Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 6/12/2009
Publication Date: 6/12/2009
Citation: Payton, P.R., Kottapalli, K.R., Rowland, D., Faircloth, W., Guo, B., Burow, M., Puppala, N., Gallo, M. 2009. Gene expression profiling in peanut using high density oligonucleotide microarrays. Biomed Central (BMC) Genomics. 10:Article 265. Interpretive Summary: Cultivated peanut or groundnut (Arachis hypogaea L.) is the second-most important legume in the world, with a total global production of 38 million tons. Legumes are the second-most important food crop, following grains, representing an important source protein for humans and livestock in the North and South America, Africa, and Asia. Additionally, when considering oil production for cooking and fuels, peanut represents one of the highest value-added crops, with an annual worth of $1 billion to farmers and $6 billion to the overall economy in the U.S. alone. Recent progress in functional genomics has enabled the study of plant responses to environmental perturbation or during key developmental stages at multigenic levels, revealing the complex nature of transcriptome responses in plants. While genes and proteins expressed differentially under abiotic stress have been identified in model plant systems such as Arabidopsis, studies on stress-induced or developmentally regulated genes in crop plants have been limited. Positional cloning and candidate gene approaches have begun to identify a limited number of structural genes or transcription factors controlling the larger response to abiotic and biotic stimuli. Identification of such genes will have a significant effect on varietal development by traditional breeding and genetic engineering. To follow suit, greater attention is needed for genomic development in the Leguminosae. Despite its importance as both a cash crop and important staple, little is known about the genetic mechanisms in peanut that control disease resistance or susceptibility, stress tolerance, or pod development. One of the major reasons is the relatively small amount of available genomic information. Although significant efforts have gone into legume genomics, there is a paucity of genomic data for peanut, bean, and chickpea compared to alfalfa, soybean, and Lotus japonicus. In peanut, marker technology is relatively young and only recently have genetics maps been published. As part of our ongoing effort to investigate the molecular mechanisms underlying peanut development and response to abiotic stress, we have developed an oligonucleotide microarray using all publicly available peanut ESTs. To test the utility of this array for expression studies in both vegetative and reproductive tissues and identify putatively pod-specific genes, we compared transcript abundance in pod, leaf, stem, root, and peg tissues. 2344 transcripts were identified as pod-abundants, i.e. having a greater than 2-fold difference in mRNA compared to stem, leaf, root, or peg. Of these, 153 were detected in pods only and categorized as pod-specific. Conversely, of the 2367 transcripts identified as more abundant in leaf, stem, root, or peg, 143 were not detected or significantly more abundant in relative to pod and classified as vegetative-specific. Interestingly, no genes were identified as significantly more abundant in root compared to pod tissue. We interpret this as a result of the lack of available root-derived ESTs in the public domain. This represents the first large-scale publicly available peanut microarray and establishes the foundation for investigation of molecular responses on a transcriptome scale.
Technical Abstract: Transcriptome expression analysis in peanut to date has been limited to a relatively small set of genes and only recently have a moderately significant number of ESTs 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 putively 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. The transcripts significantly over-represented in pod include genes responsible for seed development and desiccation (late-embryogenesis proteins, aquaporins, legumin B), reactive oxygen scavenging, oil production, and dormancy. Additionally, almost half of the pod-abundant genes represent unknown genes allowing for the possibility of associating putative function to these previously uncharacterized genes. 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.