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An efficient RNA isolation procedure and identification of reference genes for normalization of gene expression in blueberry

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Abstract

Application of transcriptomics approaches can greatly enhance our understanding of blueberry physiology. The success of transcriptomics approaches is dependent on the extraction of high-quality RNA which is complicated by the abundance of polyphenolics and polysaccharides in blueberry. Additionally, transcriptomics requires the accurate quantification of transcript abundance. Quantitative real-time polymerase chain reaction (qRT-PCR) is a robust method to determine transcript abundance. Normalization of gene expression using stably expressed reference genes is essential in qRT-PCR. An evaluation of the stability of expression of reference genes has not yet been reported in blueberry. The objectives of this study were to develop an effective procedure for extracting RNA from different organs and to evaluate potential reference genes for qRT-PCR analyses in blueberry. RNA of high quality and yield was extracted from eight and six organs of rabbiteye and southern highbush blueberry, respectively, using a modified cetyltrimethyl ammonium bromide-based method. The expression stability of 12 reference genes was evaluated. UBIQUITIN-CONJUGATING ENZYME (UBC28), RNA HELICASE-LIKE (RH8), CLATHRIN ADAPTER COMPLEXES MEDIUM SUBUNIT FAMILY PROTEIN (CACSa), and POLYUBIQUITIN (UBQ3b) were the most stably expressed genes across multiple organs in both blueberry species. Further, the expression stability of the reference genes in the branch abscission zone following treatment with fruit abscission-inducing compounds was analyzed. CACSa, RH8, and UBC28 were the most stably expressed genes in the abscission zone under abscission-inducing conditions. We suggest a preliminary evaluation of UBC28, CACSa, RH8, and UBQ3b to identify the most suitable reference genes for the experimental conditions under consideration in blueberry.

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Acknowledgments

This study was supported by a United States Department of Agriculture (USDA)—Specialty Crop Research Initiative (SCRI) Grant (2008-51180-19579).

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Authors and Affiliations

  1. Horticulture Department, University of Georgia, Athens, GA, 30602, USA

    Tripti Vashisth, Lisa Klima Johnson & Anish Malladi

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  1. Tripti Vashisth
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  2. Lisa Klima Johnson
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  3. Anish Malladi
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Corresponding author

Correspondence to Anish Malladi.

Additional information

Communicated by P. Lakshmanan.

T. Vashisth and L. K. Johnson contributed equally to this work.

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Vashisth, T., Johnson, L.K. & Malladi, A. An efficient RNA isolation procedure and identification of reference genes for normalization of gene expression in blueberry. Plant Cell Rep 30, 2167–2176 (2011). https://doi.org/10.1007/s00299-011-1121-z

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