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Transcriptome analysis of Prunus spp. plants under flooding stress

ABSTRACT: Purpose: The State of Rio Grande do Sul is the largest producer of peaches from Brazil. However, it still has low values of productivity when compared to other States. One of the problems associated to it this is the occurrence of drainage soils problems, which can suffer flooding situations potentially hampering the development and productivity such culture. For studies to assist in the selection of flood tolerant genotypes, it is essential to understand the physiological and molecular changes of the plants in situations of oxygen deprivation. Using Illumina Hiseq2500 we performed transcriptome analysis of leaves from ‘Capdeboscq’ (Prunus persica) and ‘Julior’ (Prunus insititia x Prunus domestica) rootstocks under flooding for 48 hours. Methods: The mRNA of Prunus spp. plants cv. Capdeboscq e Julior was generated using deep sequencing, in triplicate, using Illumina Hi-Seq 2500, for the following treatments:I) control: plants received irrigation daily until field capacity; and II) plants exposed to flood stress, maintaining a water level of approximately 3 cm above the ground. The sequence reads that passed quality filters were analyzed at the transcript level using this method: Mapping using STAR and identification of differentially expressed genes (DEGs) was performed with the edgeR (false discovery rates - FDRs of <0.05). RT–qPCR validation was performed using SYBR Green assays. Results: Flooding stress causes important high transcriptional changes in the ‘Capdeboscq’ compared to 'Julior' and this is mainly due to their sensitivity/tolerance levels. ‘Capdeboscq’ had photosynthesis as the most affected physiological process at the molecular level, showing a large number of down-regulated enriched GOs, even though it activated cellular signaling pathways under flooding. 'Julior' was more efficient in defense responses, which include the activation of flavonoid biosynthesis pathways. Conclusions: The analysis of two Prunus spp. rootstocks contrasting to the level of tolerance / sensitivity provide new insights into the process of plant flood stress tolerance.

ORGANISM(S): Prunus domestica x Prunus domestica subsp. insititia

PROVIDER: GSE150756 | GEO | 2020/05/19

REPOSITORIES: GEO

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Project description:The deficit of oxygen in plants is a frequent phenomenon in nature. The main causes may be due to flooding or excessive irrigation or to an excess of aerobic microflora in the soil. The Intergovernmental Panel on Climate Change (IPCC) reported that the anthropogenically induced change of world climate increases the frequency of heavy precipitation and tropical cyclone activity. This is likely to engender more frequent flooding events in river flood plains and arable farmland, particularly affecting the world’s poorest farmers. The stress caused by lack of oxygen in plants mainly produces a reduction of the respiration, and then a low energy production and accumulation of toxic compounds of anaerobic metabolism. To alleviate this problem plants have developed morphological and metabolic adaptations, the main of which include the induction of anaerobic and fermentative pathways. In the present study we used a Combimatrix platform, made up of around 8,000 ESTs of roots isolated in citrus and its rootstocks. The chip was hybridized with RNA wild type Carrizo citrange roots and a transgenic line highly expressing a transcription factor involved in the response to the deficiency of oxygen in Oryza sativa. The aim of the work consists in the study of the up and down expressed genes in wild type and transgenic lines subjected and not to anaerobiosis, in order to understand the mechanisms that are activated under anoxia. In general, the hybridization of the chip has led to the activation of 492 genes, of which 28.95% is involved in redox processes, 28.41% in the response to stress, 18.28% in response to chemical stimuli. The up and down-regulation of differentially expressed transcripts in response to oxygen deficiency were confirmed through real-time RT-PCR The results obtained showed the activation of main genes involved in the glycolytic and fermentative pathways, such as pyruvate decarboxylase, alcohol dehydrogenase and sucrose synthase. In transgenic plants of Carrizo the response to oxygen deficit appears to be more pronounced, therefore genes of glycolytic, fermentation and pentose phosphate pathway are activated.

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Transcriptome analysis of Prunus spp. plants under flooding stress

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