain length, silique number, and silique
length. No diversity was found in the coding region of TaTEF-7A, but 16 single nucleotide polymorphisms and Indels were detected in the promoter regions of different cultivars. Markers
based on sequence variations in the promoter regions (InDel-629 and InDel-604) were developed, and three haplotypes were identified
based on those markers. Haplotype–trait association analysis of the Chinese wheat mini core collection revealed that TaTEF-7A was significantly associated with grain number per spike. Phenotyping of near-isogenic lines (NILs) confirmed that TaTEF-7A increases potential grain yield and yield-related traits. Frequency changes in favoured haplotypes gradually increased in
cultivars released in China from the 1940s. Geographic distributions of favoured haplotypes were characterized in six major
wheat production regions worldwide. The presence of Hap-7A-3, the favoured haplotype, showed a positive correlation with yield in a global set of breeding lines. These results suggest
that TaTEF-7A is a functional regulatory factor for grain number per spike and provide a basis for marker-assisted selection.
Heat is considered to be a major stress limiting crop growth and yields. While important findings on the impact of heat on crop yield have been made based on experiments in controlled environments, little is known about the effects under field conditions at larger scales. The study of Deryng et al (2014 Global crop yield response to extreme heat stress under multiple climate change futures Environ. Res. Lett. 9 034011), analysing the impact of heat stress on maize, spring wheat and soya bean under climate change, represents an important contribution to this emerging research field. Uncertainties in the occurrence of heat stress under field conditions, plant responses to heat and appropriate adaptation measures still need further investigation.
De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms. We also present Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes. In the procedure, we provide a workflow for genome-independent transcriptome analysis leveraging the Trinity platform. The software, documentation and demonstrations are freely available from http://trinityrnaseq.sourceforge.net. The run time of this protocol is highly dependent on the size and complexity of data to be analyzed. The example data set analyzed in the procedure detailed herein can be processed in less than 5 h.
Avenin-like b proteins are a small family of wheat storage proteins, each containing 18 or 19 cysteine residues. The role of these proteins, with high numbers of cysteine residues, in determining the functional properties of wheat flour is unclear. In the present study, two transgenic lines of the bread wheat overexpressing avenin-like b gene were generated to investigate the effects of Avenin-like b proteins on dough mixing properties. Sodium dodecyl sulfate sedimentation (SDSS) test and Mixograph analysis of these lines demonstrated that overexpression of Avenin-like b proteins in both transgenic wheat lines significantly increased SDSS volume and improved dough elasticity, mixing tolerance and resistance to extension. These changes were associated with the increased proportion of polymeric proteins due to the incorporation of overexpressed Avenin-like b proteins into the glutenin polymers. The results of this study were critical to confirm the hypothesis that Avenin-like b proteins could be integrated into glutenin polymers by inter-chain disulphide bonds, which could help understand the mechanism behind strengthening wheat dough strength.
Abiotic stress causes abrupt increase in the expression of stress-associated proteins, which provide tolerance by modulating the defense mechanism of plants. Small heat shock proteins (sHSPs) and anti-oxidant enzymes are important for environmental stress tolerance of the plants. In this study, two full-length cDNAs encoding small heat shock protein (sHSP) and superoxide dismutase (SOD), designated as TasHSP and SODI were identified and characterized from C-306 (thermotolerant) and PBW343 (thermosusceptible) cultivars of wheat (Triticum aestivum L.). An alpha crystalline domain was observed in TasHSP and manganese/iron binding domain in case of SODI. Quantitative real-time PCR showed very high transcript level of TasHSP and SOD in C-306 compared to PBW343 at different stages of growth and against differential heat stress (HS). Under differential HS at milky-dough stage, the fold change in transcript of both TasHSP and SOD was observed maximum in C-306, compared to PBW343. Protein profiling and isoenzymes analysis showed the expression of several heat-stable proteins and prominent isoenzymes of SOD in C-306, compared to PBW343. Scanning electron microscopy (SEM) of starch granules showed globular, well-shaped and more numbers of endospermic cells in C-306, compared to defragmented, irregular shaped and shrunken granules in case of PBW343 under HS treatment (42 degrees C for 2 h). Diurnal change in soluble starch synthase (SSS) activity showed an increase in the activity during afternoon (35 degrees C), compared to morning (29 degrees C) and evening (32 degrees C) in both the cultivars. Under heat stress (42 degrees C for 2 h), a drastic decrease in the SSS activity was observed, due to the thermal denaturation of the enzyme. Thermotolerance capacity analyzed using cell membrane stability (CMS) showed significantly higher CMS in case of C-306, compared to PBW343 at different stages of growth. Findings suggest that abundance of TasHSP and SODI during milky-dough stage plays a very important role in starch granule biosynthesis. The mechanism may be further exploited to develop tolerant wheat cultivar with high quality seeds.
