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Triticale is tolerant of many environmental stresses, especially highly resistant to salt stress. However, the molecular regulatory mechanism of triticale seedlings under salt stress conditions is still unclear so far. In this study, a salt-responsive transcriptome analysis was conducted to identify candidate genes or transcription factors related to salt tolerance in triticale. The root of salt-tolerant triticale cultivars TW004 with salt-treated and non-salt stress at different time points were sampled and subjected to de novo transcriptome sequencing. Total 877,858 uniquely assembled transcripts were identified and most contigs were annotated in public databases including nr, GO, KEGG, eggNOG, Swiss-Prot and Pfam. 59,280, 49,345, and 85,922 differentially expressed uniquely assembled transcripts between salt treated and control triticale root samples at three different time points (C12_vs_T12, C24_vs_T24, and C48_vs_T48) were identified, respectively. Expression profile and functional enrichment analysis of DEGs found that some DEGs were significantly enriched in metabolic pathways related to salt tolerance, such as reduction–oxidation pathways, starch and sucrose metabolism. In addition, several transcription factor families that may be associated with salt tolerance were also identified, including AP2/ERF, NAC, bHLH, WRKY and MYB. Furthermore, 14 DEGs were selected to validate the transcriptome profiles via quantitative RT-PCR. In conclusion, these results provide a foundation for further researches on the regulatory mechanism of triticale seedlings adaptation to salt stress in the future.

Background YABBY is a plant-specific transcription factor (TF) that belongs to the zinc finger protein superfamily and is composed of a C2–C2 domain at the N-terminus and a YABBY domain at the C-terminus. It plays a role in plant development and growth. Methods In this study, 20 YABBY TFs were identified in the wheat genome. Phylogenetic relationships, collinearity relationships, gene structures, conserved motifs, and expression patterns were analyzed. Results Twenty TaYABBY TFs were distributed unevenly on 15 chromosomes. Collinearity analysis showed that these genes have a close relationship with monocot plants. The phylogenetic tree of wheat YABBYs classified these TaYABBYs into FIL, YAB2, INO, and CRC clades. Gene structure and conserved motif analyses showed that they share similar components in the same clades. Expression profile analysis showed that many TaYABBY genes have high expression levels in leaf tissues and are regulated by abiotic stresses, especially salt stress. Our results provide a basis for further functional characterization of the YABBY gene family.

Silicon plays a vital role in plant growth. However, molecular mechanisms in response to silicon have not previously been studied in wheat. In this study, we used RNA-seq technology to identify differentially expressed genes (DEGs) in wheat seedlings treated with silicon. Results showed that many wheat genes responded to silicon treatment, including 3057 DEGs, of which 6.25% (191/3057) were predicted transcription factors (TFs). Approximately 14.67% (28 out of 191) of the differentially expressed TFs belonged to the MYB TF family. Gene ontology (GO) enrichment showed that the highly enriched DEGs were responsible for secondary biosynthetic processes. According to KEGG pathway analysis, the DEGs were related to chaperones and folding catalysts, phenylpropanoid biosynthesis, and protein processing in the endoplasmic reticulum. Moreover, 411 R2R3-MYB TFs were identified in the wheat genome, all of which were classified into 15 groups and accordingly named S1–S15. Among them, 28 were down-regulated under silicon treatment. This study revealed the essential role of MYB TFs in the silicon response mechanism of plants, and provides important genetic resources for breeding silicon-tolerant wheat.

Additional file 1: Figure S1. Distribution of line and parent means for each trait in three levels of P treatments.

