Identification of HvLRX, a new dehydration and light responsive gene in Tibetan hulless barley (Hordeum vulgare var. nudum)

BACKGROUND

Tibetan hulless barley (Hordeum vulgare var. nudum), adjusting to the harsh environment on Qinghai-Tibet Plateau, is a good subject for analyzing drought tolerance mechanism. Several unannotated differentially expressed genes (DEGs) were identified through our previous RNA-Seq study using two hulless barley accessions with contrasting drought tolerance. One of these DEGs, HVU010048.2, showed up-regulated pattern under dehydration stress in both drought tolerant (DT) and drought susceptible (DS) accessions, while its function in drought resistance remains unknown. This new gene was named as HvLRX (light responsive X), because its expression was induced under high light intensity while suppressed under dark.

OBJECTIVE

To provide preliminary bioinformatics prediction, expression pattern, and drought resistance function of this new gene.

METHODS

Bioinformatics analysis of HvLRX were conducted by MEGA, PlantCARE, ProtParam, CELLO et al. The expression pattern of HvLRX under different light intensity, dehydration shock, gradual drought stress, NaCl stress, polyethylene glycol (PEG) 6000 stress and abscisic acid (ABA) treatment was investigated by quantitative reverse transcription-polymerase chain reaction (RT-qPCR). The function of HvLRX was analyzed by virus induced gene silencing (VIGS) in hulless barley and by transgenic method in tobacco.

RESULTS

Full cDNAs of HvLRX were cloned and compared in three hulless barley accessions. Homologues of HvLRX protein in other plants were excavated and their phylogenetic relationship was analyzed. Several light responsive elements (ATC-motif, Box 4, G-box, Sp1, and chs-CMA1a) were identified in its promoter region. Its expression can be promoted under high light intensity, dehydration shock, gradual drought stress, PEG 6000, and NaCl stress, but was almost unchanged in ABA treatment. HvLRX-silenced plants had a higher leaf water loss rate (WLR) and a lower survival rate (SR) compared with controls under dehydration stress. The infected leaves of HvLRX-silenced plants lost their water content quickly and became withered at 10 dpi. The SR of HvLRX overexpressed transgenic tobacco plants was significantly higher than that of wild-type plants. These results indicated HvLRX play a role in drought resistance. Besides, retarded vegetative growth was detected in HvLRX-silenced hulless barley plants, which suggested that this gene is important for plant development.

CONCLUSIONS

This study provided data of bioinformatics, expression pattern, and function of HvLRX. To our knowledge, this is the first report of this new dehydration and light responsive gene.

Dehydration induced transcriptomic responses in two Tibetan hulless barley (Hordeum vulgare var. nudum) accessions distinguished by drought tolerance

Background

The harsh environment on the Qinghai-Tibetan Plateau gives Tibetan hulless barley (Hordeum vulgare var. nudum) great ability to resist adversities such as drought, salinity, and low temperature, and makes it a good subject for the analysis of drought tolerance mechanism. To elucidate the specific gene networks and pathways that contribute to its drought tolerance, and for identifying new candidate genes for breeding purposes, we performed a transcriptomic analysis using two accessions of Tibetan hulless barley, namely Z772 (drought-tolerant) and Z013 (drought-sensitive).

Results

There were more up-regulated genes of Z772 than Z013 under both mild (5439-VS-2604) and severe (7203-VS-3359) dehydration treatments. Under mild dehydration stress, the pathways exclusively enriched in drought-tolerance genotype Z772 included Protein processing in endoplasmic reticulum, tricarboxylic acid (TCA) cycle, Wax biosynthesis, and Spliceosome. Under severe dehydration stress, the pathways that were mainly enriched in Z772 included Carbon fixation in photosynthetic organisms, Pyruvate metabolism, Porphyrin and chlorophyll metabolism. The main differentially expressed genes (DEGs) in response to dehydration stress and genes whose expression was different between tolerant and sensitive genotypes were presented in this study, respectively. The candidate genes for drought tolerance were selected based on their expression patterns.

Conclusions

The RNA-Seq data obtained in this study provided an initial overview on global gene expression patterns and networks that related to dehydration shock in Tibetan hulless barley. Furthermore, these data provided pathways and a targeted set of candidate genes that might be essential for deep analyzing the molecular mechanisms of plant tolerance to drought stress.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4152-1) contains supplementary material, which is available to authorized users.

