Identification of novel C-repeat binding factor (CBF) genes in rye (Secale cereale L.) and expression studies

Genome-wide identification of the plant homeodomain-finger family in rye and ScPHD5 functions in cold tolerance and flowering time

KEY MESSAGE

111 PHD genes were newly identified in rye genome and ScPHD5's role in regulating cold tolerance and flowering time was suggested. Plant homeodomain (PHD)-finger proteins regulate the physical properties of chromatin and control plant development and stress tolerance. Although rye (Secale cereale L.) is a major winter crop, PHD-finger proteins in rye have not been studied. Here, we identified 111 PHD genes in the rye genome that exhibited diverse gene and protein sequence structures. Phylogenetic tree analysis revealed that PHDs were genetically close in monocots and diverged from those in dicots. Duplication and synteny analyses demonstrated that ScPHDs have undergone several duplications during evolution and that high synteny is conserved among the Triticeae species. Tissue-specific and abiotic stress-responsive gene expression analyses indicated that ScPHDs were highly expressed in spikelets and developing seeds and were responsive to cold and drought stress. One of these genes, ScPHD5, was selected for further functional characterization. ScPHD5 was highly expressed in the spike tissues and was localized in the nuclei of rye protoplasts and tobacco leaves. ScPHD5-overexpressing Brachypodium was more tolerant to freezing stress than wild-type (WT), with increased CBF and COR gene expression. Additionally, these transgenic plants displayed an extremely early flowering phenotype that flowered more than two weeks earlier than the WT, and vernalization genes, rather than photoperiod genes, were increased in the WT. RNA-seq analysis revealed that diverse stress response genes, including HSPs, HSFs, LEAs, and MADS-box genes, were also upregulated in transgenic plants. Our study will help elucidate the roles of PHD genes in plant development and abiotic stress tolerance in rye.

Genome-wide identification and expression analysis of the CBF transcription factor family in Lolium perenne under abiotic stress

C-repeat binding factor (CBF) subfamily genes encoding transcriptional activators are members of the AP2/ERF superfamily. CBFs play important roles in plant tolerance to abiotic stress. In this study, we identified and analyzed the structure, phylogeny, conserved motifs, and expression profiles of 12 CBFs of the grass species Lolium perenne cultured under abiotic stress. The identified LpCBFs were grouped into three phylogenetic clades according to their protein structures and motif organizations. LpCBF expression was differentially induced by cold, heat, water deficit, salinity, and abscisic acid, among which cold treatment induced LpCBF gene expression significantly. Furthermore, association network analysis indicated that different proteins, including certain stress-related proteins, potentially interact with LpCBFs. Altogether, these findings will enhance our understanding of LpCBFs protein structure and function in the regulation of L. perenne stress responses. Our results will provide valuable information for further functional research of LpCBF proteins in L. perenne stress resistance.

The Triticeae CBF Gene Cluster-To Frost Resistance and Beyond

The pivotal role of CBF/DREB1 transcriptional factors in Triticeae crops involved in the abiotic stress response has been highlighted. The CBFs represent an important hub in the ICE-CBF-COR pathway, which is one of the most relevant mechanisms capable of activating the adaptive response to cold and drought in wheat, barley, and rye. Understanding the intricate mechanisms and regulation of the cluster of CBF genes harbored by the homoeologous chromosome group 5 entails significant potential for the genetic improvement of small grain cereals. Triticeae crops seem to share common mechanisms characterized, however, by some peculiar aspects of the response to stress, highlighting a combined landscape of single-nucleotide variants and copy number variation involving CBF members of subgroup IV. Moreover, while chromosome 5 ploidy appears to confer species-specific levels of resistance, an important involvement of the ICE factor might explain the greater tolerance of rye. By unraveling the genetic basis of abiotic stress tolerance, researchers can develop resilient varieties better equipped to withstand extreme environmental conditions. Hence, advancing our knowledge of CBFs and their interactions represents a promising avenue for improving crop resilience and food security.

Identification and Analysis of the CBF Gene Family in Three Species of Acer under Cold Stress

