Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Insights into gene expression changes during ice encasement in perennial grasses

ABSTRACT: The predicted increase in frequency and duration of winter warming episodes (WWEs) at the higher northern latitudes is expected to negatively impact the forage production in this region. The formation of non-permeable ice cover due to WWEs could subject the plants to hypoxic or anoxic conditions leading to severe winter damages. Knowledge about molecular mechanisms underlaying various winter stress is crucial to develop cultivars with better winter survival under changing climatic conditions. In the current study, we aimed at identifying genes involved in ice encasement stress responses in a perennial forage grass timothy and study gene expression differentiation due to field survival using timothy cultivars from diverse genetic backgrounds. The LD50 (the number of days under ice that kill 50% of the plants) varied across cultivars and origin. The expression of many genes involved in hypoxia and freezing stress responses were highly upregulated under ice encasement conditions. Functional analysis of DEGs revealed that the upregulated genes were linked to glycolysis, pyruvate metabolism, carbon metabolism, biosynthesis of amino acids while downregulated genes were related to photosynthesis, phenylpropanoid biosynthesis and flavonoid biosynthesis pathways. The results from a current study indicate a substantial overlap of ice encasement stress responses with those of hypoxic and freezing stresses. In addition, the potential strategies leading to higher ice encasement tolerance of timothy are outlined. Furthermore, differences in gene expression between field survivors and original material and the differences between ice encasement responses of northern adapted cultivar and southern adapted cultivar are briefly discussed.

INSTRUMENT(S): Illumina NovaSeq 6000, TruSeq RNA Sample Prep Kit

ORGANISM(S): Phleum pratense

SUBMITTER: Mallikarjuna rao Kovi

PROVIDER: E-MTAB-13705 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The sustainable production of perennial grasses in Northern Norway is at risk due to the ongoing climate change. The predicted increase in temperatures and variable weather patterns are further expected to create challenges for winter survival of timothy. Therefore, knowledge about the molecular mechanisms underlying freezing tolerance is crucial for developing robust cultivars. The current study is aimed at identifying genes involved in the freezing stress response of Timothy and studying gene expression differentiation due to field selection in contrasting environments. Four timothy cultivars, namely Engmo, Noreng, Grindstad and Snorri were field tested for three years at locations Tromsø and Vesterålen in Northern Norway. The surviving material from the field tests along with plants raised from the original seed lots were subjected to freezing tests. Following the tests, crown tissue was collected for RNA extraction. All samples from different treatment points were paired-end sequenced at 20 million reads/sample. LT50 values varied across cultivars and materials. Plant material from cold-acclimated (CA) samples was used as controls, while two pools for each cultivar were made of plant material from temperature points below the LT50, one with the higher temperatures termed Treatment 1 (T1) and one with the lower temperatures termed Treatment 2 (T2). Many genes coding for transcription factors and proteins which are known to play an important role in freezing tolerance like dehydrins, c-repeat binding factors, late embryogenesis abundant proteins are upregulated with decreasing temperatures. Moreover, genes associated with glycolysis/gluconeogenesis, TCA cycle, glutathione metabolism, proteasome, glyoxylate and dicarboxylate metabolism pathways and genes encoding heat shock proteins, autophagy-related, plasma membrane-associated proteins, sugar and amino acid transporters had elevated expression in field survivors compared to plants raised from the original material. These DEGs might be crucial for winter survival of timothy in a changing climate. Furthermore, differences in freezing stress response between northern and southern adapted cultivars, and surviving material from two field trial locations are discussed briefly

Project description:Winter survival and maintenance strategy is crucial in temperate woody plants. Here, we demonstrate novel aspects of the transcriptional regulations adopted by perennial tree species in winter/dormancy, employing a biochemical and whole transcriptome analysis. As expected, genes related to cold hardiness and defense are over-represented. Interestingly, carbohydrate biosynthesis and transport-related genes were very actively expressed in winter/dormancy. Further biochemical analyses verified the dormancy/winter transcription phenotype. Furthermore, dormancy/winter preferential expression of genes involved in the cell wall biosynthesis/modification, circadian rhythm, the indirect transcriptional regulation (RNA metabolism), and chromatin modification/remodeling were identified. Taken together, regulation of gene expression in the winter survival and maintenance may include not only controlled by promoter binding transcription factors but may also be regulated at the post-transcriptional and chromatin levels. In the first step towards the understanding of molecular mechanisms underlying the winter survival and maintenance of perennial trees, we examined the characteristics of transcription phenotype of the dormancy/winter stem compared to the active growth/summer stem by using a whole transcriptome analysis (GeneChip Poplar Genome Array; Affymetrix). Poplar Genome Array has a total of 61,251 probe sets, representing 57,423 poplar gene models, and allows us to interrogate a total of 41,558 unique gene models because of the probe set redundancy. Slight redundancy of the probe sets within a single chip gave us a unique opportunity to have internal comparisons of the particular genes. Very high reproducibility (R2 > 0.97) between the replicated samples was found. Further confirmation of the GeneChip data was made by semi-quantitative RT-PCR analysis using several genes showing the summer or winter biased expression. Based on these results, further analysis of winter stem transcriptome against summer stem was performed.

Project description:Systems responses of mature leaves from 4 reference cultivars of a larger collection of European potato cultivars (Solanum tuberosum L.) are investigated by metabolome profiling and RNA-Sequencing. The chosen reference cultivars, Milva, Alegria, Desiree, and Saturna, vary in ascending order in regard to drought tolerance. Systems analyses are based on 3 independent field trials and 3 paralleled greenhouse trials. Robust responses across all cultivars and conditions to natural seasonal drought stress comprise proline, raffinose, galactinol, arabitol, arabinonic acid, chlorogenic acid, and 102 transcripts which consist to a high proportion of heat shock proteins and genes with signaling or regulatory functions, such as a homolog of abscisic acid receptor PYL4. Constitutive differences of the tolerant cultivars, Desiree and Saturna, compared to the sensitive cultivars include arbutin (hydroquinone-beta-D-glucopyranoside), octopamine (p-hydroxyphenylethanolamine), ribitol and 248 differential transcripts. Many of these transcripts are disease related, receptor kinases, or regulatory genes, for example a homolog of the Arabidopsis FOUR LIPS MYB-regulator of stomatal cell proliferation. Functional enrichment analyses imply that heat stress is a major acclimation component of potato leaves to agronomical relevant drought stress. Enhanced leaf heat stress is a result of drought caused by loss of transpiration cooling. This effect and CO2-limitation are the main dilemmas of drought- or ABA-induced stomatal closure. Constitutive differences between tolerant and sensitive cultivars indicate partially synergistic interactions of drought and biotic stress responses. We suggest that drought tolerance of the potato reference cultivars may be caused by general resistance mechanisms which are part of previously selected pathogen tolerance. Transcriptome profiling by RNA-sequencing of 48 leaf samples from 4 potato cultivars grown under control or drought stress conditions in 6 independent experiments

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Insights into gene expression changes during ice encasement in perennial grasses

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