Background: Reducing the dependence of crop production on chemical fertilizer with its associated costs, carbon footprint and other environmental problems is a challenge for agriculture. New solutions are required to solve this problem, and crop breeding for high nitrogen use efficiency or tolerance of low nitrogen availability has been widely considered to be a promising approach. However, the molecular mechanisms of high nitrogen use efficiency or low-nitrogen tolerance in crop plants are still to be elucidated, including the role of long non-coding RNAs (lncRNAs). Results: In this study, we identified 498 lncRNAs in barley (Hordeum vulgare) landrace B968 (Liuzhutouzidamai), of which 487 were novel, and characterised 56 that were responsive to low-nitrogen stress. For functional analysis of differentially-expressed lncRNAs, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment of co-expressed and co-located protein-coding genes were analyzed, and interactions with annotated co-expressed protein coding genes or micro RNAs (miRNAs) were further predicted. Target mimicry prediction between differentially-expressed lncRNAs and miRNAs identified 40 putative target mimics of lncRNAs and 58 target miRNAs. Six differentially-expressed lncRNAs were further validated by qPCR, and one in particular showed consistent differential expression using both techniques. Expression levels of most of the lncRNAs were found to be very low, and this may be the reason for the apparent inconsistency between RNA-seq and qPCR data. Conclusions: The analysis of lncRNAs that are differentially-expressed under low-nitrogen stress, as well as their co-expressed or co-located protein coding genes and target mimics, could elucidate complex and hitherto uncharacterised mechanisms involved in the adaptation to low-nitrogen stress in barley and other crop plants.

Background: Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signalling, in some cases involving the stress hormone, abscisic acid (ABA). The burgeoning and divergence of the plant gene family has led to the evolution of three subfamilies,SnRK1,SnRK2andSnRK3, of whichSnRK2andSnRK3are unique to plants. Therefore, the study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions. In the present study, we describe theSnRKgene family of barley (Hordeum vulgare), the widespread cultivation of which can be attributed to its good adaptation to different environments.Results: The barleyHvSnRKgene family was elucidated in its entirety from publicly-available genome data and found to comprise 50 genes. Phylogenetic analyses assigned six of the genes to theHvSnRK1subfamily, 10 toHvSnRK2and 34 toHvSnRK3. The search was validated by applying it to Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome data, identifying 50SnRKgenes in rice (fourOsSnRK1, 11OsSnRK2and 35OsSnRK3) and 39 in Arabidopsis (threeAtSnRK1, 10AtSnRK2and 26AtSnRK3). Specific motifs were identified in the encoded barley proteins, and multiple putative regulatory elements were found in the gene promoters, with light-regulated elements (LRE), ABA response elements (ABRE) and methyl jasmonate response elements (MeJa) the most common. RNA-seq analysis showed that many of theHvSnRKgenes responded to ABA, some positively, some negatively and some with complex time-dependent responses.Conclusions: The barleyHvSnRKgene family is large, comprising 50 members, subdivided intoHvSnRK1(6 members),HvSnRK2(10 members) andHvSnRK3(34 members), showing differential positive and negative responses to ABA.

The excess use of nitrogen fertilizers causes many problems, including higher costs of crop production, lower nitrogen use efficiency, and environmental damage. Crop breeding for low-nitrogen tolerance, especially molecular breeding, has become the major route to solving these issues. Therefore, in crops such as barley (Hordeum vulgare L.), it is crucial to understand the mechanisms of low-nitrogen tolerance at the molecule level. In the present study, two barley cultivars, BI-04 (tolerant to low nitrogen) and BI-45 (sensitive to low nitrogen), were used for gene expression analysis under low-nitrogen stress, including 10 genes related to primary nitrogen metabolism. The results showed that the expressions of HvNIA2 (nitrite reductase), HvGS2 (chloroplastic glutamine synthetase), and HvGLU2 (ferredoxin-dependent glutamate synthase) were only induced in shoots of BI-04 under low-nitrogen stress, HvGLU2 was also only induced in roots of BI-04, and HvGS2 showed a rapid response to low-nitrogen stress in the roots of BI-04. The expression of HvASN1 (asparagine synthetase) was reduced in both cultivars, but it showed a lower reduction in the shoots of BI-04. In addition, gene expression and regulation differences in the shoots and roots were also compared between the barley cultivars. Taken together, the results indicated that the four above-mentioned genes might play important roles in low-nitrogen tolerance in barley.