The C-Repeat Binding Factor (CBF) gene family has been identified and characterized in multiple plant species, and it plays a crucial role in responding to low temperatures. Presently, only a few studies on tree species demonstrate the mechanisms and potential functions of CBFs associated with cold resistance, while our study is a novel report on the multi-aspect differences of CBFs among three tree species, compared to previous studies. In this study, genome-wide identification and analysis of the CBF gene family in Acer truncatum, Acer pseudosieboldianum, and Acer yangbiense were performed. The results revealed that 16 CBF genes (five ApseCBFs, four AcyanCBFs, and seven AtruCBFs) were unevenly distributed across the chromosomes, and most CBF genes were mapped on chromosome 2 (Chr2) and chromosome 11 (Chr11). The analysis of phylogenetic relationships, gene structure, and conserved motif showed that 16 CBF genes could be clustered into three subgroups; they all contained Motif 1 and Motif 5, and most of them only spanned one exon. The cis-acting elements analysis showed that some CBF genes might be involved in hormone and abiotic stress responsiveness. In addition, CBF genes exhibited tissue expression specificity. High expressions of ApseCBF1, ApseCBF3, AtruCBF1, AtruCBF4, AtruCBF6, AtruCBF7, and ApseCBF3, ApseCBF4, ApseCBF5 were detected on exposure to low temperature for 3 h and 24 h. Low expressions of AtruCBF2, AtruCBF6, AtruCBF7 were detected under cold stress for 24 h, and AtruCBF3 and AtruCBF5 were always down-regulated under cold conditions. Taken together, comprehensive analysis will enhance our understanding of the potential functions of the CBF genes on cold resistance, thereby providing a reference for the introduction of Acer species in our country.

Transcription-associated metabolomic profiling reveals the critical role of frost tolerance in wheat

BACKGROUND

Low temperature is a crucial stress factor of wheat (Triticum aestivum L.) and adversely impacts on plant growth and grain yield. Multi-million tons of grain production are lost annually because crops lack the resistance to survive in winter. Particularlly, winter wheat yields was severely damaged under extreme cold conditions. However, studies about the transcriptional and metabolic mechanisms underlying cold stresses in wheat are limited so far.

RESULTS

In this study, 14,466 differentially expressed genes (DEGs) were obtained between wild-type and cold-sensitive mutants, of which 5278 DEGs were acquired after cold treatment. 88 differential accumulated metabolites (DAMs) were detected, including P-coumaroyl putrescine of alkaloids, D-proline betaine of mino acids and derivativ, Chlorogenic acid of the Phenolic acids. The comprehensive analysis of metabolomics and transcriptome showed that the cold resistance of wheat was closely related to 13 metabolites and 14 key enzymes in the flavonol biosynthesis pathway. The 7 enhanced energy metabolites and 8 up-regulation key enzymes were also compactly involved in the sucrose and amino acid biosynthesis pathway. Moreover, quantitative real-time PCR (qRT-PCR) revealed that twelve key genes were differentially expressed under cold, indicating that candidate genes POD, Tacr7, UGTs, and GSTU6 which were related to cold resistance of wheat.

CONCLUSIONS

In this study, we obtained the differentially expressed genes and differential accumulated metabolites in wheat under cold stress. Using the DEGs and DAMs, we plotted regulatory pathway maps of the flavonol biosynthesis pathway, sucrose and amino acid biosynthesis pathway related to cold resistance of wheat. It was found that candidate genes POD, Tacr7, UGTs and GSTU6 are related to cold resistance of wheat. This study provided valuable molecular information and new genetic engineering clues for the further study on plant resistance to cold stress.

Association mapping of autumn-seeded rye (Secale cereale L.) reveals genetic linkages between genes controlling winter hardiness and plant development

Winter field survival (WFS) in autumn-seeded winter cereals is a complex trait associated with low temperature tolerance (LTT), prostrate growth habit (PGH), and final leaf number (FLN). WFS and the three sub-traits were analyzed by a genome-wide association study of 96 rye (Secale cereal L.) genotypes of different origins and winter-hardiness levels. A total of 10,244 single nucleotide polymorphism (SNP) markers were identified by genotyping by sequencing and 259 marker-trait-associations (MTAs; p < 0.01) were revealed by association mapping. The ten most significant SNPs (p < 1.49e−04) associated with WFS corresponded to nine strong candidate genes: Inducer of CBF Expression 1 (ICE1), Cold-regulated 413-Plasma Membrane Protein 1 (COR413-PM1), Ice Recrystallization Inhibition Protein 1 (IRIP1), Jasmonate-resistant 1 (JAR1), BIPP2C1-like protein phosphatase, Chloroplast Unusual Positioning Protein-1 (CHUP1), FRIGIDA-like 4 (FRL4-like) protein, Chalcone Synthase 2 (CHS2), and Phenylalanine Ammonia-lyase 8 (PAL8). Seven of the candidate genes were also significant for one or several of the sub-traits supporting the hypothesis that WFS, LTT, FLN, and PGH are genetically interlinked. The winter-hardy rye genotypes generally carried additional allele variants for the strong candidate genes, which suggested allele diversity was a major contributor to cold acclimation efficiency and consistent high WFS under varying field conditions.

