Plant reference genes for development and stress response studies

Abstract

Many reference genes are used by different laboratories for gene expression analyses to indicate the relative amount of input RNA/DNA in the experiment. These reference genes are supposed to show least variation among the treatments and with the control sets in a given experiment. However, expression of reference genes varies significantly from one set of experiment to the other. Thus, selection of reference genes depends on the experimental conditions. Sometimes the average expression of two or three reference genes is taken as standard. This review consolidated the details of about 120 genes attempted for normalization during comparative expression analysis in 16 different plants. Plant species included in this review are Arabidopsis thaliana, cotton (Gossypium hirsutum), tobacco (Nicotiana benthamiana and N. tabacum), soybean (Glycine max), rice (Oryza sativa), blueberry (Vaccinium corymbosum), tomato (Solanum lycopersicum), wheat (Triticum aestivum), potato (Solanum tuberosum), sugar cane (Saccharum sp.), carrot (Daucus carota), coffee (Coffea arabica), cucumber (Cucumis sativus), kiwi (Actinidia deliciosa) and grape (Vitis vinifera). The list includes model and cultivated crop plants from both monocot and dicot classes. We have categorized plant-wise the reference genes that have been used for expression analyses in any or all of the four different conditions such as biotic stress, abiotic stress, developmental stages and various organs and tissues, reported till date. This review serves as a guide during the reference gene hunt for gene expression analysis studies.

Selection and Validation of Appropriate Reference Genes for Real-Time Quantitative PCR Analysis in Needles of Larix olgensis under Abiotic Stresses

“…Similar to geNorm, NormFinder indicated that ADP was the least stable gene in all treatments. Although there were some differences in Forests 2020, 11,193 9 of 17 rankings between geNorm and NormFinder, the top five most stable genes were relatively consistent between them. NormFinder analysis: the NormFinder approach provides a stability value for each gene based on inter-and intra-group variation in expression [15].…”

“…Forests 2020, 11,193 7 of 18 heat stress. The ranking of gene stability by average CV values across all treatments was PP2A (Table 2).…”

“…These species include Arabidopsis thaliana [5], Oryza sativa [6], Solanum lycopersicum [7], Malus domestica [8], and Populus euramericana cv [9]. RGs are often housekeeping genes that are associated with basic cellular processes and Forests 2020, 11,193 3 of 17…”

“…The outside box is determined from 25th to 97.5th percentiles. The top and bottom whiskers represent the highest and lowest Cq values, respectively.Forests 2020,11, 193 7 of 18…”

Selection and Validation of Reference Genes for the qRT-PCR Assays of Populus ussuriensis Gene Expression under Abiotic Stresses and Related ABA Treatment

“…As shown in Figure 2 and Table 2, all 14 RGs showed average M values less than 1.5 under drought, high salinity, cold stress, and ABA treatment. Sometimes a single RG does not meet the stability requirements for use in normalization, and two or more RGs are therefore needed to reduce error and obtain more accurate results [28]. geNorm can determine the optimal number of candidate RGs based on the calculation of pairwise variation (Vn/Vn+1).…”