Selection of Reliable Reference Genes for Gene Expression Studies of a Promising Oilseed Crop, Plukenetia volubilis, by Real-Time Quantitative PCR

• Published in: International journal of molecular sciences Vol. 16; no. 6; pp. 12513 - 12530
• Main Authors: Niu, Longjian, Tao, Yan-Bin, Chen, Mao-Sheng, Fu, Qiantang, Li, Chaoqiong, Dong, Yuling, Wang, Xiulan, He, Huiying, Xu, Zeng-Fu
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 03-06-2015; MDPI
• Subjects: Algorithms; biofuels; Crops; Crops, Agricultural - chemistry; Crops, Agricultural - genetics; Crops, Agricultural - growth & development; Euphorbiaceae - chemistry; Euphorbiaceae - genetics; Euphorbiaceae - growth & development; flower development; Flowers - genetics; Gene expression; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Genes; Oils & fats; Organ Specificity; Plant Oils; Plant Proteins - genetics; Plukenetia volubilis; Quantitative genetics; Real time; Real-Time Polymerase Chain Reaction - methods; Real-Time Polymerase Chain Reaction - standards; reference gene; Reference Standards; RT-qPCR; seed development; Seeds - genetics; reference gene; seed development; flower development; biofuels; Plukenetia volubilis; RT-qPCR
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms160612513

Real-time quantitative PCR (RT-qPCR) is a reliable and widely used method for gene expression analysis. The accuracy of the determination of a target gene expression level by RT-qPCR demands the use of appropriate reference genes to normalize the mRNA levels among different samples. However, suitable reference genes for RT-qPCR have not been identified in Sacha inchi (Plukenetia volubilis), a promising oilseed crop known for its polyunsaturated fatty acid (PUFA)-rich seeds. In this study, using RT-qPCR, twelve candidate reference genes were examined in seedlings and adult plants, during flower and seed development and for the entire growth cycle of Sacha inchi. Four statistical algorithms (delta cycle threshold (ΔCt), BestKeeper, geNorm, and NormFinder) were used to assess the expression stabilities of the candidate genes. The results showed that ubiquitin-conjugating enzyme (UCE), actin (ACT) and phospholipase A22 (PLA) were the most stable genes in Sacha inchi seedlings. For roots, stems, leaves, flowers, and seeds from adult plants, 30S ribosomal protein S13 (RPS13), cyclophilin (CYC) and elongation factor-1alpha (EF1α) were recommended as reference genes for RT-qPCR. During the development of reproductive organs, PLA, ACT and UCE were the optimal reference genes for flower development, whereas UCE, RPS13 and RNA polymerase II subunit (RPII) were optimal for seed development. Considering the entire growth cycle of Sacha inchi, UCE, ACT and EF1α were sufficient for the purpose of normalization. Our results provide useful guidelines for the selection of reliable reference genes for the normalization of RT-qPCR data for seedlings and adult plants, for reproductive organs, and for the entire growth cycle of Sacha inchi.