Nucleoredoxin Gene TaNRX1 Positively Regulates Drought Tolerance in Transgenic Wheat (Triticum aestivum L.)

Cadmium and copper-induced metabolic and proteomic changes in the root tip during early maize growth

In this study, the metabolic adjustments performed by maize (Zea mays L.) seminal roots exposed to 25 µM Cd2+ or 25 µM Cu2+ at pre-emergence are compared, focusing on the proteomic changes after metal exposure. Root width was increased, and root length was decreased after 72 h of metal treatment. Both metals induced H2O2 accumulation and lipid peroxidation in the root tip. These changes were accompanied by increases in lipoxygenase activity and 4-hydroxy-2-nonenal content. NMR spectroscopy revealed that the abundance of 38 water-soluble metabolites was significantly modified by Cd and Cu exposure; this set of metabolites comprised carboxylic acids, amino acids, carbohydrates, and unidentified phenolic compounds. Linoleic acid content significantly decreased in Cu-treated samples. The total amount of proteins detected in maize root apexes was 2,171. Gene ontology enrichment analysis of the differentially accumulated proteins was performed to detect pathways probably affected by metal additions. Both metals altered redox homeostasis, up-regulated oxylipins biosynthetic process, and shifted metabolism towards the oxidative pentose-phosphate in the root apexes. However, the methionine salvage pathway appears as a key metabolic module only under Cd stress. The integrative analysis carried out in this study suggests that most molecular features behind the reprogramming of maize root tips to cope with cadmium and copper toxicity are common, but some are not.

Functional analysis of polyphenol oxidase 1 gene in common wheat

Polyphenol oxidase (PPO) activity is a major cause of the undesirable brown color of wheat-based products. Ppo1, a major gene for PPO activity, was cloned based on sequence homology in previous studies; however, its function and regulation mechanism remain unclear. In this study, the function and genetic regulation of Ppo1 were analyzed using RNA interference (RNAi) and Targeting Induced Local Lesions IN Genomes (TILLING) technology, and superior mutants were identified. Compared with the control, the level of Ppo1 transcript in RNAi transgenic lines was drastically decreased by 15.5%-60.9% during grain development, and PPO activity was significantly reduced by 12.9%-20.4%, confirming the role of Ppo1 in PPO activity. Thirty-two Ppo1 mutants were identified in the ethyl methanesulfonate (EMS)-mutagenized population, including eight missense mutations, 16 synonymous mutations, and eight intron mutations. The expression of Ppo1 was reduced significantly by 6.7%-37.1% and 10.1%-54.4% in mutants M092141 (G311S) and M091098 (G299R), respectively, in which PPO activity was decreased by 29.7% and 28.8%, respectively, indicating that mutation sites of two mutants have important effects on PPO1 function. Sequence and structure analysis revealed that the two sites were highly conserved among 74 plant species, where the frequency of glycine was 94.6% and 100%, respectively, and adjacent to the entrance of the hydrophobic pocket of the active site. The M092141 and M091098 mutants can be used as important germplasms to develop wheat cultivars with low grain PPO activity. This study provided important insights into the molecular mechanism of Ppo1 and the genetic improvement of wheat PPO activity.

Identification of novel putative alleles related to important agronomic traits of wheat using robust strategies in GWAS

Principal component analysis (PCA) is widely used in various genetics studies. In this study, the role of classical PCA (cPCA) and robust PCA (rPCA) was evaluated explicitly in genome-wide association studies (GWAS). We evaluated 294 wheat genotypes under well-watered and rain-fed, focusing on spike traits. First, we showed that some phenotypic and genotypic observations could be outliers based on cPCA and different rPCA algorithms (Proj, Grid, Hubert, and Locantore). Hubert's method provided a better approach to identifying outliers, which helped to understand the nature of these samples. These outliers led to the deviation of the heritability of traits from the actual value. Then, we performed GWAS with 36,000 single nucleotide polymorphisms (SNPs) based on the traditional approach and two robust strategies. In the conventional approach and using the first three components of cPCA as population structure, 184 and 139 marker-trait associations (MTAs) were identified for five traits in well-watered and rain-fed environments, respectively. In the first robust strategy and when rPCA was used as population structure in GWAS, we observed that the Hubert and Grid methods identified new MTAs, especially for yield and spike weight on chromosomes 7A and 6B. In the second strategy, we followed the classical and robust principal component-based GWAS, where the first two PCs obtained from phenotypic variables were used instead of traits. In the recent strategy, despite the similarity between the methods, some new MTAs were identified that can be considered pleiotropic. Hubert's method provided a better linear combination of traits because it had the most MTAs in common with the traditional approach. Newly identified SNPs, including rs19833 (5B) and rs48316 (2B), were annotated with important genes with vital biological processes and molecular functions. The approaches presented in this study can reduce the misleading GWAS results caused by the adverse effect of outlier observations.

Genome-wide identification, characterization, evolution, and expression pattern analyses of the typical thioredoxin gene family in wheat (Triticum aestivum L.)