Transcriptome analysis revealed the drought-responsive genes in Tibetan hulless barley

Background

Hulless barley, also called naked barley, is an important cereal crop worldwide, serving as a healthy food both for human consumption and animal feed. Nevertheless, it often suffered from drought stress during its growth and development, resulting in a drastic reduction in barley yields. Therefore, study on molecular mechanism of hulless barley drought-tolerance is very important for increasing barley production. To investigate molecular mechanism of barley drought-resistance, this study examined co-regulated mRNAs that show a change in expression pattern under early well water, later water deficit and finally water recovery treatments, and to identify mRNAs specific to water limiting conditions.

Results

Total of 853 differentially expressed genes (DEGs) were detected and categorized into nine clusters, in which VI and VIII were apparently up-regulated under low relative soil moisture content (RSMC) level. The majority of genes in these two clusters was relevant to abiotic stress responses in abscisic acid (ABA) dependent and independent signaling pathway, including NCED, PYR/PYL/RCAR, SnRK2, ABF, MYB/MYC, AP2/ERF family, LEA and DHN. In contrast, genes within clusters II and IV were generally down-regulated under water stress; cluster IX genes were up-regulated during water recovery response to both low and high RSMC levels. Genes in implicated in tetrapyrrole binding, photosystem and photosynthetic membrane were the most affected in cluster IX.

Conclusion

Taken together, our findings indicate that the responses of hulless barley to drought stress shows differences in the pathways and genes activated. Furthermore, all these genes displayed different sensitivities to soil water deficit and might be profitable for future drought tolerance improvement in barley and other crops.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2685-3) contains supplementary material, which is available to authorized users.

Physiological and molecular changes in barley and wheat under salinity

In this study, it was aimed to compare salinity-induced changes in barley (Hordeum vulgare L. cv. Bornova-92) and bread wheat (Triticum aestivum L. cv. Gerek-79). Seeds were germinated under saline conditions (0, 50, 100, 250, and 500 mM NaCl) for 2 days and recovered under non-saline conditions for 2 days. At the end of the salt treatment, germination, water content (WC), total soluble protein content, and catalase (CAT, EC 1.11.1.6) activity were affected in both species, while superoxide dismutase (SOD, EC 1.15.1.1) activity was affected in barley. Salinity affected WC, protein content, and CAT activity in both species, while it affected germination in barley and affected fresh weight and SOD activity in wheat after recovery. Physiological responses of both species were correlated. Expression of α-tubulin, Atls1, and Lls1 genes was down-regulated in barley after 250 mM NaCl treatment. HVA1 gene was highly (more than 50-fold) stimulated by salinity in barley. However, α-tubulin and Atls1 genes were down-regulated, and Lls1 gene was up-regulated in wheat after recovery from 250-mM NaCl treatment. Increase in HVA1 expression was not significant in wheat. The expression profiles of barley and wheat under salinity are different, and barley tended to regulate gene expression faster than wheat.

[Molecular cloning and protein structure prediction of barley (Hordeum vulgare L.) Dhn6 gene and its expression pattern under dehydration conditions]

Dehydrins (DHNs), proteins with protective functions encoded by the late embryogenesis abundant (LEA), are differentially up-regulated at the transcriptional level under environmental stresses such as water deficit, salinity, and low temperature or in response to ABA. Data involving protein structure and expression of dehydrins could elucidate their functional roles under dehydration conditions in plants. Dhn6 gene of 1767 bp with an intron (92 bp) in six-rowed barley, a member of LEA D11, was cloned into pMD18-T vector in the present study. It shared 93.18% identity with Hordeum vulgare ssp. vulgare (GenBank accession: AF043091), encoding a protein composed of 523 amino acid residues with the predicted molecular weight of 49.68 kDa and the theoretical isoelectric point of 8.04. Analyses of domain and structure indicated that the protein was dominantly composed of 83% hydrophillic amino acid residues, with numerous imperative curls and three loosed helixes. Three-dimensional measurement revealed that the water-soluble lipid-associating protein was attributed to its twisted cable formed by reverse paralleled chains. Moreover, the putative amphipathic α-helices formed by K-segments might play roles in protecting membrane structure in barley. Significantly, relatively high accumulations of Dhn6 gene were detected after 8 h of water deficit by real-time quantitative RT-PCR. These results possibly suggested that the accumulation of Dhn6 gene could be critical for resistant dehydration in plants.