A comparative proteomic analysis of drought-responsive proteins during grain development of two wheat varieties Kauz (strong resistance to drought stress) and Janz (sensitive to drought stress) was performed by using linear and nonlinear 2-DE and MALDI-TOF mass spectrometry technologies. Results revealed that the nonlinear 2-DE had much higher resolution than the linear 2-DE. A total of 153 differentially expressed protein spots were detected by both 2-DE maps, of which 122 protein spots were identified by MALDI-TOF and MALDI-TOF/TOF mass spectrometry. The identified differential proteins were mainly involved in carbohydrate metabolism (26%), detoxification and defense (23%), and storage proteins (17%). Some key proteins demonstrated significantly different expression patterns between the two varieties. In particular, catalase isozyme 1, WD40 repeat protein, LEA and alpha-amylase inhibitors displayed an upregulated expression pattern in Kauz, whereas they were downregulated or unchanged in Janz. Small and large subunit ADP glucose pyrophosphorylase, ascorbate peroxidase and G beta-like protein were all downregulated under drought stress in Janz, but had no expression changes in Kauz. Sucrose synthase and triticin precursor showed an upregulated expression pattern under water deficits in both varieties, but their upregulation levels were much higher in Kauz than in Janz. These differentially expressed proteins could be related to the biochemical pathways for stronger drought resistance of Kauz.
Background:
α-Amylase inhibitors (α-AIs) belong to the discrete classes, and exhibited differential specificities against α-amylases from various sources. Several α-amylases and their complexes with inhibitors at the molecular level have been studied in detail. Interestingly, some α-AIs depict specific and selective interactions amid different insect α-amylases.
Scope of review:
There are studies to understand evolutionary variability and functional differentiation of insect α-amylases and their cognate inhibitors. We have examined sequence, structural, and interaction diversity between various α-amylases and α-AIs. Based on these analyses, we are providing a potential basis for the functional differentiation among certain insect α-amylases concerning mammalian counterparts and their interactions with different proteinaceous α-AIs.
Major conclusions:
Insect α-amylases have conserved domain architecture with differences in length, number of disulfide bonds, and secondary structure. Furthermore, few of them exhibit variable characteristics like chloride dependent activity, the presence of N-terminal glutamine residue to protect against proteolytic degradation, and loop variations near the enzyme active site. Conformation of α-AI protein could be an essential factor for their specificity and binding affinities towards target α-amylase(s). Furthermore, variation into the enzyme binding pocket residues might contribute to differential interactions with inhibitors.
General significance:
Molecular insights in the interactions between insect α-amylases and plant α-AI will provide the details of mechanisms assisting the inhibitor specificity. Furthermore, this information will help to design potent and effective α-AIs against specific α-amylase.
