RNAi and CRISPR/Cas9 as Functional Genomics Tools in the Neotropical Stink Bug, Euschistus heros

Simple Summary

Understanding the biology of insect pests is an important step towards developing appropriate control strategies. In this study, a CRISPR/Cas9 gene knockout work flow was established for the first time and was together with RNAi used as tools to study gene functions in the Neotropical stink bug, Euschistus heros. RNAi was first employed to study the function of three genes, abnormal wing disc (awd), tyrosine hydroxylase (th) and yellow (yel). Targeting awd and th resulted in distinct malformed phenotypes such as a deformed wing or a lighter cuticle pigmentation/defects in cuticle sclerotization, respectively. However, no distinct phenotype was observed for yel. To further investigate the function of yel, a CRISPR/Cas9 gene editing protocol was developed for E. heros. A total of 719 eggs were microinjected with single-guide (sgRNA) and Cas9 and total of six insects hatched. Out of these six nymphs, one insect showed mutation in yel but no clear phenotype was visible. Although, we were unable to generate insects with a distinct phenotype for yel, a successful gene editing workflow was established to complement RNAi for future functional gene studies in E. heros. Additionally, we provided recommendations to improve the established gene editing workflow.

Abstract

The Neotropical brown stink bug, Euschistus heros, is one of the most important stink bug pests in leguminous plants in South America. RNAi and CRISPR/Cas9 are important and useful tools in functional genomics, as well as in the future development of new integrated pest management strategies. Here, we explore the use of these technologies as complementing functional genomic tools in E. heros. Three genes, abnormal wing disc (awd), tyrosine hydroxylase (th) and yellow (yel), known to be involved in wing development (awd) and the melanin pathway (th and yel) in other insects, were chosen to be evaluated using RNAi and CRISPR/Cas9 as tools. First, the genes were functionally characterized using RNAi knockdown technology. The expected phenotype of either deformed wing or lighter cuticle pigmentation/defects in cuticle sclerotization was observed for awd and th, respectively. However, for yel, no obvious phenotype was observed. Based on this, yel was selected as a target for the development of a CRISPR/Cas9 workflow to study gene knockout in E. heros. A total of 719 eggs were injected with the Cas9 nuclease (300 ng/µL) together with the sgRNA (300 ng/µL) targeting yel. A total of six insects successfully hatched from the injected eggs and one of the insects showed mutation in the target region, however, the phenotype was still not obvious. Overall, this study for the first time provides a useful CRISPR/Cas9 gene editing methodology to complement RNAi for functional genomic studies in one of the most important and economically relevant stink bug species.

1. Introduction

An increase in genome and transcriptome sequence databases for non-model insects, coupled to the development of high-throughput techniques for gene expression profiling and functional characterization has made it possible to study the biology of non-model insects. This is particularly interesting for pest insect species where understanding the underlying mechanisms in their biology through functional genomics could lead to the development of potential pest control strategies. Euschistus heros (Hemiptera: Pentatomidae) is one of the most important stink bug species present in South America and is responsible for causing severe damage to several crops, especially soybean, mainly during the reproductive period [1,2,3]. The recently published transcriptome of E. heros [4] provides a good starting basis to explore the biology of this important pest species. However, this will require the adaptation of current available functional genomics tools, including CRISPR/Cas9 gene editing, for studies in E. heros.

Post-transcriptional gene silencing also known as RNA interference (RNAi) was first elucidated in 1998 [5] and has since then been widely used as a tool in the study of gene function. In the hemipteran group, RNAi has been used to study the role of genes in insect development/reproduction of several species, such as Oncopeltus fasciatus [6,7], Nezara viridula ([8], Diaphorina citri [9], Halyomorpha halys [10], among others. RNAi is a highly conserved mechanism among eukaryotic organisms, in which the messenger RNA (mRNA) is cleaved by the RNAi machinery, leading to the inactivation of gene expression [11]. However, RNAi efficiency can vary between different insect groups, developmental stages or tissues [12] and due to its transient characteristic, it might not be suitable for studying some candidate genes.