Identification of genes for tolerance against phosphorus (P) deficiency is important for wheat production in P-deficient soils. Nine root system architecture (RSA) and root biomass-related traits (RBT) in 198 double haploid lines derived from cross between Yangmai 16/Zhongmai 895 were characterized under zero (control), low, and high P treatments (KH2PO4 contents: 0, 0.005, 0.25 mmol/L, respectively) in hydroponic culture, and the DH lines and parents were genotyped using Wheat 660K SNP array. All traits showed significant variations among the DH lines with high heritabilities (0.76 to 0.91) and high correlations (r =0.59 to 0.98) with each other. Inclusive composite interval mapping using 10,242 markers identified 34 QTLs for all traits in the three P treatments. Of these, 11 QTLs under low P condition on chromosomes 2BL, 4BS (2 QTLs), 4DS (2), 6BL (2), 7AL (2), and 7BL (2) for root length (RL), root tip number (RTN) and ratio of root to shoot dry weight (RRS) explained 4.6 - 20.4% of the phenotypic variances. QRRS.caas-4DS (16.64 - 30.66 Mb) was detected in all three P treatments and accounted for 8.4 to 20.4% of the phenotypic variances. Seven QTLs clusters (C1 to C7) were mapped on chromosomes 3DL, 4BS, 4DS, 6BL, 7AS, 7AL and 7BL, of which five (C3 to C7) were detected under low P condition. Cluster C5 on chromosome 7AS (AX-109955164 - AX-109445593) played the key role in modulating RL, RTN and ROSA, with the favorable allele coming from Zhongmai 895. SNPs closely linked to QTLs and clusters could be used for improving root nutrient-use efficiency traits in future breeding.

Proteinaceous α-amylase inhibitors have specialized activities that make some strong inhibition of α-amylases. New α-amylase inhibitors continue to be discovered so far. A proteinaceous α-amylase inhibitor CL-AI was isolated and identified from chickpea seeds. CL-AI, encoded by Q9SMJ4, was a storage legumin precursor containing one α-chain and one β-chain, and each chain possessed a same conserved cupin domain. Amino acid mutation and deficiency of cupin domain would lead to loss of α-amylase inhibitory activity, indicating that it was essential for inhibitory activity. CL-AI(α + β) in its single stranded state in vivo had inhibitory activity. After it was processed into one α-chain and one β-chain, the two chains were connected to each other via disulfide bond, which would cover the cupin domains and lead to the loss of inhibitory activity. The CL-AI(α + β), α-chain and β-chain could inhibit various α-amylases and delay the seed germination of wheat, rice and maize as well as the growth and development of potato beetle larva. Two cupin proteins, Glycinin G1 in soybean and Glutelinin in rice were also found to have inhibitory activity. Our results indicated that the cupin domain is involved in α-amylase inhibitory activity and the proteins with a cupin domain may be a new kind of proteinaceous α-amylase inhibitor.

As a large family of regulatory proteins, NAC (for NAM, ATAF1,2 and CUC2) proteins play important roles in various plant developmental processes and response to environmental stresses. Several studies have investigated the role of NAC transcription factors during these processes. In the present study, a gene encoding a NAC protein from chickpea (Cicer arietinum L.), CarNAC2, which encodes a putative protein of 191 amino acids, was isolated and characterized. Analyses of mRNA levels revealed that the expression of CarNAC2 was up-regulated by drought and ABA (abscisic acid). CarNAC2::GFP fusion protein was localized in the nucleus. Yeast one-hybrid assay showed that CarNAC2 possesses transcriptional activation activity which was located in the C-terminal region. Overexpression of CarNAC2 enhanced drought tolerance in transgenic Arabidopsis plants. In addition, transgenic plant overexpressing CarNAC2 displayed lower germination vigor and later blooming than wild type plants. Overall, our findings suggest that CarNAC2 protein as a transcriptional activator is involved in response to drought stress and various developmental processes in chickpea.

Haloxylon ammodendron (Chenopodiaceae) is a dominant shrubby or sub-arboreal perennial. During the torrid and arid summer, annual assimilative branches of H. ammodendron are often observed slow growing (even ceasing growth) and gradually turning in color from green to brilliant yellow, even with some drying up and falling off. The pivotal factor causing this phenomenon is still unknown. Here we report that it is the high desert surface layer (0–5 cm) temperature (DSLT) that causes H. ammodendron plants to display this phenomenon. Damage is caused by high DSLT around the stem basal part of H. ammodendron plants, with stress threshold value being 55 °C. Based on the color changes of the annual assimilative branches, damage responses of H. ammodendron could be broadly divided into three degrees of mild, moderate and high damage that visually can be detected. DSLT stress also destroys the redox homeostasis in H. ammodendron plants, bringing about physiological damages. Since high DSLT is one of the inherent factors of desert habitat conditions, our results suggest that it will have importance to investigate the direct effect of high DSLT stress also on other desert plants.