Drought is an environmental stress that severely affects plant growth and crop production. Different studies have focused on drought responses but the molecular bases that regulate these mechanisms are still unclear. We report the participation of Aspartic Protease (APA1) in drought tolerance. Overexpressing APA1 Arabidopsis plants (OE-APA1), showed a phenotype more tolerant to drought compared with WT. On the contrary, apa1 insertional lines were more sensitive to this stress compared to WT plants. Morphological and physiological differences related with the water loss were observed between leaves of OE- APA1 and WT plants. OE-APA1 leaves showed lower stomata index and stomata density as well as a smaller of the stomatic aperture compared to WT plants. qPCR analysis in OE-APA1 leaves, showed higher expression levels of genes related to ABA signaling and synthesis. Analysis of plant lines expressing APA1 promoter fused to GUS showed that APA1 is expressed in epidermal and stomata cells. In summary, this work suggests that APA1 is involved in ABA-dependent response that its overexpression confers drought tolerance in Arabidopsis.
High temperatures adversely impact productivity and quality (nutritional and functional) of wheat grains. Anthesis and post-anthesis developmental stages are more sensitive to heat stress, with the grain-filling stage being crucial for sustained grain yield and quality. Comparative transcriptome profiling of the developing grain of three wheat genotypes (contrasting for heat stress tolerance) during early- (14-dpa (days post anthesis)) and late-grain filling (30-dpa) was studied to identify key genes involved in imparting heat tolerance. Heat stress during grain-filling (early- and late-) significantly down-regulated key genes in the genotypes, Gregory and Banks, found to be more heat susceptible. Upregulation of the cluster of genes comprising 6-phosphogluconate dehydrogenase, S6 RPS6-2 ribosomal protein, peptidylprolyl isomerase, plasma membrane proton ATPase, Heat shock cognate-70, FtsH protease, RuBisCO activase B, methionine synthase, cytochrome C (class I), and HMW-glutenin in the genotype Fang-60 during heat stress was found to be associated with heat stress tolerance in this genotype. Upregulation of β-glucanase (1,3 & 1,4), triose phosphate isomerase and calnexin at 14-dpa; and downregulation of Na⁺/H⁺antiporter, glucose-1-phosphate adenylyltransferase, ips1 riboregulator and AraC family transcriptional regulator at 30-dpa was observed specifically in the heat susceptible genotypes. Hsp-family, ascorbate peroxidase, β-amylase, γ-gliadin-2 and LMW-glutenin were heat stress responsive and were upregulated during stress across 14- and 30-dpa in all three genotypes. This study provides insights into genes that may be involved in regulating heat tolerance in a tolerant genotype and those that are responsive to heat in the developing wheat grain of tolerant and susceptible genotypes. The genotype Fang-60 was demonstrated to be a potential source of heat stress tolerance for use in wheat breeding.
Maize is an important food crop. Chilling stress can decrease maize production by affecting seed germination and seedling growth, especially in early spring. We analysed chlorophyll fluorescence, membrane lipids, secondary metabolites and the transcriptome of two maize inbred lines (chilling-tolerant M54 and chilling-sensitive 753F) after 0, 4 and 24 h cold stress. M54 showed better ability to protect PSII and accumulate secondary metabolites. From RNA sequencing data, we determined that the majority of cold-affected genes were involved in photosynthesis, secondary metabolism, and signal transduction. Genes important for maintaining photosystem structure and for regulating electron transport were less affected by cold stress in M54 than in 753F. Expression of genes related to secondary metabolism and unsaturated fatty acid synthesis were upregulated more strongly in M54 than in 753F and M54 accumulated more unsaturated fatty acids and secondary metabolites. As a result, M54 achieved relatively high cold tolerance by protecting the photosystems and maintaining the stability of cell membranes.
Plants counter an array of stresses by generation of a group of stress-related proteins, often referred to as the chaperones. Expression of these chaperones is induced in response to almost all kinds of stress. However, there are numerous evidences showing that these chaperones are vital for survival even under normal physiological conditions. They act as key modulators in physiological stress response and acquired tolerance. Research carried out over the past several years has clearly established that these chaperones are involved in diverse cellular functions such as folding, accumulation, translocation and degradation of proteins. Thus, these evolutionary conserved proteins affect a broad array of cellular processes. Gaining knowledge about this cellular chaperone machinery is of immense significance to understand the mechanism of interdependent stress-related cross talk in plants and ultimately, for the crop improvement programs.