On the other hand, Clustered Regularly Interspaced Palindromic Repeats/CRISPR-associated protein 9, known as CRISPR/Cas9, is a genetic tool that allows researchers to do very specific modification at a genomic level. The CRISPR/Cas9 system is formed by three main components—a molecule of approximately 21 nucleotides called CRISPR RNA (crRNA), the trans-activating CRISPR RNA (tracrRNA) and the Cas9 enzyme. The crRNA and tracrRNA form the sgRNA (single-guide RNA), which guides the Cas9 enzyme to the complementary DNA sequence in the genome, near the PAM (protospacer adjacent motif) sequence—NGG. Once the system finds the complementary region, the Cas9 endonuclease cleaves the two DNA strands, generating a double-strand break (DSB) in the target sequence [13,14]. The DSB can be repaired by two different approaches: error-prone non-homologous end joining (NHEJ) or homology-directed repair (HDR). The repair by the NHEJ can result in either deletions or insertions known as “indels” or generate nucleotide substitutions, leading to the creation of a mutant version of the target gene [15,16,17]. On the other hand, HDR is mainly used to generate repair based on a donor template, leading to a gene knock-in repair process [16,18].

In this study, we explored the use of RNAi and CRISPR/Cas9 as complementary functional genomics tools to elucidate the role of genes in E. heros. Prior to the genome editing experiments, abnormal wing disc (awd), tyrosine hydroxylase (th) and yellow (yel) were evaluated in E. heros by exploiting RNAi-mediated knockdown technology. Awd is a gene involved in wing development in several species [9,19,20], while th and yel are genes involved in the melanin pathway [21]. Based on the lack of an obvious phenotype following the knockdown of yel, a CRISPR/Cas9 gene editing workflow was developed for the first time for E. heros to complement RNAi in the study of yel. Additionally, we provide recommendations to further improve the gene editing workflow presented in this study for future mutagenesis studies in stink bugs.

2. Materials and Methods

2.1. Insects

A colony of E. heros was kept under standard mass-rearing conditions of 25 ± 2 °C, 60 ± 10% relative humidity and a light/dark photoperiod of 14:10 h at the Laboratory of Agrozoology, Ghent University. The insects were kept in plastic boxes and fed ad libitum with a mixture of fresh green bean pods (Phaseolus vulgaris (L.)), raw shelled peanuts (Arachis hypogaea (L.)) and soybean seeds (Glycine max (L.)) [22]. The supplies were replenished every 3-days. Eggs were removed and placed in Petri dishes for five days, then transferred to plastic boxes and reared until they reached adulthood.

2.2. Target Gene Identification and Expression Profile

The protein sequences for awd, th and yel from the pea aphid Acyrthosiphon pisum (NP_001119625.1, XP_008182999.1 and XP_001948479.1, respectively) was used as query to identify homologs of the candidate genes in an own published E. heros transcriptome database [4], using the tBLASTn tool. We then detected the open reading frames (ORFs) in the retrieved E. heros homologs using the ORF Finder from the National Center for Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih.gov/orffinder/). The Protein Basic Local Alignment Tool (Protein BLAST) was used for protein homology searches against the insect non-redundant protein database at NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi). To confirm the identity of the identified genes, their protein sequences were aligned against those of other insect species using MUSCLE with default settings [23] and a phylogenetic tree was constructed using maximum likelihood with default settings in the software MEGA7 [24].

To evaluate the stage-specific expression of awd, th and yel, samples from different developmental stages including eggs (dissected from female ovaries, <24 h old and 7 days old), nymphs (1st-, 2nd-, 3rd-, 4th-, 5th-instar) and adults (male and female) were prepared (Table S1). Briefly, total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) and treated with DNase I (Ambion, Austin, TX, USA) to remove residual genomic DNA. RNA was quantified using a NanoDrop ND-1000 (Nanodrop Technologies, Wilmington, DE, USA), visualized in a 1.5% agarose gel and stored in −80 °C until further use. cDNA was synthesized using a SuperScript IV kit (Invitrogen, Carlsbad, CA, USA) with an oligo d(T) primer in a final volume of 20 μL, according to the manufacturer’s instructions.

