Selection of Reference Genes for qPCR Analyses of Gene Expression in Ramie Leaves and Roots across Eleven Abiotic/Biotic Treatments

Quantitative real-time PCR (qPCR) is commonly used for deciphering gene functions. For effective qPCR analyses, suitable reference genes are needed for normalization. The objective of this study is to identify the appropriate reference gene(s) for qPCR analyses of the leaves and roots of ramie (Boehmeria nivea L.), an important natural fiber crop. To accomplish this goal, we investigated the expression patterns of eight common plant qPCR reference genes in ramie leaves and roots under five abiotic stresses, five hormonal treatments, and one biotic stress. The relative expression stabilities of the eight genes were evaluated using four common but different approaches: geNorm, NormFinder, BestKeeper, and RefFinder. Across the 11 tested conditions, ACT1 was the most stably expressed among the eight genes while GAPDH displayed the biggest variation. Overall, while variations in the suggested reference genes were found for different tissue x treatment combinations, our analyses revealed that together, genes ACT1, CYP2, and UBQ can provide robust references for gene expression studies of ramie leaves under most conditions, while genes EF-1α, TUB, and ACT1 can be used for similar studies of ramie roots. Our results should help future functional studies of the genes in ramie genome across tissues and environmental conditions.