Heat stress has an adverse effect on the quality and quantity of agriculturally important crops, especially wheat. The tolerance mechanism has not been explored much in wheat and very few genes/ TFs responsive to heat stress is available on public domain. Here, we identified, cloned and characterized a putative TaHSFA6e TF gene of 1.3 kb from wheat cv. HD2985. We observed an ORF of 368 aa with Hsf DNA binding signature domain in the amino acid sequence. Single copy number of TaHSFA6e was observed integrated in the genome of wheat. Expression analysis of TaHSFA6e under differential HS showed maximum transcripts in wheat cv. Halna (thermotolerant) in response to 38ºC for 2 h during pollination and grain-filling stages, as compared to PBW343, HD2329 and HD2985. Putative target genes of TaHSFA6e (HSP17, HSP70 and HSP90) showed upregulation in response to differential HS (30 & 38ºC, 2 h) during pollination and grain-filling stages. Small HSP17 was observed most triggered in Halna under HS. We observed increase in the catalase, guaiacol peroxidase, total antioxidant capacity (TAC), and decrease in the lipid peroxidation in thermotolerant cvs. (Halna, HD2985), as compared to thermosusceptible (PBW343, HD2329) under differential HS. Multiple stresses (heat - 38ºC, 2 h, and drought - 100 mL of 20% polyethylene Glycol 6000) during seedling stage of wheat showed positive correlation between the expression of TaHSFA6e, putative targets (HSP70, HSP90, HSP17) and TAC. Halna (thermotolerant) performed better, as compared to other contrasting cvs. TaHSFA6e TF can be used as promising candidate gene for manipulating the heat stress-tolerance network.
Increasing temperature and consequent changes in climate adversely affect plant growth and development, resulting in catastrophic loss of wheat productivity. For each degree rise in temperature, wheat production is estimated to reduce by 6%. A detailed overview of morpho-physiological responses of wheat to heat stress may help formulating appropriate strategies for heat-stressed wheat yield improvement. Additionally, searching for possible management strategies may increase productivity and sustainability of growing wheat. The major findings from this review are as follows: (1) heat stress significantly reduces seed germination and seedling growth, cell turgidity, and plant water-use efficiency; (2) at a cellular level, heat stress disturbs cellular functions through generating excessive reactive oxygen species, leading to oxidative stress; (3) the major responses of wheat to heat stress include the enhancement of leaf senescence, reduction of photosynthesis, deactivation of photosynthetic enzymes, and generation of oxidative damages to the chloroplasts; (4) heat stress also reduces grain number and size by affecting grain setting, assimilate translocation and duration and growth rate of grains; (5) effective approaches for managing heat stress in wheat include screening available germplasm under field trials and/or employing marker-assisted selection, application of exogenous protectants to seeds or plants, mapping quantitative trait locus conferring heat resistance and breeding; (6) a well-integrated genetic and agronomic management option may enhance wheat tolerance to heat. However, the success of applying various techniques of heat stress management requires greater understanding of heat tolerance features, molecular cloning, and characterization of genes. The overall success of the complex plant heat stress management depends on the concerted efforts of crop modelers, molecular biologists, and plant physiologists.
The wheat avenin-like proteins (ALP) are considered atypical gluten constituents and have shown positive effects on dough properties revealed using a transgenic approach. However, to date the genetic architecture of ALP genes is unclear, making it impossible to be utilized in wheat breeding. In the current study, three genes of type-b ALPs were identified and mapped to chromosomes 7AS, 4AL and 7DS. The coding gene sequence of both TaALP-7A and TaALP-7D was 855 bp long, encoding two identical homologous 284 amino acid long proteins. TaALP-4A was 858 bp long, encoding a 285 amino acid protein variant. Three alleles were identified for TaALP-7A and four for TaALP-4A. TaALP-7A alleles were of two types: type-1, which includes TaALP-7A1 andTaALP-7A2, encodes mature proteins, while type-2, represented byTaALP-7A3, contains a stop codon in the coding region and thus does not encode a mature protein. Dough quality testing of 102 wheat cultivars established a highly significant association of the type-1 TaALP-7A allele with better wheat processing quality. This allelic effects were confirmed among a range of commercial wheat cultivars. Our research makes the ALP be the first of such genetic variation source that can be readily utilized in wheat breeding.