Quantitative real-time PCR (qRT-PCR) analysis was performed with a CFX 96TM real-time system and the CFX manager software (Bio-Rad, Hercules, CA, USA). qRT-PCR primers were designed using PrimerQuest Tool from IDT (https://www.idtdna.com/pages) (Table S2) and a standard curve based on a serial dilution of cDNA was done to determine the primer annealing efficiency and a melting curve analysis with a temperature range from 60 to 95 °C. The qRT-PCR reaction was done in a 20 μL-reaction system, containing 8 μL of cDNA samples, 10 μL of GoTaq qPCR Master Mix (Promega, Madison, WI, USA) and 1 μL of each primer (10 μM). The reactions were set-up in 96-well format Microseal PCR plates (Bio-Rad). The amplification conditions were 3 min at 95 °C followed by 39 cycles of 10 s at 95 °C and 30 s at 60 °C. After the amplification, a melting curve analysis with a temperature gradient of 0.1 °C/s from 60 to 95 °C was performed to confirm that only the specific product was amplified. The endogenous controls, ribosomal protein 18S and RPL32, were used for normalization of the qRT-PCR data. A no-template control was also included in the assay. All experiments were performed in three biological replicates. Relative expression values of genes were calculated using the equation ratio 2^−ΔΔCt [25].

2.3. RNAi-Mediated Gene Silencing Assay

Primers were designed using the PrimerQuest Tool from Integrated DNA Technologies (IDT) (https://www.idtdna.com/pages) and T7 promoter sequences placed at the 5′-ends of both forward and reverse primers (Table S2). DNA templates were amplified using Taq DNA polymerase (Invitrogen) and cDNA as a template. Green fluorescent protein (GPF) was amplified from a plasmid containing the GFP insert (Genbank ID: NC_011521.1). The DNA templates were purified using the Wizard clean-up system (Promega). The dsRNAs were synthesized using the MEGAscript RNAi kit (Ambion) following the manufacturer’s instructions. The dsRNA was quantified on a NanoDrop ND-1000 (Nanodrop Technologies) and integrity analyzed in an electrophoresis gel.

Third instar nymphs were microinjected using a microinjector (FemtoJet, Eppendorf, Hamburg, Germany), equipped with an injection needle prepared with capillary glass tubes. Each nymph was injected with 1.0 µL of a 1 µg/μL dsRNA solution, based on an established protocol [4,26]. The nymphs were anesthetized with ether for 2 min and then injected on the ventral metathoracic region, near to the hind coxa. DsRNA targeting GFP was used as a negative control. Twenty-six nymphs were injected per gene-specific dsRNA treatment and the experiment was repeated twice (N = 52 in total). After microinjections, nymphs were put in Petri dishes containing green bean slices and kept under standard mass-rearing conditions. Insects were supplied with fresh green beans and seeds every 2–3 days. Insects were checked for phenotype under a stereomicroscope (Leica DFC295, Wetzlar, Germany).

Gene expression was measured 72 h post-microinjection. Three groups of two pooled insects/group were sampled from each gene-specific treatment group and used for the qRT-PCR measurements. This was done for the two experiment repeats (N = 6 groups in total). For all samples, total RNA isolation and qRT-PCR analysis were done as described above. The qRT-PCR reactions were performed in the CFX 96TM real-time system (Bio-Rad) following the steps described above.

2.4. CRISPR/Cas9 Gene Editing Assay

The sequence for the yel gene was obtained from the E. heros transcriptome (PRJNA488833) and its open reading frame (ORF) was predicted using the ORFfinder tool from NCBI (https://www.ncbi.nlm.nih.gov/orffinder/) as mentioned above. The retrieved coding sequences were used to design a guide RNA target sequence (gRNA) that targeted both isoforms, according to the criteria: 5′-GG-(N)18-NGG-3′ [27]. The IDT Custom Alt-R CRISPR-Cas9 guide RNA design tool (https://eu.idtdna.com/site/order/designtool/index/CRISPR_CUSTOM) was used to predict the sgRNA with the lowest potential for off-target-risk and a high on-target potential. Additionally, in the absence of a publicly available genome database for E. heros, potential off-targets were checked in the transcriptome using the predicted sgRNA through BLAST analysis.

