For detection and quantification of GM contents, techniques
based on nucleic acid analysis have been widely applied,
including conventional PCR and TaqMan real-time PCR
analysis [8]. The efficient and accurate quantification of host
genome DNA copy numbers using endogenous reference
genes is very important during the process [9]. In general, GM
contents are expressed as mass/mass ratio or copy number
ratio of GM over non-GM of the assayed organism. Therefore,
endogenous reference genes and their real-time PCR assays
are referred to as “golden standards” in GMO analysis [8]. One
desirable endogenous reference gene and its real-time PCR
assay should have three characteristics: species specificity,
single or low copy number in the genome, and low
heterogeneity among different lines [10]. In general, low
heterogeneity is determined by minimum number of single
nucleotide polymorphisms (SNPs) in the target DNA sequence
and high PCR amplification performance among different lines
[11,12].