Dataset Information

Comparative Solanum wild species transcription profiles under controlled water stress conditions

ABSTRACT: The aim of the present work is to apply microarrays to identify candidate genes associated with the strategies adopted by different Solanum wild species to maintain their metabolism and limit the harm under water stress conditions. Wild genotypes are a rich source of novel genes for introduction into cultivated species to enhance stress tolerance. The mechanisms in which genes act can involve different pathways inside the cell, resulting in the expression of stress responsive genes. We will identify genes whose expression change in the leaves of potato plants subjected to drought stress. We will analyze different Solanum genotypes in six moments of water stress (0,1,3,5,7 & 10 days after initiation of stress). We will selected 4 time-points (days 0,5,7 & 10) and 2 genotypes (with divergence behavior) for microarrays analysis. The candidate genes obtained with this approach will be validated by semi-quantitative northern blot analysis (Typhoon scanner) and/or RT-PCR in each time-point of treatment and with all wild genotypes in study. This will help us to get a better understanding respect the dynamics of expression of a great number of genes in response to stress, as well as to establish functional relations between the involved genes. Research Plan: 5-weeks-old Solanum wild species plants were randomly sorted in 2 groups (25 plants per group). One group was submitted to non-irrigated conditions, withholding water and the other was normally watered. For microarray analysis, leaflets tissue from 4 plants per group of 4 time-points (days 0,5,7, & 10) were pooled, frozen in liquid nitrogen and stored at –80°C.RNA of the pool was extracted following TRIZOL method (Invitrogen). RNA integrity was verified on agarose gel. Hybridizations were performed with n genotypes,t time-points and r repeats. The hybridizations proposed in this experiment to enhance statistical robustness of data will be: 32 slides = n*t*r ; (2 genotypes; 4 time-points; 4 repeats (dye-swap). Keywords: Direct comparison

ORGANISM(S): Solanum tuberosum

PROVIDER: GSE10481 | GEO | 2008/02/13

SECONDARY ACCESSION(S): PRJNA107925

REPOSITORIES: GEO

ACCESS DATA

Similar Datasets

Project description:Six months old seed grown under well-watered greenhouse conditions were used in the current study. The seedlings of the two wild emmer wheat genotypes were vernalized on a moist germination paper (Hofman Manufacturing, Inc, Jefferson, OR, USA) for three weeks in the dark at 4oC, followed by three days acclimation at 24oC. Seedlings were then transplanted into 5L pots containing a mixture of pure quartz sand and peat (4:1 v/v), supplemented with a slow release fertilizer (2 g/L, Osmocote® Standard 14-14-14, Scotts-Sierra Horticulture, Marysville, OH, USA) and by a weekly application of 100 ml/pot of 0.5X Murashigi and Skoog growth solution (Sigma Chemical Co., St Louis, MO, USA). Pots were placed in a screen-house under natural winter conditions (December to February; 5-18°C) in Haifa, Israel (Mt. Carmel; 35o01′ E, 32o45′ N; 480 m above sea level) for 10 weeks and irrigated daily by a drip irrigation system. Three weeks prior to application of terminal drought stress, the pots were transferred to a controlled environment greenhouse (22/18 oC; 12 h day/12 h night) in order to prevent rainfall during the drought experiment. Five pots per genotype served as biological replicates, plants of three pots of each genotype/treatment were used for transcriptome study whereas two additional pots were used for quantitative PCR analysis (altogether five biological replicated of were used for quantitative real time PCR). Three individual plants were grown in each pot, one plant was used for measurements of leaf relative water content (RWC) (Barrs and Weatherley 1968), whereas the other two plants were used for sampling of flag leaf tissue for RNA extraction. Terminal drought stress (D) was applied at inflorescence emergence stage (Zadoks 50-60), (Zadoks et al. 1974), after emergence of 1-2 spikes in all biological replicates of both genotypes. The time from transplanting to inflorescence emergence stage was not significantly different between genotypes (70 days in the S genotype and 72 days in the R genotype). Drought stress application initiated after irrigation with excess amount of water in order to assure that all pots start the experiment at the same soil water capacity. Drought stress was imposed by withholding water for eight days until stress symptoms (i.e. leaf rolling and wilting symptoms) were visible in plants of both genotypes. Stress symptoms were more visible in the S genotype, however, leaf relative water content (RWC), measured after eight days of drought stress was low but was not significantly different between the two genotypes (49.68%±1.48 in the R genotype and 53.34%±1.83 in the S genotype). The well-watered control (C) plants were irrigated daily by ample amount of water. Flag leaf tissues of drought-stressed plants and well-watered control plants were harvested, immediately frozen in liquid nitrogen, and stored at -80ºC for RNA extraction. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Krugman Tamar. The equivalent experiment is TA33 at PLEXdb.]

Dataset Information

Comparative Solanum wild species transcription profiles under controlled water stress conditions

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure