Research article

Gene expression profiling in peanut using high density oligonucleotide microarrays

Paxton Payton¹ , Kameswara Rao Kottapalli^1,2 , Diane Rowland³ , Wilson Faircloth³ , Baozhu Guo⁴ , Mark Burow^2,5 , Naveen Puppala⁶ and Maria Gallo⁷

¹  United States Department of Agriculture Cropping Systems Research Laboratory, Lubbock, Texas 79415, USA

²  Texas Tech University, Department of Plant and Soil Science, Lubbock, Texas 79409, USA

³  United States Department of Agriculture, National Peanut Research Laboratory, Dawson, Georgia, USA

⁴  Crop Protection and Research Management Laboratory, Tifton, Georgia, 31793, USA

⁵  Texas Agrilife Research, Lubbock, Texas 79403, USA

⁶  New Mexico State University Agricultural Science Center, Clovis, New Mexico 88101, USA

⁷  Institute of Food and Agricultural Sciences and the Genetics Institute, University of Florida, Gainesville, Florida 32611, USA

author email corresponding author email

BMC Genomics 2009, 10:265doi:10.1186/1471-2164-10-265

Published:	12 June 2009

Abstract

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.

Conclusion

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.