Identification and characterization of AnICE1 and AnCBFs involved in cold tolerance from Ammopiptanthus nanus

The ICE-CBF-COR pathway plays a vital role in improving the cold tolerance of plants. As an evergreen small shrub, Ammopiptanthus nanus has a high tolerance to cold stress because of its special growth conditions. Regrettably, no cold-responsive genes in the ICE-CBF-COR pathway have been reported in A. nanus. In the current study, we isolated AnICE1, AnCBF1, and AnCBF2 in A. nanus and analyzed their sequence structure. Evolutionary analysis indicated that these genes are most closely related to those from Ammopiptanthus mongolicus, Glycine max, Spatholobus suberectus, and Cajanus cajan, all belonging to the Fabaceae. Expression analysis showed that the expression levels of these genes were induced under cold stress and treatment with several plant hormones. As a critical upstream regulator in the ICE-CBF-COR pathway, the function of AnICE1 was further identified. The subcellular localization indicated that AnICE1 is predominantly localized in the plasma membrane and less in the nucleus. Overexpression of AnICE1 in Arabidopsis thaliana improved seed germination and growth of transgenic seedlings during cold stress. Moreover, some physiological indices such as relative electrical conductivity, contents of proline and malondialdehyde, catalase activity, and Nitro Blue tetrazolium and 3.3'-diaminobenzidine staining were investigated by transient expression in A. nanus seedlings and stable overexpression in A. thaliana. These results indicated that AnICE1 enhanced cold tolerance in A. nanus and transgenic A. thaliana. This study is significant for understanding the cold-resistant mechanism of ICE and CBF genes in A. nanus.

Physiological effects of different stubble height and freeze-thaw stress on Secale cereale L. seedlings

BACKGROUND

As a biennial plant, Secale cereale L is usually harvested in the autumn in the northern part of China where the temperature difference between day and night is of great disparity Through the pot experiment, the seedlings were cut to 2, 6 and 10 cm stubble height, and the simulated freeze-thaw (FT) stress (10/- 5 °C) was carried out after 6 days regrowth. The physiological effects of FT with different stubble height were revealed by analyzing the relative water content (RWC), osmotic adjustment substance concentration (soluble sugar and protein), membrane peroxidation (MDA) and catalase (CAT) activity.

RESULTS

The results demonstrated that under freeze stress (- 5 °C), the content of soluble protein and MDA decreased and the seedlings of 2 cm treatment kept higher level of soluble protein and MDA, while the seedlings of 6 and 10 cm treatments kept higher level of the RWC, soluble sugar content, and CAT activity. After FT stress, the content of soluble sugar and protein, RWC in the 6 cm treatment were higher than those in 2 cm and 10 cm treatments, and the CAT activity in 10 cm treatment was the highest while the MDA content is lower.

CONCLUSION

These data suggest that keeping high stubble height is more adaptive for short-term FT stress.

AP2/ERF, an important cold stress-related transcription factor family in plants: A review

Increasing the vulnerability of plants especially crops to a wide range of cold stress reduces plant growth, development, yield production, and plant distribution. Cold stress induces physiological, morphological, biochemical, phenotypic, and molecular changes in plants. Transcription factor (TF) is one of the most important regulators that mediate gene expression. TF is activated by the signal transduction pathway, together with cis-acting element modulate the transcription of cold-responsive genes which contribute to increasing cold tolerance in plants. Here, AP2/ERF TF family is one of the most important cold stress-related TF families that along with other TF families, such as WRKY, bHLH, bZIP, MYB, NAC, and C2H2 interrelate to enhance cold stress tolerance. Over the past decade, significant progress has been found to solve the role of transcription factors (TFs) in improving cold tolerance in plants, such as omics analysis. Furthermore, numerous studies have identified and characterized the complexity of cold stress mechanisms among TFs or between TFs and other factors (endogenous and exogenous) including phytohormones, eugenol, and light. The role, function, and relationship among these TFs or between TFs and other factors to enhance cold tolerance still need to be clarified. Here, the current study analysed the role of AP2/ERF TF and the linkages among AP2/ERF with MYB, WRKY, bZIP, bHLH, C2H2, or NAC against cold stress tolerance.

Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential

Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.

Assessment of economic traits’ inheritance of winter rye at intraspecific hybridization

Intraspecific hybridization in winter rye selection (Secale cereale L. ssp. cereale) is a source of intrapopulation genotypic variability with the possibility of using the effect of interpopulation heterosis. The inheritance of the crop yield, the regeneration degree after overwintering and the weight of 1000 grains in reciprocal and back winter rye F1 intervarietal hybrids was established. Different types of inheritance prevailed in reciprocal and back crossings. The regeneration inheritance and the weight of 1000 grains had a specificity. Traits’ overdominance prevailed in reciprocal crossings (45% of hybrids). The yield of reciprocal hybrids was inherited mainly according to the overdominance type (68% of the hybrids), the weight of 1000 grains - according to the intermediate type (50%), regeneration - according to the overdominance type and transitionally - equally (36% each). Intermediate traits’ inheritance prevailed in back crossings (62% of hybrids). The rarest type of traits’ inheritance was complete dominance of the best parent (2 hybrids). 4 F1 hybrids with the greatest overdominance in yield, regeneration, weight of 1000 grains were allocated. The degree of true and competitive heterosis of reciprocal F1 hybrids in terms of yield was determined. The level of true heterosis of F1 hybrids in terms of yield varied within 6-123%. Economically significant competitive heterosis in terms of yield was established in 7 F1 hybrids.