Eggs were collected within a maximum of 1 h after oviposition and quickly lined up in preparation for injection. Glass slides used for microinjection were prepared as follows: two glass slides stuck together using double tape, with a 3 cm overlapping space. On this overlapping space, eggs were lined up (longitudinal orientation) against the top glass slide, quickly covered with nuclease-free water (~1.5 mL) [28] and then wrapped with plastic film with the aim to fix the eggs in position on the glass slide. An injection solution containing 300 ng/µL sgRNA and 300 ng/µL Alt-R Cas9 protein (IDT) was prepared and the eggs were injected using a microinjector (about 2 nL per egg) (FemtoJet, Eppendorf), equipped with a needle prepared from a capillary glass tube. Controls were injected with nuclease-free water. During injection, the needle was inclined at an angle of about 30° relative to the microscope stage. After injection, the eggs were placed into Petri dishes, underlaid by a slightly moist filter paper soaked with water + Nipagin (1%) to avoid fungal growth, especially at the injection point on the eggs. The Petri dishes were then sealed with a plastic film and returned to the incubator under standard rearing conditions as described above. The injected eggs were monitored for 8 days for nymph hatching, after which the nymphs were transferred to new Petri dishes and fed with fresh green beans ad libitum.

Upon hatching, the nymphs were observed and assessed under the microscope (Leica DFC295, Wetzlar, Germany). Genomic DNA from three nymphs from the yel treatment and three nymphs from the control were individually extracted using QIAamp DNA Mini Kit (Qiagen) and used as a template for PCR amplification of the yel gene region containing the sgRNA target site (Table S2). The PCR conditions were: 95 °C for 2 min, 35 cycles of 95 °C for 30 s, 55 °C for 30 s and 72C for 1 min, followed by a final extension of 10 min at 72 °C. The resulting PCR product from each E. heros individual was sequenced (LGC Genomics, Berlin, Germany) to verify for mutation in yel. The wild-type sequence used for mutation analysis originated from control embryos injected with water.

2.5. Data Analysis

The data were checked for normality and homoscedasticity using the Shapiro-Wilk and Levene’s tests. Failing these assumptions, they were compared using the Kruskal-Wallis test followed by Dunn’s multiple comparison test using GraphPad Prism Software. The results of the survival bioassays were subjected to survival analysis, which was performed using Kaplan-Meier estimators (log-rank method) with SigmaPlot 12.0 (Systat Software, San Jose, CA, USA).

