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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Commodity Protection and Quality Research » Research » Publications at this Location » Publication #408575
Research Project: Improved Systems-based Approaches that Maintain Commodity Quality and Control of Arthropod Pests Important to U.S. Agricultural Production, Trade and Quarantine

Location: Commodity Protection and Quality Research

Title: Gene expression patterns to identify stable reference genes for expression analyses in Carpophilus hemipterus (L.) (Coleoptera: Nitidulidae)

Author
item Bansal, Raman
item Burks, Charles - Chuck
item Walse, Spencer

Submitted to: Gene Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/11/2024
Publication Date: 7/25/2024
Citation: Bansal, R., Burks, C.S., Walse, S.S. 2024. Gene expression patterns to identify stable reference genes for expression analyses in Carpophilus hemipterus (L.) (Coleoptera: Nitidulidae). Gene Reports. 36(2024). Article 101982. https://doi.org/10.1016/j.genrep.2024.101982.
DOI: https://doi.org/10.1016/j.genrep.2024.101982

Interpretive Summary: The dried fruit beetle (DFB) is one of the common pests of figs, raisins, prunes, dates as well as stone fruits in central California. There are no validated reference genes to normalize the gene expression for real-time quantitative PCR in this insect. We selected and validated 12 commonly used reference genes for their stability across developmental stages, sexes, and under thermal stress conditions. Two genes UBE3A (Ubiquitin E3 ligase) and RPL9 (Ribosomal protein L9) were identified as the most stable across the treatments, and thus were recommended for normalizing the real time gene expression data. These findings will support genomics investigations into developmental biology to reveal the fundamental and applied biological aspects in this important beetle species.

Technical Abstract: Dried fruit beetle, Carpophilus hemipterus, (Linnaeus, 1758) (Coleoptera: Nitidulidae) is a serious pest of ripened fresh fruit in the orchard and dried fruit in post-processing storage. Despite the economic significance and widespread distribution of C. hemipterus, there is a lack of functional genomics research seeking to elucidate features of developmental biology and molecular physiology for improved pest management. Performing such functional genomics studies requires validated, stably expressed reference genes for accurate normalization of real-time quantitative reverse transcription-PCR (qRT-PCR) data. Here, we identified and validated 12 common insect reference genes (RPL6, RPL4, RPL9, RPS13, RPS18, RPSA, TUB, UBE3A, RPS23, GLU, EF1A, and RBP) for expression stability in C. hemipterus. These genes were assessed across developmental stages and sexes (egg, three larval instars, prepupa, pupa, adult male, and adult female) as well as thermal stress conditions. Stability of candidate genes was estimated using software algorithms geNorm, NormFinder, BestKeeper, comparative delta-Ct, and RefFinder. Two genes UBE3A and RPL9 showed the highest stability across the treatments, and thus were proposed for normalizing the qRT-PCR raw data. Results of this study will strengthen the application of genomics to reveal the fundamental and applied biological aspects in this important beetle species.