Transcription profiling of leaves of Populus nigra × P. maximowiczii growing in monoculture and stands mixed with Robinia at poor and rich soil sites
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 4000
ORGANISM(S): Populus maximowiczii x Populus nigra
SUBMITTER: Dennis Janz
PROVIDER: E-MTAB-9039 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:P. nigra × P. maximowiczii plants were grown in the field, each in monoculture and in stands mixed with Robinia pseudoacacia, at two locations differing in soil nutrient levels. After 3 years of growing under ambient weather conditions, leaf samples were harvested and analyzed by RNA-seq.
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Project description:This study was designed to identify changes in gene expression that occur when corn was grown on different landscape features. Specifically on the backslope or summit/shoulder of a hill. In rolling landscapes, plant available water varies drastically by location and soil type. Almost simultaneously, plants may be flooded out in footslope locations whereas plants in summit locations may be suffering from severe drought. The objective of this study was to determine the influence of landscape position on corn (Zea mays) productivity and gene regulation. Corn was sampled at V12 for plant growth characteristics and transcriptome analysis at summit/shoulder and lower backslope positions. Plants at the summit had 16% less leaf area and biomass compared with plants at the toeslope. Gene expression analysis using microarray chips, transcriptome analysis, and qPCR indicated that plants at the summit had 708 genes down-regulated and 399 genes up-regulated compared to control plants at the lower back slope. GSEA (Gene Set Enrichment Analysis) indicated tolerance to cold, salt, and drying were increased in summit/should plants compared to control toeslope plants. However, nutrient uptake, recovery from wounding, pest and fungal disease resistance, along with photosynthetic capacity were all down-regulated in moderate water stresses plants. These responses suggest that corn preferentially responses to water stress as the expense of its ability to respond to other stresses. Three biological replicates for the control (backslope) and six biological replicate of summit/shoulder-grown plants were collected. The resulting labeled cDNA was hybridized to the 46,000-element maize microarray chip developed by the University of Arizona using their protocol (International Microarray Workshop Handbook, 2009Gardiner et al. 2005). The hybridization scheme was a dual hybridization using a rolling circle balanced dye swap design. Thus we had three to six biological replicates for each growth condition and two technical replicates for each biological sample.
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