Winter Wheat Freeze Survival: Transcription Factors; Co-Expression and Co-Regulation of Genes: A Microarray Story (original) (raw)
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BMC Plant Biology, 2009
Background: In order to identify genes that might confer and maintain freeze resistance of winter wheat, a comparative transcriptome analysis was performed between control and 4 wk coldacclimated crown tissue of two winter wheat lines that differ in field freeze survival. The lines, generated by azide mutagenesis of the winter wheat cultivar 'Winoka' were designated FR (75% survival) and FS (30% survival). Using two winter lines for this comparative analysis removed the influence of differential expression of the vernalization genes and allowed our study to focus on Cbf genes located within the Fr-A2 allele independent of the effect of the closely mapped Vrn allele.
Genes & Genetic Systems, 2005
The cold acclimation process in plants is primarily regulated through the signal transduction pathways that lead to the induction and enhancement of expression of different sets of Cor / Lea genes. Winter wheat 'Mironovskaya 808' (M808) exhibited a much higher level of freezing tolerance than spring wheat 'Chinese Spring' (CS), and the difference became clearer after the long-term cold acclimation. To understand the molecular basis of this cultivar difference, we isolated two CBF/DREB1 homologs, Wcbf2 , which are the candidate gene for a transcription factor of the Cor / Lea genes. Expression of the Wcbf2 gene was induced rapidly by low temperature (LT) and drought but not by abscisic acid (ABA). The gene expression was temporal and at least twice up-regulated by LT. The first up-regulation occurred within 1-4 h, which might correspond to the rapid response to LT, while the second up-regulation occurred during 2-3 weeks of cold acclimation. After the second up-regulation, the amount of Wcbf2 transcript greatly decreased in CS, while it increased again in M808 after 4 weeks until 9 weeks (end of the test period). The maintenance of this high level of the Wcbf2 transcript might represent the long-term effect of cold acclimation. The activation of Cor/Lea genes followed the accumulation of Wcbf2 transcript suggested direct involvement of the Wcbf2 gene in the induction and enhancement of the Cor/Lea gene expression. The cultivar difference in freezing tolerance developed during different stages of cold acclimation can be at least partly explained by the differential and coordinated regulation of the predicted Cor/Lea gene signal transduction pathway that is mediated by the CBF/DREB1 transcription factors in common wheat.
Journal of Experimental Botany, 2005
Vrn-1/Fr-1 chromosomal regions of common wheat possess major QTLs for both winter hardiness (Fr) and vernalization requirement (Vrn). The Vrn-1/Fr-1 intervals are assigned to long arms of the homoeologous group 5 chromosomes. To investigate the role of the Vrn-1/Fr-1 intervals on the low-temperature (LT) inducibility of wheat Cor/Lea genes and its putative transcription factor gene Wcbf2, LT response of these genes was monitored using near-isogenic lines (NILs) for the Vrn-1 loci. The Wcbf2 transcript accumulated rapidly after LT treatment and remained at a high level in lines without any dominant Vrn-1 alleles. By contrast, the Wcbf2 transcript level was greatly reduced in lines carrying the Vrn-1 alleles. The Vrn-1 NILs accumulated much lower amounts of Cor/Lea transcripts and COR/LEA proteins than the non-carrier line. The observed patterns and levels of gene expression, particularly in the Vrn-A1 NIL, agreed with the higher sensitivity to freezing damage in this line than in the noncarrier line. Up-regulation of the expression of the WAP1 gene, a candidate of the Vrn-1 loci, was much delayed in the non-carrier line than all the NILs carrying the Vrn-1 loci. Neither positive nor negative relationships were found between the WAP1 expression and the Cbf2/Cor/ Lea expression. These results support the intimate relationship between the Cbf2/Cor/Lea expression and the level of freezing tolerance, and suggest that a functional Fr-A1 allele linked to the vrn-A1 allele, instead of the vernalization gene itself, plays a major role in regulating the CBF-mediated Cor/lea gene expression in wheat.
Physiologia Plantarum, 2004
Expression profiles of a set of Cor/Lea genes were assessed during early stages of cold acclimation in seedlings of two wheat cultivars, which showed contrasting levels of freezing tolerance. These Cor/Lea family members consisted of three EST clones and 13 previously identified cDNA clones of wheat and rye. Northern blot analysis using RNA extracted from seedling leaves and roots showed that most of the genes exhibited a quite similar time-course of expression, although with different expression levels: They rapidly responded to low temperature and their transcript levels reached high plateaus within 3-5 days. The overall gene expression profiles were correlated with the time-dependent development and the level of freezing tolerance under low temperature in the two cultivars. Western blot analysis of protein accumulation further verified this observation. Abscissic acid response was proved for at least four genes. Light was stimulatory to most of the genes, and this positive light response associated with low temperature occurred not only in leaf-specific genes but also in leaf/root-expressed genes. Taken together, the present results suggest that the Cor/Lea gene family represents a major group of downstream genes involved in the ABA-dependent and -independent signal pathways and that most of them are co-regulated in determining freezing tolerance in wheat seedlings.
Plant Molecular Biology, 2007
Freezing tolerance in plants develops through acclimation to cold by growth at low, above-freezing temperatures. Wheat is one of the most freezing-tolerant plants among major crop species and the wide range of freezing tolerance among wheat cultivars makes it an excellent model for investigation of the genetic basis of cold tolerance. Large numbers of genes are known to have altered levels of expression during the period of cold acclimation and there is keen interest in deciphering the signaling and regulatory pathways that control the changes in gene expression associated with acquired freezing tolerance. A 5740 feature cDNA amplicon microarray that was enriched for signal transduction and regulatory genes was constructed to compare changes in gene expression in a highly cold-tolerant winter wheat cultivar CDC Clair and a less tolerant spring cultivar, Quantum. Changes in gene expression over a time course of 14 days detected over 450 genes that were regulated by cold treatment and were differentially regulated between spring and winter cultivars, of these 130 are signaling or regulatory gene candidates, including: transcription factors, protein kinases, ubiquitin ligases and GTP, RNA and calcium binding proteins. Dynamic changes in transcript levels were seen at all periods of cold acclimation in both cultivars. There was an initial burst of gene activity detectable during the first day of CA, during which 90% of all genes with increases in transcript levels became clearly detectable and early expression differential between the two cultivars became more disparate with each successive period of cold acclimation.
BMC Genomics, 2011
Background To identify the genes involved in the development of low temperature (LT) tolerance in hexaploid wheat, we examined the global changes in expression in response to cold of the 55,052 potentially unique genes represented in the Affymetrix Wheat Genome microarray. We compared the expression of genes in winter-habit (winter Norstar and winter Manitou) and spring-habit (spring Manitou and spring Norstar)) cultivars, wherein the locus for the vernalization gene Vrn-A1 was swapped between the parental winter Norstar and spring Manitou in the derived near-isogenic lines winter Manitou and spring Norstar. Global expression of genes in the crowns of 3-leaf stage plants cold-acclimated at 6°C for 0, 2, 14, 21, 38, 42, 56 and 70 days was examined. Results Analysis of variance of gene expression separated the samples by genetic background and by the developmental stage before or after vernalization saturation was reached. Using gene-specific ANOVA we identified 12,901 genes (at p < 0.001) that change in expression with respect to both genotype and the duration of cold-treatment. We examined in more detail a subset of these genes (2,771) where expression was highly influenced by the interaction between these two main factors. Functional assignments using GO annotations showed that genes involved in transport, oxidation-reduction, and stress response were highly represented. Clustering based on the pattern of transcript accumulation identified genes that were up or down-regulated by cold-treatment. Our data indicate that the cold-sensitive lines can up-regulate known cold-responsive genes comparable to that of cold-hardy lines. The levels of expression of these genes were highly influenced by the initial rate and the duration of the gene's response to cold. We show that the Vrn-A1 locus controls the duration of gene expression but not its initial rate of response to cold treatment. Furthermore, we provide evidence that Ta.Vrn-A1 and Ta.Vrt1 originally hypothesized to encode for the same gene showed different patterns of expression and therefore are distinct. Conclusion This study provides novel insight into the underlying mechanisms that regulate the expression of cold-responsive genes in wheat. The results support the developmental model of LT tolerance gene regulation and demonstrate the complex genotype by environment interactions that determine LT adaptation in winter annual cereals.