The third edition of the Handbook of Proteolytic Enzymes is a fully revised and updated major reference work in Elsevier's canon. For the first time the Handbook will be available as an online via Elsevier's ScienceDirect platform as well as a three-volume book. The online version will have the enhanced options including online multimedia, cross-referencing capabilities, integrated online delivery and closer integration with the online MEROPS database of peptidases and their inhibitors. This reference work is intended for university libraries, researchers and students, and will be of great interest to the pharmaceutical and biotechnology companies. The new edition will feature articles on approximately 1000 different proteolytic enzymes written by acknowledged experts in the field. Each article will be a full but concise summary, including details of activity and specificity, structural chemistry, preparation and biological aspects. There are also introductory chapters on peptidase classification and mechanisms and a comprehensive index. The one-stop resource for proteolytic enzymes Contains over 830 chapters Covers new research in therapeutics and drug trials Supplies content written by experts in the field.
Respected and known worldwide in the field for his research in plant nutrition, Dr. Horst Marschner authored two editions of Mineral Nutrition of Higher Plants. His research greatly advanced the understanding of rhizosphere processes and trace element uptake by plants and he published extensively in a variety of plant nutrition areas. While doing agricultural research in West Africa in 1996, Dr. Marschner contracted malaria and passed away, and until now this legacy title went unrevised. Despite the passage of time, it remains the definitive reference on plant mineral nutrition. Great progress has been made in the understanding of various aspects of plant nutrition and in recent years the view on the mode of action of mineral nutrients in plant metabolism and yield formation has shifted. Nutrients are not only viewed as constituents of plant compounds (constructing material), enzymes and electron transport chains but also as signals regulating plant metabolism via complex signal transduction networks. In these networks, phytohormones also play an important role. Principles of the mode of action of phytohormones and examples of the interaction of hormones and mineral nutrients on source and sink strength and yield formation are discussed in this edition. Phytohormones have a role as chemical messengers (internal signals) to coordinate development and responses to environmental stimuli at the whole plant level. These and many other molecular developments are covered in the long-awaited new edition. Esteemed plant nutrition expert and Horst Marschner's daughter, Dr. Petra Marschner, together with a team of key co-authors who worked with Horst Marschner on his research, now present a thoroughly updated and revised third edition of Marschner's Mineral Nutrition of Higher Plants, maintaining its value for plant nutritionists worldwide. A long-awaited revision of the standard reference on plant mineral nutrition Features full coverage and new discussions of the latest molecular advances Contains additional focus on agro-ecosystems as well as nutrition and quality.
DEAD-box RNA helicases play important roles in all types of processes in RNA metabolism. This report characterizes a stress-responsive transcript termed TaRH1 (Triticum aestivum RNA helicase) that encodes a putative ATP-dependent RNA helicase and is a member of the DEAD box family. Quantitative real-time PCR (qRT-PCR) analysis indicated that the TaRH1 gene was differentially expressed under both biotic and several abiotic stresses. The characteristics are given of the TaRH1-catalysed unwinding of duplex RNA following TaRH1 expression in Escherichia coli BL 21. These results suggest that the TaRH1 gene may participate in the plant stress response.
When small RNA is sequenced on current sequencing machines, the resulting reads are usually longer than the RNA and therefore contain parts of the 3' adapter. That adapter must be found and removed error-tolerantly from each read before read mapping. Previous solutions are either hard to use or do not offer required features, in particular support for color space data. As an easy to use alternative, we developed the command-line tool cutadapt, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features.
Cutadapt, including its MIT-licensed source code, is available for download at http://code.google.com/p/cutadapt/