Typical thioredoxin (TRX) plays an important role in maintaining redox balance in plants. However, the typical TRX genes in wheat still need to be comprehensively and deeply studied. In this research, a total of 48 typical TaTRX genes belonging to eight subtypes were identified via a genome-wide search in wheat, and the gene structures, protein conserved motifs, and protein 3D structures of the same subtype were very similar. Evolutionary analysis showed that there are two pairs of tandem duplication genes and 14 clusters of segmental duplication genes in typical TaTRX family members; TaTRX15, TaTRX36, and TaTRX42 had positive selection compared with the orthologs of their ancestral species; rice and maize have 11 and 13 orthologous typical TRXs with wheat, respectively. Gene Ontology (GO) analysis indicated that typical TaTRXs were involved in maintaining redox homeostasis in wheat cells. Estimation of ROS content, determination of antioxidant enzyme activity, and gene expression analysis in a line overexpressing one typical TaTRX confirmed that TRX plays an important role in maintaining redox balance in wheat. A predictive analysis of cis-acting elements in the promoter region showed that typical TaTRXs were extensively involved in various hormone metabolism and response processes to stress. The results predicted using public databases or verified using RT-qPCR show that typical TaTRXs were able to respond to biotic and abiotic stresses, and their expression in wheat was spatiotemporal. A total of 16 wheat proteins belonging to four different families interacting with typical TaTRXs were predicted. The above comprehensive analysis of typical TaTRX genes can enrich our understanding of this gene family in wheat and provide valuable insights for further gene function research.

Candidate Genes Associated with Abiotic Stress Response in Plants as Tools to Engineer Tolerance to Drought, Salinity and Extreme Temperatures in Wheat: An Overview

Wheat represents one of the most important staple food crops worldwide and its genetic improvement is fundamental to meeting the global demand of the growing population. However, the environmental stresses, worsened by climate change, and the increasing deterioration of arable land make it very difficult to fulfil this demand. In light of this, the tolerance of wheat to abiotic stresses has become a key objective of genetic improvement, as an effective strategy to ensure high yields without increasing the cultivated land. Genetic erosion related to modern agriculture, whereby elite, high-yielding wheat varieties are the product of high selection pressure, has reduced the overall genetic diversity, including the allelic diversity of genes that could be advantageous for adaptation to adverse environmental conditions. This makes traditional breeding a less effective or slower approach to generating new stress-tolerant wheat varieties. Either mining for the diversity of not-adapted large germplasm pools, or generating new diversity, are the mainstream approaches to be pursued. The advent of genetic engineering has opened the possibility to create new plant variability and its application has provided a strong complement to traditional breeding. Genetic engineering strategies such as transgenesis and genome editing have then provided the opportunity to improve environmental tolerance traits of agronomic importance in cultivated species. As for wheat, several laboratories worldwide have successfully produced transgenic wheat lines with enhanced tolerance to abiotic stresses, and, more recently, significant improvements in the CRISPR/Cas9 tools available for targeted variations within the wheat genome have been achieved. In light of this, the present review aims to provide successful examples of genetic engineering applications for the improvement of wheat adaptation to drought, salinity and extreme temperatures, which represent the most frequent and most severe events causing the greatest losses in wheat production worldwide.

Genome-wide identification of foxtail millet's TRX family and a functional analysis of SiNRX1 in response to drought and salt stresses in transgenic Arabidopsis

Thioredoxins (TRXs) are small-molecule proteins with redox activity that play very important roles in the growth, development, and stress resistance of plants. Foxtail millet (Setaria italica) gradually became a model crop for stress resistance research because of its advantages such as its resistance to sterility and its small genome. To date, the thioredoxin (TRX) family has been identified in Arabidopsis thaliana, rice and wheat. However, studies of the TRX family in foxtail millet have not been reported, and the biological function of this family remains unclear. In this study, 35 SiTRX genes were identified in the whole genome of foxtail millet through bioinformatic analysis. According to phylogenetic analysis, 35 SiTRXs can be divided into 13 types. The chromosome distribution, gene structure, cis-elements and conserved protein motifs of 35 SiTRXs were characterized. Three nucleoredoxin (NRX) members were further identified by a structural analysis of TRX family members. The expression patterns of foxtail millet's SiNRX members under abiotic stresses showed that they have different stress-response patterns. In addition, subcellular localization revealed that SiNRXs were localized to the nucleus, cytoplasm and membrane. Further studies demonstrated that the overexpression of SiNRX1 enhanced Arabidopsis' tolerance to drought and salt stresses, resulting in a higher survival rate and better growth performance. Moreover, the expression levels of several known stress-related genes were generally higher in overexpressed lines than in the wild-type. Thus, this study provides a general picture of the TRX family in foxtail millet and lay a foundation for further research on the mechanism of the action of TRX proteins on abiotic stresses.

Transcriptomic Identification of Wheat AP2/ERF Transcription Factors and Functional Characterization of TaERF-6-3A in Response to Drought and Salinity Stresses

AP2/ERF (APETALA2/ethylene responsive factor) is a family of plant-specific transcription factors whose members are widely involved in many biological processes, such as growth, development, and biotic and abiotic stress responses. Here, 20 AP2/ERF genes were identified based on wheat RNA-seq data before and after drought stress, and classified as AP2, ERF, DREB, and RAV. The analysis of gene structure revealed that about 85% of AP2/ERF family members had lost introns, which are presumed to have been lost during the formation and evolution of the wheat genome. The expression of 20 AP2/ERF family genes could be verified by qRT-PCR, which further supported the validity of the RNA-seq data. Subsequently, subcellular localization and transcriptional activity experiments showed that the ERF proteins were mainly located in the nucleus and were self-activating, which further supports their functions as transcription factors. Furthermore, we isolated a novel ERF gene induced by drought, salt, and cold stresses and named it TaERF-6-3A. TaERF-6-3A overexpression increased sensitivity to drought and salt stresses in Arabidopsis, which was supported by physiological and biochemical indices. Moreover, the expression of stress- and antioxidant-related genes was downregulated in TaERF-6-3A-overexpressing plants. Overall, these results contribute to the further understanding of the TaERF-6-3A gene function in wheat.