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ARS Home » Midwest Area » Madison, Wisconsin » Cereal Crops Research » Research » Publications at this Location » Publication #346544

Research Project: Improvement of Barley Seed Quality Through Molecular and Functional Genomic Gene Expression

Location: Cereal Crops Research

Title: Evaluation and selection of internal reference genes from two- and six-row U.S. malting barley varieties throughout micromalting for use in RT-qPCR

Author
item Walling, Jason
item Zalapa (tirado), Leslie
item Vinje, Marcus

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/30/2018
Publication Date: 5/8/2018
Citation: Walling, J.G., Zalapa, L.A., Vinje, M.A. 2018. Evaluation and selection of internal reference genes from two- and six-row U.S. malting barley varieties throughout micromalting for use in RT-qPCR. PLoS One. 13(5)/e0196966. https://doi.org/10.1371/journal.pone.0196966.
DOI: https://doi.org/10.1371/journal.pone.0196966

Interpretive Summary: RT-qPCR is a relatively modern technique that is commonly employed to measure gene transcript abundance. In order to use RT-qPCR effectively, researchers must first run preliminary experiments that identify genes that are stably expressed to use as a normalizer. Malting is the controlled germination of barley grains that is necessary pre-requisite for use in the multi-billion dollar malting, brewing, and distilling industries. Micromalting is a scaled down version of malting commonly used by malting researchers. In this study, we have tested 13 potential genes for stability throughout micromalting in both two- and six-row malting barley varieties. We identified the most stable genes to study gene expression in micromalting as Actin and Heat Shock Protein 70. Additionally, we have determined that only two genes are required for sufficient normalization under micromalting conditions.

Technical Abstract: Reverse Transcription quantitative Polymerase Chain Reaction (qRT-PCR) is a popular method for measuring transcript abundance. The most commonly used method of interpretation is relative quantification and thus necessitates the use of normalization controls (i.e. reference genes) to standardize transcript abundance. The most popular gene targets for RT-qPCR are housekeeping genes because they are thought to maintain a static transcript level among a variety of samples. However, more recent studies have shown, several housekeeping genes are not reliably stable. This is the first study to examine the potential of several reference genes for using in qPCR normalization during barley malting. The process of malting barley mechanizes the imbibition and subsequent germination of barley seeds under controlled conditions. Malt quality is controlled by many pleiotropic genes that are determined by examining the result of physiological changes the barley seed undergoes during the malting process. We compared the stability of 13 reference genes across both two-and six-row malting barleys (Conrad and Legacy, respectfully) throughout the entirety of the malting process. Initially, primer target specificity, amplification efficiency and average Ct values were determined for each of the selected primer pairs. Three statistical programs (geNorm, NormFinder, and BestKeeper) were used to rank the stability of each reference gene. Rankings provided from the three programs were similar between the two-row and the six-row and with exception of BestKeeper’s ranking of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). A consensus ranking among programs was determined using RefFinder. Our results show that Actin (ACT) and Heat Shock Protein 70 (HSP70) were the most stable throughout micromalting, while Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and Cyclophilin (CYP) were the least stable. Two reference genes are necessary for stable transcript normalization according to geNorm and the best two reference genes (ACT and HSP70) provided a sufficient level of stability.