Isolation and expression analysis of two novel C-repeat binding factor (CBF) genes involved in plant growth and abiotic stress response in mangrove Kandelia obovata

Kandelia obovata is one of the cold tolerant mangrove plants along the China coast. To reveal the cold tolerant mechanism of K. obovata, the present work isolated two CBF/DREB1 genes (designated KoCBF1 and KoCBF3) from cold-stressed K. obovata and characterized their expression profiles in various organs and in response to multiple abiotic stresses. The deduced proteins of KoCBF1 and 3 all contain specific features of CBFs, and show high similarity to AmCBF1 and 3 from Avicennia marina, respectively. Different expression patterns of the two CBF orthologous under various abiotic stresses and exogenous hormone suggested that they may have different regulators and be involved in different regulatory pathway. The high basal and cold induced expression of the two genes indicated that they may all play important roles in growth and cold resistance of plants. The significant induction of KoCBF3 after salt and lead (Pb²⁺) treatments suggested that this CBF gene may also participate in response to salinity and heavy metal stresses. This study will provide a better understanding of CBF-regulated stress-resistant mechanism, which may be benefit in mangrove biotechnological breeding, high-latitude transplanting, and bioremediation of heavy metal pollutions.

Influence of CNV on transcript levels of HvCBF genes at Fr-H2 locus revealed by resequencing in resistant barley cv. 'Nure' and expression analysis

Resequencing in resistant cultivar 'Nure' and structural comparison with the same region of susceptible 'Morex' was performed in order to gain a better insight into barley Frost-resistance-H2 locus. Accurate annotation showed copy number variation (CNV) in the proximal part of the locus. In 'Nure', two exact copies of the HvCBF4-HvCBF2A region and one of the HvCBF4-HvCBF2B segment were observed, while in 'Morex' the corresponding region harboured a single HvCBF4-HvCBF2A (22 kb) segment. Abundance and diversity of repetitive element classes, gene function gain/losses, regulatory motifs and SNPs in gene sequences were identified. An expression study of key HvCBFs with/without CNV on selected genotypes contrasting for frost resistance and estimated HvCBF4-HvCBF2B copy number (2-10 copies) was also performed. Under light stimulus at warm temperature (23 °C), CNV of HvCBF2A and HvCBF4 correlated with their expression levels and reported frost resistance of genotypes; moreover, expression levels of HvCBF2A and HvCBF14 were strongly correlated (r = 0.908, p < 0.01). On the other hand, frost resistance correlated to HvCBF14 expression (r = 0.871, p < 0.01) only after cold induction (6°C) in the dark. A complex interplay of HvCBFs expression levels under different light/temperature stimuli is discussed in light of CNV and presence/number of regulatory elements that integrate different signal transduction pathways.

Identification of CBF Transcription Factors in Tea Plants and a Survey of Potential CBF Target Genes under Low Temperature

C-repeat binding factors (CBFs) are key signaling genes that can be rapidly induced by cold and bind to the C-repeat/dehydration-responsive motif (CRT/DRE) in the promoter region of the downstream cold-responsive (COR) genes, which play a vital role in the plant response to low temperature. However, the CBF family in tea plants has not yet been elucidated, and the possible target genes regulated by this family under low temperature are still unclear. In this study, we identified five CsCBF family genes in the tea plant genome and analyzed their phylogenetic tree, conserved domains and motifs, and cis-elements. These results indicate that CsCBF3 may be unique in the CsCBF family. This is further supported by our findings from the low-temperature treatment: all the CsCBF genes except CsCBF3 were significantly induced after treatment at 4 °C. The expression profiles of eight tea plant tissues showed that CsCBFs were mainly expressed in winter mature leaves, roots and fruits. Furthermore, 685 potential target genes were identified by transcriptome data and CRT/DRE element information. These target genes play a functional role under the low temperatures of winter through multiple pathways, including carbohydrate metabolism, lipid metabolism, cell wall modification, circadian rhythm, calcium signaling, transcriptional cascade, and hormone signaling pathways. Our findings will further the understanding of the stress regulatory network of CsCBFs in tea plants.