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Evaluation of Four Genes in Rice for Their Suitability As Endogenous Reference Standards in Quantitative PCR

文献类型： 外文期刊

作者： Wang, Chong 1 ; Jiang, Lingxi 2 ; Rao, Jun 1 ; Liu, Yinan 1 ; Yang, Litao 1 ; Zhang, Dabing 1 ;

作者机构： 1.Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, SJTU Bor Luh Food Safety Ctr, GMO Detect Lab, Shanghai 200240, Peoples R China

2.Shanghai Acad Agr Sci, Agrobiotech Res Ctr, Shanghai 201106, Peoples R China

3.Shanghai Jiao Tong Univ, Minist Educ, Key Lab Genet & Dev & Neuropsychiat Dis, Bio X Ctr, Shanghai 200240, Peoples R China

关键词： Real-time PCR;rice endogenous reference gene;GeNorm analysis;single nucleotide polymorphism

期刊名称：JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY （ 影响因子：5.279； 五年影响因子：5.269 ）

ISSN：

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收录情况： SCI

摘要： The genetically modified (GM) food/feed quantification depends on the reliable detection systems of endogenous reference genes. Currently, four endogenous reference genes including sucrose phosphate synthase (SPS), GOS9, phospholipase D (PLD), and ppi phosphofructokinase {ppi-PPF) of rice have been used in GM rice detection. To compare the applicability of these four rice reference genes in quantitative PCR systems, we analyzed the target nucleotide sequence variation in 58 conventional rice varieties from various geographic and phylogenic origins, also their quantification performances were evaluated using quantitative real-time PCR and GeNorm analysis via a series of statistical calculation to get a "M value" which is negative correlation with the stability of genes. The sequencing analysis results showed that the reported GOS9 and PLD taqman probe regions had detectable single nucleotide polymorphisms (SNPs) among the tested rice cultivars, while no SNPs were observed for SPS and ppi-PPF amplicons.. Also, poor quantitative performance was detectable in these cultivars with SNPs using GOS9 and PLD quantitative PCR systems. Even though the PCR efficiency of ppi-PPF system was slightly lower, the SPS and ppi-PPF quantitative PCR systems were shown to be applicable for rice endogenous reference assay with less variation among the Q values, good reproducibility in quantitative assays, and the low M values by the comprehensive quantitative PCR comparison and GeNorm analysis.

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