Somatic embryogenesis receptor-like kinases (SERKs), a subfamily of receptor-like kinases, showed important roles in plant response to abiotic and biotic stresses in addition to embryogenesis and organogenesis in numerous plant species. In the present study, three orthologs of SERK genes (HvSERK1/2/3) were isolated from barley, and their expression patterns during in vitro culture of microspores as well as their responses to different stresses including salinity and powdery mildew were characterized. Sequence analysis suggested that three HvSERK genes were highly conserved in the grass family. Subcellular localization showed the HvSERK1 protein located on the plasma membrane. The HvSERK1 transcript was up-regulated during the microspore culture period, suggesting its roles in microspore embryogenesis. HvSERK1 and HvSERK3 showed the highest expression level in the leaves; however no difference was detected for HvSERK2 expression in different plants’ tissues. Under salt stress, all three HvSERK genes were quickly induced in microspore-derived embryogenic calli, whereas only HvSERK1 was up-regulated in the roots of barley seedlings. Moreover, only HvSERK2 was induced in the barley leaves upon powdery mildew inoculation. These results suggest that barley SERK genes may participate in barley microspores’ development and plant response toward salt and fungal stress, and the function of them has some evolutionary changes.

Crop breeding for high nitrogen use efficiency (NUE) or tolerance to low nitrogen fertilization is thought to be an ideal solution to reduce the cost, carbon footprint, and other environmental problems caused by the excess use of nitrogen fertilizers. As a model plant for cereal crops, barley has many advantages, including good adaptability, a short growth period, and high natural stress resistance or tolerance. Therefore, research on improving NUE in barley is not only beneficial for nitrogen-efficient barley breeding but will also inform NUE improvement in other cereal crops. In this review, recent progress in understanding barley’s response to nitrogen nutrition, evaluation of NUE or low-nitrogen tolerance, quantitative trait loci (QTL) mapping and gene cloning associated with improving NUE, and breeding of nitrogen-efficient barley is summarized. Furthermore, several biotechnological tools that could be used for revealing the molecular mechanisms of NUE or breeding for improving NUE in barley are introduced, including GWAS, omics, and gene editing. The latest research ideas in unraveling the molecular mechanisms of improving NUE in other crops are also discussed. Thus, this review provides a better understanding of improving the NUE of barley and some directions for future research in this area.

Barley yellow mosaic disease, caused mainly by Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus, is a devastating disease of barley and is a threat to Eurasian barley production. Early detection is essential for effective management of the pathogens and to assure food security. In this study, a simple, rapid, specific, sensitive, and visual method was developed to detect BaYMV using loop-mediated isothermal amplification (LAMP). Two pairs of oligonucleotide primers (inner and outer primers) were designed to amplify the gene encoding the coat protein of BaYMV. The optimal conditions for the LAMP method were determined, and a one-step reverse transcription (RT)-LAMP method was also developed. Subsequently, the fastest processing time for RT-LAMP was determined. Among eight plant viruses examined using the LAMP method, only BaYMV was detectable, suggesting that the assay was highly specific. The RT-LAMP method was 10 times more sensitive than the RT-PCR method in the sensitivity test. To further shorten the virus detection process, a dye was added to the RT-LAMP products, and positive reactions were simply read by the naked eye via a color change (from orange to light green) under visible light. Barley samples from the middle and lower reaches of the Yangtze River basin, where BaYMV broke out very seriously in 1970s, were detected by the newly established RT-LAMP method. The results showed that all samples were positive for BaYMV, indicating the potential risk of the virus in these areas. This newly established LAMP/RT-LAMP method could be a promising tool for barley protection and food security control.