ABSTRACT
Objective:To screen out stable internal reference genes suitable for real-time quantitative polymerase chain reaction（Real-time PCR） analysis of different parts of<italic> Cinnamomum cassia</italic> and <italic>C. cassia</italic> var. <italic>macrophyllum</italic>，in order to provide stable internal reference genes for gene expression analysis of three different parts of and <italic>C. cassia</italic> var.<italic> macrophyllum</italic> branches and leaves. Method:With 6 different tissues and organs， such as bark，branches and leaves of two plants of <italic>C. cassia</italic> and <italic>C. cassia</italic> var. <italic>macrophyllum</italic> as experimental materials，Real-time PCR technology was used to detect the five internal reference genes， namely glyceraldehyde-3-phosphate dehydrogenase（GAPDH），actin，ubiquitin-ligase enzymes（UBE），histone and tubin（TUB）. The analysis of the expression of the data. Furthermore， three commonly used internal reference gene analysis software，namely geNorm，NormFinder and BestKeeper，was used to analyze and evaluate the stability of the candidate internal reference gene. Result:The internal five reference genes were expressed in the bark，branches and leaves of the two plants，but with differences in stability. Comprehensive analysis showed that the expression stability of candidate internal reference genes was in the order of GAPDH>actin>UBE>histone>TUB. The internal reference genes of the two plants were analyzed separately，and the optimal internal reference gene was still GAPDH，indicating that GAPDH was the most suitable internal reference gene. TUB and histone ranked low in the three software，and should be eliminated in the screening of reference genes. They were not suitable for gene expression analysis of <italic>C. cassia </italic>and <italic>C. cassia</italic> var. <italic>macrophyllum</italic>. Conclusion:The most suitable internal reference gene for different parts of cinnamon，branches，and leaves of <italic>C. cassia</italic> and <italic>C. cassia</italic> var. <italic>macrophyllum</italic> was GAPDH. In this study，a screening system for internal reference genes of Real-time PCR of <italic>C. cassia</italic> and <italic>C. cassia</italic> var. <italic>macrophyllum</italic> was established to provide theoretical basis for studying functional regulation and expression of genes during the accumulation of effective components in different parts.