Chickpea (Cicer arietinum L.) is an important pulse crop grown mainly in the arid and semi-arid regions of the world. Due to its taxonomic proximity with the model legume Medicago truncatula and its ability to grow in arid soil, chickpea has its unique advantage to understand how plant responds to drought stress. In this study, an oligonucleotide microarray was used for analyzing the transcriptomic profiles of unigenes in leaf and root of chickpea seedling under drought stress, respectively. Microarray data showed that 4,815 differentially expressed unigenes were either ≥ 2-fold up- or ≤ 0.5-fold down-regulated in at least one of the five time points during drought stress. 2,623 and 3,969 unigenes were time-dependent differentially expressed in root and leaf, respectively. 110 pathways in two tissues were found to respond to drought stress. Compared to control, 88 and 52 unigenes were expressed only in drought-stressed root and leaf, respectively, while nine unigenes were expressed in both the tissues. 1,922 function-unknown unigenes were found to be remarkably regulated by drought stress. The expression profiles of these time-dependent differentially expressed unigenes were useful in furthering our knowledge of molecular mechanism of plant in response to drought stress.

Late-embryogenesis abundant (LEA) proteins have been reported to be closely correlated with the acquisition of desiccation tolerance during seed development and response of plant to drought, salinity, and freezing, etc. In this study, a LEA gene, CarLEA4 (GenBank accession no. GU247511), was isolated from chickpea based on a cDNA library constructed with chickpea seedling leaves treated by polyethylene glycol (PEG). CarLEA4 contained two exons and one intron within genomic DNA sequence and encoded a putative polypeptide of 152 amino acids. CarLEA4 had a conserved pfam domain, and showed high similarity to the group 4 LEA proteins in secondary structure. It was localized in the nucleus. The transcripts of CarLEA4 were detected in many chickpea organs including seedling leaves, stems, roots, flowers, young pods, and young seeds. CarLEA4 was inhibited by leaf age and showed expression changes in expression during seed development, pod development and germination. Furthermore, the expression of CarLEA4 was strongly induced by drought, salt, heat, cold, ABA, IAA, GA(3) and MeJA. Our results suggest that CarLEA4 encodes a protein of LEA group 4 and may be involved in various plant developmental processes and abiotic stress responses.

We studied the diversity of endophytic fungi associated with Ferula sinkiangensis K. M. Shen.Endophytic fungi from different years (1-2 years, 3-4 years and5 years) and different parts (root, stemand leaf) of Ferula sinkiangensis K. M. Shen were isolated by tissue expand method. Strains were classified by morphology and similarity of internal transcribed spacer (ITS) sequence by Clustal X method. Composition, diversity and preference of endophytic fungal community were analyzed by the isolation rate (IR), isolation frequency (IF), Shannon-Wiener biodiversity index (H'), Margalef Richness index (R).In total 140 endophytic fungi were isolated from F. sinkiangensis K. M. Shen and classified into 18 genera. Among the 140 isolates, Aureobasidium (25.7%), Alternaria (16.4%) and Phyllosticta (15.7%) were the dominant genera. The isolation results show that there were some notable differences between distribution and composition of the endophytic fungi isolated from different years and different parts of Ferula sinkiangensis K. M. Shen. Meanwhile, a certain degree of years and tissue preference were also obvious.The results obtained in this study will be helpful to exploit the endophytic fungal resources of Ferula sinkiangensis K. M. Shen, which can also provide a new way for the realization of the artificial breeding of Ferula sinkiangensis K. M. Shen.

F-box protein family has been found to play important roles in plant development and abiotic stress responses via the ubiquitin pathway. In this study, an F-box gene CarF-box1 (for Cicer arietinum F-box gene 1, Genbank accession no. GU247510) was isolated based on a cDNA library constructed with chickpea seedling leaves treated by polyethylene glycol. CarF-box1 encoded a putative protein with 345 amino acids and contained no intron within genomic DNA sequence. CarF-box1 is a KFB-type F-box protein, having a conserved F-box domain in the N-terminus and a Kelch repeat domain in the C-terminus. CarF-box1 was localized in the nucleus. CarF-box1 exhibited organ-specific expression and showed different expression patterns during seed development and germination processes, especially strongly expressed in the blooming flowers. In the leaves, CarF-box1 could be significantly induced by drought stress and slightly induced by IAA treatment, while in the roots, CarF-box1 could be strongly induced by drought, salinity and methyl jasmonate stresses. Our results suggest that CarF-box1 encodes an F-box protein and may be involved in various plant developmental processes and abiotic stress responses.