3. Results

3.1. RNAi-Mediated Knockdown for Functional Genomics in E. heros

Before starting with the bioassays in E. heros, we first confirmed the identity of the candidate genes (awd, th and yel) in this species through phylogenetic analysis, where they were observed to cluster on distinct branches together with their respective homologs in other insect species (Figure S1). Life stage-specific expression of awd, yel and th at the mRNA level was also evaluated, with the aim to select the best time-point for dsRNA treatment. Although the expression level of awd in the different developmental stages was more or less stable (1.34 ± 0.15) (Figure S2), its expression in the eggs dissected from the ovary was higher (7.34 ± 0.84) when compared to less than one day old laid eggs (0.42 ± 0.10). The expression level of th was higher in E. heros females (2.98 ± 0.94) compared to E. heros males (<0.01 ± 0.001), whereas no difference was found in its expression between the different developmental stages (0.51 ± 0.23). Similar to th, the expression level of yel was higher in females (3.47 ± 0.66) when compared to males (0.01 ± 0.004) and also eggs dissected from the ovary (0.01 ± 0.003), while it remained similar between the other developmental stages (0.59 ± 0.31). Overall, no major differences were noted in the expression profiles for awd, th and yel between the different nymphal stages. As such, freshly molted 3rd-instar nymphs (<24 h old) were selected for RNAi gene silencing bioassays. Out of 40 nymphs treated with dsawd, 18 died as 3rd-instar nymphs during the expected molting period (45%), 20 successfully molted to 5th-instar nymphs (50%) and 17 reached adulthood (43%) (Figure 1a). Moreover, 15% (6 adults) of the adults showed abnormalities in wing formation (Figure 1b) which could appear extremely shortened in some individuals (Figure S3). Out of 40 nymphs treated with dsth, 31 molted to the 4th-instar (78%), 16 molted to the 5th-instar (40%) and only 3 reached adulthood (8%). Moreover, defects in cuticle sclerotization, a curved abdomen, malformed antenna and legs were observed in dsth-treated nymphs (Figure 1b). Out of 40 dsyel-treated nymphs, 22 insects reached adulthood (55%) (Figure 1a). Treatment with dsyel, did not result in any obvious difference in cuticle development nor pigmentation when compared to the normal phenotype observed in the control (dsGFP) (Figure 1b). For the insects treated with dsGFP, 35 insects (88%) successfully molted to 4th-instar and 26 reached adulthood (65%) (Figure 1a). Treatment with dsth resulted in a lighter pigmentation of the nymph cuticle compared to the control (dsGFP) of the same life stage (Figure 1b).

To verify RNAi-mediated silencing of awd, th and yel in the treated insects, their transcript levels were evaluated by qRT-PCR. A respective significant reduction of 98.5, 98.4 and 91.1% in the transcript level of awd, th and yel was observed in the target gene-specific dsRNA-treated insects when compared to the control (dsGFP) (p < 0.001) (Figure 1c–e).

Survival of the treated insects was evaluated for 27 days. Dsawd-, dsyel- and dsGFP-treated groups showed similar survival levels in contrast to the dsTh-treated group (Holms-Sidak’s statistics < 32.1, p < 0.0001) (Figure 2). The mortality rate of dsawd-, dsyel- and dsGFP-treated insects at 27 days after microinjection was 57, 45 and 35%, respectively (Holms-Sidak’s statistics < 3.61, p = 0.1). The mortality rate of dsth-treated insects was quite high (92%) when compared to that in the control dsGFP-treated insects (Holms-Sidak’s statistics < 32.1, p < 0.0001).

3.2. CRISPR/Cas9 Gene Editing for Functional Genomics in E. heros

A CRISPR/Cas9 workflow for gene knockout in E. heros was established. The entire workflow consisted of 9 steps, from egg collection through embryo injection to screening of the genotype and phenotype in hatched nymphs (1-day old) and lasted for 8 days (Figure 3).

Based on the results from the previous RNAi bioassay, where knocking down the expression of yel did not lead to any obvious phenotype, yel was selected as the target for a CRISPR/Cas9 gene knockout experiment with the aim of maybe getting a distinct visible phenotype. The yel gene has two isoforms in E. heros, hence ensuring successful disruption of the expression of both isoforms, a single-guide RNA was designed within the coding sequence for gene knockout (File S1). A total of 719 E. heros eggs were injected with sgRNA (300 ng/µL) and Cas9 protein (300 ng/µL), however, only 6 successfully hatched to 1st-instar nymphs (~1% hatching rate). In the control, 276 eggs were injected with water of which 28 successfully hatched into 1st-instar nymphs (10% hatching rate).

All of the hatched 1st-instar nymphs from the test group were carefully examined under the microscope. Unfortunately, no obvious distinct phenotype from the control 1st-instar nymphs was observed (Figure S4). Out of the six 1st-instar nymphs from the test group, three were randomly selected and sequenced (Yel-Nymph0, Yel-Nymph1 and Yel-Nymph3). The sequencing data revealed deletions in the targeted region in one of the three nymphs (Figure 4a,b). The remaining nymphs (Yel-Nymph2, 4 and 5) died within four days after hatching.

