Gene expression profiling in peanut using high density oligonucleotide microarrays.
BACKGROUND
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.


RESULTS
We have developed a high-density oligonucleotide microarray for peanut using 49,205 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 demonstrate the utility of this array for expression profiling in a variety of peanut tissues, we compared transcript levels in pod, peg, leaf, stem, and root tissues. Results from this experiment showed 108 putatively pod-specific/abundant genes, as well as transcripts whose expression was low or undetected in pod compared to peg, leaf, stem, or root. The transcripts significantly over-represented in pod include genes responsible for seed storage proteins and desiccation (e.g., late-embryogenesis abundant proteins, aquaporins, legumin B), oil production, and cellular defense. Additionally, almost half of the pod-abundant genes represent unknown genes allowing for the possibility of associating putative function to these previously uncharacterized genes.


CONCLUSIONS
The peanut oligonucleotide array represents the majority of publicly available peanut ESTs and can be used as a tool for expression profiling studies in diverse tissues.
Payton
Paxton
P
United States Department of Agriculture Cropping Systems Research Laboratory, Lubbock, Texas 79415, USA. paxton.payton@ars.usda.gov
Kottapalli
Kameswara Rao
KR
Rowland
Diane
D
Faircloth
Wilson
W
Guo
Baozhu
B
Burow
Mark
M
Puppala
Naveen
N
Gallo
Maria
M
D010367:Arachis / Q000235:genetics*; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D017343:Genes, Plant; D018745:Genome, Plant; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D018749:RNA, Plant / Q000235:genetics
D018749:RNA, Plant