Poole Rebecca, Barker Gary, Wilson Ian D, Coghill Jane A, Edwards Keith J
School of Biological Sciences, University of Bristol, Bristol, UK.
Funct Integr Genomics. 2007 Jul;7(3):207-19. doi: 10.1007/s10142-007-0046-7. Epub 2007 Mar 16.
The number of global gene expression studies has increased significantly in recent years. It is assumed that the different techniques employed report similar levels of gene expression for each sequence type. While this may be true for many species, polyploids containing homoeologous and paralogous gene copies represent a unique situation. In this paper, we describe the comparison of the Affymetrix GeneChip Wheat Genome Array, an in-house custom-spotted complementary DNA array and quantitative reverse transcription-polymerase chain reaction (PCR) for the study of gene expression in hexaploid wheat. Analysis of the data generated from each platform revealed little concordance and suggested that global comparisons are not possible. Potential causes of these inter-platform discrepancies were investigated and revealed to be due to the inability of the platforms to discriminate between different but related transcripts. Our results also showed that the traditionally used array validation technique, quantitative reverse transcription PCR, differs in its discriminatory ability, resulting in the poor confirmation rates seen in previous polyploid studies. These findings have implications for gene expression studies in polyploid organisms and highlight the need for homoeologous- and paralogous-specific arrays when investigating polyploid gene expression.
近年来，全球基因表达研究的数量显著增加。人们认为，所采用的不同技术对于每种序列类型报告的基因表达水平相似。虽然这对许多物种可能是正确的，但含有同源和旁系同源基因拷贝的多倍体代表了一种独特的情况。在本文中，我们描述了Affymetrix基因芯片小麦基因组阵列、一种内部定制点样互补DNA阵列和定量逆转录-聚合酶链反应（PCR）在六倍体小麦基因表达研究中的比较。对每个平台产生的数据进行分析后发现，一致性很低，这表明无法进行全局比较。对这些平台间差异的潜在原因进行了调查，发现是由于这些平台无法区分不同但相关的转录本。我们的结果还表明，传统使用的阵列验证技术——定量逆转录PCR，其区分能力不同，导致在先前的多倍体研究中确认率较低。这些发现对多倍体生物的基因表达研究具有启示意义，并突出了在研究多倍体基因表达时对同源和旁系同源特异性阵列的需求。
