Genome-Wide Identification of Wheat KNOX Gene Family and Functional Characterization of TaKNOX14-D in Plants

The KNOX genes play important roles in maintaining SAM and regulating the development of plant leaves. However, the TaKNOX genes in wheat are still not well understood, especially their role in abiotic stress. In this study, a total of 36 KNOX genes were identified, and we demonstrated the function of the TaKNOX14-D gene under mechanical injury and cold stress. Thirty-six TaKNOX genes were divided into two groups, and thirty-four TaKNOX genes were predicted to be located in the nucleus by Cell-PLoc. These genes contained five tandem duplications. Fifteen collinear gene pairs were exhibited in wheat and rice, one collinear gene pair was exhibited in wheat and Arabidopsis. The phylogenetic tree and motif analysis suggested that the TaKNOX gene appeared before C3 and C4 diverged. Gene structure showed that the numbers of exons and introns in TaKNOX gene are different. Wheat TaKNOX genes showed different expression patterns during the wheat growth phase, with seven TaKNOX genes being highly expressed in the whole growth period. These seven genes were also highly expressed in most tissues, and also responded to most abiotic stress. Eleven TaKNOX genes were up-regulated in the tillering node during the leaf regeneration period after mechanical damage. When treating the wheat with different hormones, the expression patterns of TaKNOX were changed, and results showed that ABA promoted TaKNOX expression and seven TaKNOX genes were up-regulated under cytokinin and auxin treatment. Overexpression of the TaKNOX14-D gene in Arabidopsis could increase the leaf size, plant height and seed size. This gene overexpression in Arabidopsis also increased the compensatory growth capacity after mechanical damage. Overexpression lines also showed high resistance to cold stress. This study provides a better understanding of the TaKNOX genes.     

Genome-Wide Identification and Characterization of Soybean GmLOR Gene Family and Expression Analysis in Response to Abiotic Stresses

The LOR (LURP-one related) family genes encode proteins containing a conserved LOR domain. Several members of the LOR family genes are required for defense against Hyaloperonospora parasitica (Hpa) in Arabidopsis. However, there are few reports of LOR genes in response to abiotic stresses in plants. In this study, a genome-wide survey and expression levels in response to abiotic stresses of 36 LOR genes from Glycine max were conducted. The results indicated that the GmLOR gene family was divided into eight subgroups, distributed on 14 chromosomes. A majority of members contained three extremely conservative motifs. There were four pairs of tandem duplicated GmLORs and nineteen pairs of segmental duplicated genes identified, which led to the expansion of the number of GmLOR genes. The expansion patterns of the GmLOR family were mainly segmental duplication. A heatmap of soybean LOR family genes showed that 36 GmLOR genes exhibited various expression patterns in different tissues. The cis-acting elements in promoter regions of GmLORs include abiotic stress-responsive elements, such as dehydration-responsive elements and drought-inducible elements. Real-time quantitative PCR was used to detect the expression level of GmLOR genes, and most of them were expressed in the leaf or root except that GmLOR6 was induced by osmotic and salt stresses. Moreover, GmLOR4/10/14/19 were significantly upregulated after PEG and salt treatments, indicating important roles in the improvement of plant tolerance to abiotic stress. Overall, our study provides a foundation for future investigations of GmLOR gene functions in soybean.     

Genome-Wide Identification and Characterization of the Cystatin Gene Family in Bread Wheat (Triticum aestivum L.)

Cystatins, as reversible inhibitors of papain-like and legumain proteases, have been identified in several plant species. Although the cystatin family plays crucial roles in plant development and defense responses to various stresses, this family in wheat (Triticum aestivum L.) is still poorly understood. In this study, 55 wheat cystatins (TaCystatins) were identified. All TaCystatins were divided into three groups and both the conserved gene structures and peptide motifs were relatively conserved within each group. Homoeolog analysis suggested that both homoeolog retention percentage and gene duplications contributed to the abundance of the TaCystatin family. Analysis of duplication events confirmed that segmental duplications played an important role in the duplication patterns. The results of codon usage pattern analysis showed that TaCystatins had evident codon usage bias, which was mainly affected by mutation pressure. TaCystatins may be regulated by cis-acting elements, especially abscisic acid and methyl jasmonate responsive elements. In addition, the expression of all selected TaCystatins was significantly changed following viral infection and cold stress, suggesting potential roles in response to biotic and abiotic challenges. Overall, our work provides new insights into TaCystatins during wheat evolution and will help further research to decipher the roles of TaCystatins under diverse stress conditions.     

