In-depth analysis of the endogenous reference genes used in the quantitative PCR detection systems for rice

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To standardize the rice-specific PCR detection methods, five previously reported rice (Oryza sativa) taxon-specific genes were compared and evaluated. The investigated genes included the rice root-specific gene (gos9), the ppiphosphofructokinase gene (ppi-PPF), the phospholipase D gene (PLD), the starch branching enzyme gene (RBE4) and the sucrose phosphate synthase gene (SPS). Sequencing analyses revealed that among the tested rice cultivars, single-nucleotide polymorphisms (SNPs) existed in the gos9, PLD, ppi-PPF and SPS amplicons, though no statistically significant effect on their Ct values was found. The ppi-PPF and PLD systems were found to produce amplicons in non-rice species, such as sugarcane and broomcorn. The quantitative real-time PCR results revealed that this cross-reaction led to an underestimate of the GM (genetically modified) rice content. With the exception of the aforementioned shortcomings, these five endogenous reference genes all have acceptable amplification efficiencies, which ranged from 98 to 108 %, and high sensitivity within the limit of detection (LOD) values, which ranged from 5 to 10 copies of the haploid genome. In estimating the GM content in blinded rice samples, these five systems produce relatively accurate quantitative results with deviations less than 15 %, but the RBE4 system produced the most accurate quantitative results. Therefore, we have determined that the RBE4 gene is the most suitable rice reference gene, and the gos9 and SPS genes can also be used as rice reference genes because they have good commutability with the RBE4 gene. Care should be taken when interpreting results based on the PLD and ppi-PPF genes owing to their cross-reaction with other species.