Starch granule-associated proteins of hull-less barley (Hordeum vulgare L.) from the Qinghai-Tibet Plateau in China

BACKGROUND

The starch granule-associated proteins (SGAPs) are the minor components of the starch granules and a majority of them are believed to be starch biosynthetic enzymes. The Qinghai-Tibet Plateau in China, one of the centres of origin of cultivated barley, is abundant in hull-less barley resources which exhibit high polymorphism in SGAPs.

RESULTS

The SGAPs of hull-less barley from Qinghai-Tibet Plateau were analysed by one-dimensional (1-D) SDS-PAGE, 2-D PAGE and ESI-Q-TOF MS/MS. In the 1-D SDS-PAGE gel, four proteins including a 80 kDa starch synthase, actin, actin 4 and ATP synthase β-subunit were identified as novel SGAPs. A total of six different bands were identified as starch granule-bound starch synthase I (GBSSI) and the segregation of the novel GBSSI bands in F(1) and F(2) seeds derived from yf127 × yf70 was in accordance with Mendel's law. In the 2-D PAGE gel, 92 spots were identified as 42 protein species which could be classified into 15 functional groups. Thirteen protein species were identified as SGAPs for the first time and multiple spots were identified as GBSSI.

CONCLUSION

This study revealed novel SGAPs in hull-less barley from the Qinghai-Tibet Plateau in China and these will be significant in further studies of starch biosynthesis in barley.

Abscisic acid and late embryogenesis abundant protein profile changes in winter wheat under progressive drought stress

Three varieties (cv. Pobeda, Katya and Sadovo) of winter wheat (Triticum aestivum), differing in their agronomic characteristics, were analysed during progressive soil water stress and recovery at early vegetation stages. Changes in abscisic acid content, SDS-PAGE and immunoblot profiles of proteins that remained soluble upon heating were monitored. Initially higher ABA content in control Pobeda and Katya corresponded to earlier expression of the studied late embryogenesis abundant (LEA) proteins. A combination of higher ABA content, early immunodetection of dehydrins, and a significant increase of WZY2 transcript levels were observed in drought-stressed leaves of the tolerant variety Katya. One-step RT-PCR analyses of some acidic dehydrin genes (WCOR410b, TADHN) documented their relatively constant high expression levels in leaves under drought stress during early vegetative development. Neutral WZY2 dehydrin, TaLEA2 and TaLEA3 transcripts accumulated gradually with increasing water deficit. Delayed expression of TaLEA2 and TaLEA3 genes was found in the least drought-tolerant wheat, Sadovo. The expression profile of WZY2 revealed two distinct and separate bands, suggesting alternative splicing, which altered as water stress increased.

A transient assay system for the assessment of cell-autonomous gene function in dehydration-stressed barley

Drought is a serious, worldwide problem for crop production and also affects yields of barley and wheat, together with other stressors such as frost, viral diseases, or fungal pathogens. Although a number of candidate genes have been identified by transcriptome approaches in recent years, only very few have been tested in functional assays for a beneficial effect on drought tolerance. Here, a transient assay system in microprojectile-bombarded barley leaves is described that allows the functional testing of dehydration stress-related candidate genes by RNA interference (RNAi) or overexpression. Cellular stress or damage in dedydrated leaves is reported by a reduced accumulation of slowly maturing, native red-fluorescing protein DsRed that is known to be sensitive to denaturing conditions. After a dehydration-stress period of 4 d during which the relative fresh weight of leaves was kept at 60-66% of initial fresh weight, a reproducible reduction of normalized DsRed fluorescence was observed. In order to obtain proof of concept, a number of barley mRNAs homologous to drought response genes were selected and targeted by transient induced gene silencing (TIGS). TIGS of four tested genes resulted in a significantly stronger decrease of normalized DsRed fluorescence in dehydration-stressed leaves, whereas they had no effect in fully turgescent control leaves. These genes encode barley drought-responsive factor HvDRF1 (DREB2-like), dehydrin 6, late embryogenesis-abundant protein HVA1, and the vacuolar sodium/proton antiporter HvHNX1. The four targeted transcripts were also found to accumulate rapidly in dehydration-stressed barley leaf segments. The results suggest a value of the TIGS system for functional pre-screening of larger numbers of drought or dehydration stress-related candidate genes in barley.