The Glutathione Peroxidase Gene Family in Thellungiella salsuginea: Genome-Wide Identification,Classification, and Gene and Protein Expression Analysis under Stress Conditions

Glutathione peroxidases (GPX) catalyze the reduction of H₂O₂ or organic hydroperoxides to water or corresponding alcohols using reduced glutathione, which plays an essential role in ROS (reactive oxygen species) homeostasis and stress signaling. Thellungiella salsuginea (Eutrema salsugineum), a relative of Arabidopsis thaliana, displays an extremely high level of tolerance to salt, drought, cold and oxidative stresses. The enzymatic antioxidant systems may contribute to the stress tolerance of T. salsuginea. In the present study, we aimed at understanding the roles of the antioxidant enzymes in T. salsuginea by focusing on the GPX family. We identified the eight GPX genes in T. salsuginea, and the structure of the N-terminal domains indicated their putative chloroplastic, mitochondrial and cytoplasmic location. The exon-intron organization of these genes exhibited a conserved pattern among plant GPX genes. Multiple environmental stresses and hormone response related cis-acting elements were predicted in the promoters of TsGPX genes. The gene and protein expression profiles of TsGPXs in response to high level of salinity and osmotic stresses, in leaves and roots of T. salsuginea were investigated using real-time RT-PCR and western blotting analysis. Our result showed that different members of the GPX gene family were coordinately regulated under specific environmental stress conditions, and supported the important roles of TsGPXs in salt and drought stress response in T. salsuginea.     

Genome-Wide Identification,Expression Patterns and Sugar Transport of the Physic Nut SWEET Gene Family and a Functional Analysis of JcSWEET16 in Arabidopsis

The Sugars Will Eventually be Exported Transporters (SWEET) family is a class of sugar transporters that play key roles in phloem loading, seed filling, pollen development and the stress response in plants. Here, a total of 18 JcSWEET genes were identified in physic nut (Jatropha curcas L.) and classified into four clades by phylogenetic analysis. These JcSWEET genes share similar gene structures, and alternative splicing of messenger RNAs was observed for five of the JcSWEET genes. Three (JcSWEET1/4/5) of the JcSWEETs were found to possess transport activity for hexose molecules in yeast. Real-time quantitative PCR analysis of JcSWEETs in different tissues under normal growth conditions and abiotic stresses revealed that most are tissue-specifically expressed, and 12 JcSWEETs responded to either drought or salinity. The JcSWEET16 gene responded to drought and salinity stress in leaves, and the protein it encodes is localized in both the plasma membrane and the vacuolar membrane. The overexpression of JcSWEET16 in Arabidopsis thaliana modified the flowering time and saline tolerance levels but not the drought tolerance of the transgenic plants. Together, these results provide insights into the characteristics of SWEET genes in physic nut and could serve as a basis for cloning and further functional analysis of these genes.     

Genome-Wide Analysis of the Rab Gene Family in Melilotus albus Reveals Their Role in Salt Tolerance

Melilotus albus is a high-quality forage, due to its high protein content, and aboveground biomass and salt tolerance. Rab (Ras-related protein in the brain) proteins are the largest GTPase family which play a key role in intracellular membrane transport, and many Rab genes have been identified in eukaryotes. The growth and distribution of M. albus are severely hampered by soil salinization. However, little is known about candidate genes for salt tolerance in M. albus. In this study, 27 Rab family genes were identified for the first time from M. albus, and divided into eight groups (Groups A-H). The number of introns in MaRabs ranged from one to seven, with most genes containing one intron. In addition, most MaRab proteins showed similarities in motif composition. Phylogenetic analysis and structural-domain comparison indicated that Rab family genes were highly conserved in M. albus. Members of the MaRab gene family were distributed across all eight chromosomes, with the largest distribution on chromosome 1. Prediction of the protein interaction network showed that 24 Rab proteins exhibited protein–protein interactions. Analysis of the promoter cis-acting elements showed that MaRab-gene family members are extensively involved in abiotic stress responses. RNA-seq data analysis of the MaRab-gene-expression patterns suggested that the Rab gene family possesses differentially expressed members in five organs and under salt stress, drought stress, and ABA (Abscisic Acid) treatment. Differentially expressed genes under drought stress, salt stress and ABA stress were validated by quantitative real-time PCR. Furthermore, heterologous expression in yeast was used to characterize the functions of MaRab1 and MaRab17, which were upregulated in reaction to salt stress. In summary, this study provided valuable information for further research into the molecular mechanism of the response of M. albus to saline stress, as well as the possibility of developing cultivars with high salt-resistance characteristics.     

Validation of a QTL on Chromosome 1DS Showing a Major Effect on Salt Tolerance in Winter Wheat

Salt stress is one the most destructive abiotic stressors, causing yield losses in wheat worldwide. A prerequisite for improving salt tolerance is the identification of traits for screening genotypes and uncovering causative genes. Two populations of F₃ lines developed from crosses between sensitive and tolerant parents were tested for salt tolerance at the seedling stage. Based on their response, the offspring were classified as salt sensitive and tolerant. Under saline conditions, tolerant genotypes showed lower Na⁺ and proline content but higher K⁺, higher chlorophyll content, higher K⁺/Na⁺ ratio, higher PSII activity levels, and higher photochemical efficiency, and were selected for further molecular analysis. Five stress responsive QTL identified in a previous study were validated in the populations. A QTL on the short arm of chromosome 1D showed large allelic effects in several salt tolerant related traits. An expression analysis of associated candidate genes showed that TraesCS1D02G052200 and TraesCS5B02G368800 had the highest expression in most tissues. Furthermore, qRT-PCR expression analysis revealed that ZIP-7 had higher differential expressions under saline conditions compared to KefC, AtABC8 and 6-SFT. This study provides information on the genetic and molecular basis of salt tolerance that could be useful in development of salt-tolerant wheat varieties.