Gene expression profiling in peanut using oligonucleotide microarrays

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 Overall design: 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.

迄今为止，花生转录组表达分析局限于相对较小的一组基因，而直至近期，数量适中的ESTs（表达序列标签）才被公开发布。利用这些ESTs构建寡核苷酸微阵列，为我们提供了研究大规模转录响应于各类发育和环境信号的途径，从而深化了我们对植物生物学认知。本研究开发了一种基于约47,767个公开发布ESTs的高密度寡核苷酸微阵列，并测试了该阵列在花生不同组织表达谱分析中的实用性。为识别假定的组织特异性基因并探究该阵列的应用价值，我们比较了豆荚与果柄、叶片、茎和根组织中的转录水平。实验结果表明，存在一系列假定的豆荚特异性/丰富基因，以及相对于果柄、叶片或茎，在豆荚中表达水平低或未检测到的转录本。关键词：花生组织特异性基因表达；总体设计：本研究采用Agilent花生基因芯片（017430）来识别假定的组织特异性基因，并探究该阵列在花生各种组织表达谱分析中的应用。研究使用了Flavrunner 458花生基因型的豆荚、叶片、茎、果柄和根组织。在正常灌溉条件下种植的田间植株被用于样本采集。通过在相同的双色寡核苷酸阵列上杂交豆荚组织和叶片、茎、果柄及根组织的cRNA，进行了三次微阵列实验的重复。