Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression profiling in peanut using oligonucleotide microarrays

ABSTRACT: Transcriptome expression analysis in peanut to date has been limited to a relatively small set of genes and only recently have moderately significant number of ESTs has been released into the public domain. Utilization of these ESTs for the oligonucleotide microarrays provides a means to investigate large-scale transcript responses to a variety of developmental and environmental signals, ultimately improving our understanding of plant biology. We have developed a high-density oligonucleotide microarray for peanut using approximately 47,767 publicly available ESTs and tested the utility of this array for expression profiling in a variety of peanut tissues. To identify putatively tissue-specific genes and investigate the utility of this array, we compared transcript levels in pod to peg, leaf, stem, and root tissues. Results from this experiment showed a number of putatively pod-specific/abundant genes, as well as transcripts whose expression was low or undetected in pod compared to either peg, leaf, or stem. Keywords: Peanut tissue-specific gene expression We used Agilent peanut gene chips (017430) to identify putative tissue-specific genes and investigate the utility of the array for expression profiling of various peanut tissues. Pod, leaf, stem, peg and root tissues of the peanut genotype Flavrunner 458 were used in the study. Field grown plants under normal irrigation were used for sample collection. Three replications of microarray experiments were carried out by hybridizing the cRNA from pod tissue and cRNA from leaf, stem, peg and root tissues on the same dual color oligonucleotide arrays.

ORGANISM(S): Arachis hypogaea

SUBMITTER: Kameswara Rao Kottapalli

PROVIDER: E-GEOD-11365 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Gene expression profiling in peanut using high density oligonucleotide microarrays.

Payton Paxton P Kottapalli Kameswara Rao KR Rowland Diane D Faircloth Wilson W Guo Baozhu B Burow Mark M Puppala Naveen N Gallo Maria M

BMC genomics 20090612

<h4>Background</h4>Transcriptome expression analysis in peanut to date has been limited to a relatively small set of genes and only recently has a significant number of ESTs been released into the public domain. Utilization of these ESTs for oligonucleotide microarrays provides a means to investigate large-scale transcript responses to a variety of developmental and environmental signals, ultimately improving our understanding of plant biology.<h4>Results</h4>We have developed a high-density oli ...[more]

PMID: 19523230

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Project description:To gain insights into molecular mechanisms of tolerance to heat stress, we conducted a transcript profiling experiment to identify heat-responsive genes in contrasting peanut mini core accessions, either un-acclimated or acclimated to heat stress. Plants at reproductive stage were exposed to 28 °C (control), 45 °C for 15 d (un-acclimated) or 45 °C for 1 d followed by 7 d recovery and 15 d stress (acclimated). Two contrasting genotypes showing diverse response to stress were selected based on a bioassay involving chlorophyll fluorescence yield under elevated respiratory demand and membrane thermostability. Transcript profiling was performed using 8 x 15k custom oligo microarrays containing 15k peanut EST sequences. Gene enrichment analysis was performed using Blast2GO program and genes with homology to known proteins were categorized into detailed molecular functional groups. Majority of stress-responsive genes assigned to KEGG pathways belonged to starch, sucrose and galactose metabolism followed by aminoacid metabolism, and secondary metabolite biosynthesis. Differentially expressed transcripts from samples were validated in the samples from second year by quantitative real-time PCR. Transcripts of eight genes involved in terpenoid and flavanoid biosynthesis were induced after second and seventh day, respectively in leaves under heat stress. Metabolite analysis confirmed increases in metabolites of selected pathways under heat stress. The heat up-regulated genes in tolerant COC041 mini-core accession are potential candidate genes for engineering stress-tolerant peanuts and unraveling molecular mechanisms of peanut adaptation to heat stress. We used Agilent peanut microarrays to identify putative heat stress-responsive genes. Acclimated leaf tissues of the peanut genotypes COC041 (tolerant) and COC166 (susceptible) were used in the study. Three replications of microarray experiments were carried out by hybridizing the cRNA from different time points and stress conditions in a loop design on 8 x 15k microarray.

Project description:To gain insights into molecular mechanisms of tolerance to heat stress, we conducted a transcript profiling experiment to identify heat-responsive genes in contrasting peanut mini core accessions, either un-acclimated or acclimated to heat stress. Plants at reproductive stage were exposed to 28 °C (control), 45 °C for 15 d (un-acclimated) or 45 °C for 1 d followed by 7 d recovery and 15 d stress (acclimated). Two contrasting genotypes showing diverse response to stress were selected based on a bioassay involving chlorophyll fluorescence yield under elevated respiratory demand and membrane thermostability. Transcript profiling was performed using 4 x 44k custom oligo microarrays containing 22k peanut EST sequences. The microarray analysis identified 710 stress-induced and 770 stress-repressed putative heat-responsive transcripts in the tolerant genotype. Gene enrichment analysis was performed using Blast2GO program and genes with homology to known proteins were categorized into detailed molecular functional groups. Majority of stress-responsive genes assigned to KEGG pathways belonged to starch, sucrose and galactose metabolism followed by amino acid metabolism, and secondary metabolite biosynthesis. Differentially expressed transcripts from samples obtained from first year’s experiment were validated in the samples from second year by quantitative real-time PCR. Transcripts of eight genes involved in terpenoid and flavanoid biosynthesis were induced after second and seventh day, respectively, in leaves under heat stress. Metabolite analysis confirmed increases in metabolites of selected pathways under heat stress. The heat up-regulated genes in tolerant COC041 mini-core accession are potential candidate genes for engineering stress-tolerant peanuts and unraveling molecular mechanisms of peanut adaptation to heat stress. We used Agilent peanut microarrays to identify putative heat stress-responsive genes. Directly heat-stressed leaf tissues of the peanut genotypes COC041 (tolerant) and COC166 (susceptible) were used in the study. Three replications of microarray experiments were carried out by hybridizing the cRNA from different time points and stress conditions in a loop design on 4 x 44k microarray.

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Dataset Information

Gene expression profiling in peanut using oligonucleotide microarrays

Publications

Gene expression profiling in peanut using high density oligonucleotide microarrays.

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