4. Discussion

RNAi-mediated gene knockdown and CRISPR/Cas9-mediated gene knockout have been successfully used as tools for functional genomic studies in insects. However, the use of the CRISPR/Cas9 system in a non-model insect, such as E. heros has never been demonstrated before. In this study, we demonstrate the use of both RNAi and CRISPR/Cas9 as complementary tools in the elucidation of gene function in E. heros.

In a first step, RNAi-mediated knockdown experiments in E. heros targeting awd and th resulted in the insects having distinct malformed phenotypes, confirming the role of these genes in specific physiological processes. Treatment with dsawd resulted in E. heros adults with malformed wings which varied in severity. We hypothesize that this difference could be linked to several factors ranging from a difference in awd knockdown efficiency between individuals within the treated group to the length in time of the silencing signal. Nevertheless, we could confirm that awd is linked to wing development in E. heros as was also reported for other insect species such as Drosophila melanogaster [19], Bombyx mori [29], Diaphorina citri [9] and Antheraea pernyi [20]. RNAi knockdown of th transcripts in E. heros resulted in nymphs with a lighter pigmentation of the cuticle, curved abdomen, malformed antenna and lack of proper sclerotization. The th gene is known to be involved in the synthesis of black melanin precursors, which are in turn associated with the conversion of tyrosine to dihydroxyphenylalanine (DOPA) and dopamine (dihydroxyphenylethylamine) [21,30]. Similar to the phenotype observed in dsth-treated E. heros, knocking down th in the twin-spotted assassin bug Platymeris biguttatus also resulted in insects with a pale pigmentation of the cuticle confirming the role of th in the melanin pathway [21]. Contrary to th, knocking down yel did not result to any obvious change in the pigmentation of the cuticle as would be expected. Both th and yel have been reported to be involved in the melanin pathway where yel is required for the synthesis of DOPA and dopamine melanin [30]. Loss of yel in D. melanogaster caused a lack of melanin incorporation, resulting in a yellowish overall appearance of the cuticle [31]. Similar effects have been observed in other insects such as B. mori [32], P. biguttatus [21], while in Tribolium castaneum, loss of yel led to a slightly darker coloration of the cuticle, coupled with high mortality in the adults [33]. The transient gene silencing characteristic of RNAi can present a weakness to its use as a tool for functional genomics. For example, the time-point for injection and/or the duration of the gene silencing signal can affect the outcome of a phenotype [34]. This can range from no change in phenotype (despite gene silencing) through a mild to a strong phenotype in the target organism. As a result, RNAi might not be suitable alone as a tool for all types of functional genomic studies.