The expression of several Cbf genes at the FrA2 locus is linked to frost resistance in wheat
Molecular Genetics and Genomics, 2005
The C-repeat binding factor (Cbf) gene family has been shown to have a critical role in the regulation of low-temperature stress response in Arabidopsis. In Triticum monococcum, a locus carrying a family of Cbf-like genes, orthologs of Arabidopsis Cbf genes, is tightly linked to the frost tolerance locus Fr-A m 2, representing candidates for the differences in frost tolerance mapped at this locus. In this work we show that several Cbf genes have dramatically different levels of induction after cold exposure in hexaploid wheat. The Cbf-transcription levels differ between substitution and single chromosome recombinant lines carrying different 5A chromosomes or chromosome segments of the chromosome 5A from frost-tolerant and frost-sensitive wheat varieties. When the expression of eight Cbf genes, previously mapped at the Fr-A2 locus was investigated with gene specific primers using real-time RT-PCR, three Cbf sequences (Cbf1A, Cbf1C, Cbf7) showed a significantly higher relative transcription level (more than fourfold change) in lines differing for the Fr-A2 region. Differences in Cbf expression were also associated with a variation in frost tolerance. These results suggest that the amount of some Cbf mRNAs might be a critical factor for determining the level of frost tolerance in wheat.
Molecular and General Genetics, 2000
Although cold acclimation in cereals involves the expression of many cold-regulated genes, genetic studies have shown that only very few chromosomal regions carry loci that play an important role in frost tolerance. To investigate the genetic relationship between frost tolerance and the expression of cold-regulated genes, the expression and regulation of the wheat homolog of the barley cold-regulated gene cor14b was studied at various temperatures in frost-sensitive and frost-tolerant wheat genotypes. At 18/15 °C (day/night temperatures) frost-tolerant plants accumulated cor14b mRNAs and expressed COR14b proteins, whereas the sensitive plants did not. This result indicates that the threshold temperature for induction of the wheat cor14b homolog is higher in frost-resistant plants, and allowed us to use this polymorphism in a mapping approach. Studies made with chromosome substitution lines showed that the polymorphism for the threshold induction temperature of the wheat cor14b homolog is controlled by a locus(i) located on chromosome 5A of wheat, while the cor14b gene was mapped in Triticum monococcum on the long arm of chromosome 2Am. The analysis of single chromosome recombinant lines derived from a cross between Chinese Spring/Triticum spelta 5A and Chinese Spring/Cheyenne 5A identified two loci with additive effects that are involved in the genetic control of cor14b mRNA accumulation. The first locus was tightly linked to the marker psr911, while the second one was located between the marker Xpsr2021 and Frost resistance 1 (Fr1).
Transcriptome changes triggered by a short-term low temperature stress in winter wheat
Zemdirbyste-Agriculture
Abiotic stresses alter the expression of multiple genes in plants allowing them to accommodate to hostile environmental conditions. Exposure to low temperatures in the autumn prior to winter is a crucial environmental factor determining an increase in freezing tolerance and winter hardiness in temperate plants. The objective of this study was to evaluate transcriptome changes under a short-term low temperature stress using an RNA-Seq approach in winter wheat (Triticum aestivum L.). Significant alterations were observed for nuclear transcriptome of winter wheat, whereas the expression profiles of organellar genes were much less responsive to low temperature stress. In total, there were 15,042 nuclear genes with significantly (FDR < 0.05) altered expression profiles caused by exposure to low temperature. From this number, a total of 2,466 genes had a substantially (log 2 FC > 2 or log 2 FC < −2) affected expression profile. The highest number of upregulated genes was observed from chromosomes in homoeologous group 5, followed by group 2. Differentially expressed genes (DEGs) with the most extreme upregulation encompassed CBFIIId-12.1, WRKY transcription factor 55-like, and a group of genes related to jasmonate signalling pathway.
Biotechnology & Biotechnological Equipment, 2014
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