| Summary: | The oriental fruit fly is a polyphagous and highly invasive economically important pest in the world. We proposed the hypothesis that radiation treatment influence RNA expression in the larvae and leads to emergence failure. Therefore, transcriptome analyses of third-instar larvae of <i>B. dorsalis</i> ionizing, irradiated with <sup>60</sup>Co-γ at 116Gy, were conducted and compared with the controls; a total of 608 DEGs were identified, including 348 up-regulated genes and 260 down-regulated ones. In addition, 130 SNPs in 125 unigenes were identified. For the DEGs, the most significantly enriched GO item was hemolymph coagulation, and some of the enriched pathways were involved in digestive processes. The subsequent validation experiment confirmed the differential expression of six genes, including <i>sqd</i>, <i>ENPEP</i>, <i>Jhe</i>, <i>mth</i>, <i>Notch</i>, and <i>Ugt</i>. Additionally, the 3401:G->A SNP in the <i>Notch</i> gene was also successfully validated. According to previous research, this was the first comparative transcriptome study to discover the candidate genes involved in insect molt to pupae. These results not only deepen our understanding of the emerging mechanism of <i>B. dorsalis</i> but also provide new insights into the research of biomarkers for quarantine insect treatment with the appropriate dose of radiation.
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