In the second part of this study, we developed and used a CRISPR/Cas9-mediated gene knockout work flow for the first time in E. heros to complement RNAi for functional gene studies. The yel gene was selected as a target for the knockout experiments based on the lack of an obvious phenotype following RNAi knockdown. The chromatogram revealed a predominant deletion of 6 nucleotides that caused an in-frame mutation in the conserved domain of yel, which belongs to the MRJP (Major royal jelly protein) super family (PF03022). Unfortunately, the knockout of yel did not lead to an obvious change in the pigmentation of the cuticle in the sequenced mutant nymph. Considering the multicolor natural appearance of E. heros (particularly the nymphs), it might be possible that we might have missed very subtle changes in the color of the cuticle which are not obvious with mere observation under the microscope. Also, the exact role of yel in body pigmentation in E. heros is unknown. In B. mori, it is hypothesized that yel acts together with laccase 2 in the body pigmentation pathway [30]. This implies that in the absence of yel, laccase 2 may still be functional in the melanin pathway, allowing body pigmentation. Two shortcomings of the current study are that the number of genomic loci encoding yel in E. heros are unknown and also that in the absence of next generation sequence data, solely sanger sequencing results were not conclusive to confirm heterozygosity or homozygosity of yel in the mutant insect. Assuming that yel-sgRNA targeted yel only on one locus, then expression from the untargeted locus could still result to a normal wild-type phenotype. In the absence of a genome for E. heros, we recommend southern blot analysis to confirm gene copy number. Also, the expression of a recessive gene in a heterozygous mutant could still result in a normal phenotype. Another major challenge was the low hatchability rate of the yel-sgRNA injected eggs. Based on other CRISPR/Cas9 gene editing protocols developed for non-model insects, a low percentage of hatching was expected [34]. However, the percentage of hatched nymphs in the treatment with yel-sgRNA (~1%) was under the expected rates (≥10%), resulting in only one detected mutant. A possible explanation could be the unknown role of yel during embryogenesis in E. heros, where complete knockout of yel is lethal. In a similar study in the large milkweed bug Oncopeltus fasciatus, the knock-out of the white gene resulted in significant embryonic mortality [35], although its homolog in Drosophila melanogaster is widely known to be involved in eye pigmentation [36]. Depending on the stage of embryonic development when CRISPR/Cas9 components are delivered, it is not uncommon to have a mixed population of edited (somatic mutations) and unedited cells that can result to mosaic effects in generation 0 (G₀) [37]. Furthermore, depending on the target gene and which cell population (edited versus unedited) in G₀, mosaicism can either hide or render a phenotype prominent. In the Colorado potato beetle, Leptinotarsa decemlineata, a range of phenotypes was observed after the vestigial gene (vest) was knocked out with attribution to differences in the mutation level (monoallelic, biallelic or no mutations at all) [34]. Low egg hatchability in E. heros following treatment with yel-sgRNA could also be attributed to off-target mutations in essential genes necessary for embryonic development and survival. Although yel-sgRNA was verified to have no potential off-targets in the transcriptome of E. heros, there is a still high possibility of off-targets at the genome level which could have resulted in the low hatching rates observed. The generation of a genome database for E. heros will greatly facilitate the use of CRISPR/Cas9 as a tool for functional genomics in this species. Nevertheless, we successfully developed and demonstrated a working CRISPR/Cas9-mediated gene editing work flow for E. heros, paving the way for further optimization and application.

5. Conclusions and Recommendations

Until now, it is mainly RNAi that has been explored in the research of gene function in E. heros. It is well known that the efficiency of RNAi-mediated gene knockdown is not always sufficient and due to this, it may not be suitable for functional analysis of some genes and in all insect species. On the other hand, the CRISPR/Cas9 system allows us to surpass some of the challenges faced using RNAi through the generation of mutant lines by a relatively simple and inexpensive method. However, this technique is time-consuming and similar to RNAi can present low efficiency in some species. Nevertheless, both tools can complement each other in functional gene studies in insects when properly applied. In our study, we successfully demonstrated that it is possible to exploit the CRISPR/Cas9 system to generate mutants in E. heros with room for improvement. With proper optimization following some of the recommendations provided in this study (Box 1) and some adaptations, the use of the presented CRISPR/Cas9 work flow can be exploited beyond functional gene studies to generate gene drives [17] for insect pest control.

Box 1. Some recommendations for improving CRISPR/Cas9-mediated gene editing in E. heros.

• Freshly laid eggs: Cell division is a continuous process during embryonic development, hence injecting early enough (<1 h post oviposition) can reduce mosaicism.
• Needle size: Keep the needle opening small enough to not damage the egg while still being able to inject without requiring a high injection pressure.
• Nuclease-free water to cover the eggs:E. heros eggs have a very hard chorion, which protects them from environmental conditions. Adding water will temporarily render it soft, allowing the needle to penetrate without breaking and damaging the egg.
• Water + Nipagin (1%) on underlying filter paper in the Petri dishes: This will significantly reduce potential fungal growth on the eggs at the injection point.
• Target-gene choice: This will be dependent on the objective of the experiment. Essential genes for survival versus genes linked to non-lethal phenotypes.
• Multiple sgRNAs: If properly designed can significantly improve gene knockout and ease detection of mutants, based on amplicon size of the mutated gene versus the wild type.
• Ratio of Cas9 sgRNA: Ratios other than the 1:1 ratio used in this study could improve efficiency.
• Type of Cas enzyme: Depending on the objective of the experiment, other Cas enzymes could be used to target specific sites in the genome (e.g., Cas12a).