Efficient, low-cost, and noninvasive characterization of the timing, occurrence, and duration of spawning and larval rearing in Pacific Lamprey (PL) is vital to its recovery. Yet, direct surveys via electrofishing, rotary screw trapping, drift netting, and redd surveillance can be time consuming, costly, and injurious. Though comparatively cheap and efficient, noninvasive environmental DNA (eDNA) surveys are often limited to presence-absence because qPCR of genomic DNA cannot distinguish phenotypes, such as life stages, maturity, or sex. By contrast, ‘reverse transcriptase’ (RT) PCR of environmental messenger RNA (eRNA) specifically targets the transcriptome and thus quantifies gene expression, as opposed to gene identity. Thus, if phenotypes correspond to unique gene expression profiles or ‘transcript-types’ then there is potential to develop RT-PCR assays for characterizing spawning and rearing activities. The goal of this study is to develop new eRNA markers based on genes known to distinguish phenotypes in other lamprey species. Our objectives are to identify differentially expressed genes (DEGs) between larvae and mature males/females and to design RT-PCR assays that specifically target those genes. The deliverable of this study is RT-PCR assays that are diagnostic for phenotypes to help map spawning versus rearing activities of PL using eRNA.

Environmental RNA has the potential to help provide status information that is specific to life stages, which are some of the key components to effective monitoring programs and can help support targeted and streamlined recovery actions.