Population structure and genetic diversity of invasive Fall Armyworm after 2 years of introduction in India

Dominant strain shift in the invasive fall armyworm (Lepidoptera: Noctuidae) populations in Thailand as inferred from mitochondrial COI and nuclear Tpi genes

The fall armyworm, Spodoptera frugiperda (J. E. Smith, 1797) (Lepidoptera: Noctuidae), is a significant global pest, that exhibits 2 discernible strains, corn strain (CS) and rice strain (RS). After initial detection in the eastern hemisphere in 2016, the dominant strain was identified as RS based only on cytochrome C oxidase subunit I (COI) mitochondrial gene from limited samples from various countries, including Thailand. This study aimed to assess strain and haplotype variation in the S. frugiperda populations in Thailand using both mitochondrial COI and nuclear triosephosphate isomerase (Tpi) genes. Analyses of COI sequences (n = 105) revealed 2 predominant haplotypes, COICSh4 (82.86%) and COIRSh1 (17.14%), and the analyses of Tpi sequences (n = 99) revealed 6 haplotypes, with TpiCa1a (53.53%) being the most prevalent. Of the 98 caterpillar samples, the majority exhibited true CS (83.67%) for both genes. Meanwhile, interstrain hybrids, indicated by gene discordance, accounted for the minority (16.33%). Interestingly, despite the initial dominance of RS during the 2018 outbreak, the current study identified CS as the prevalent strain across all localities in Thailand. These findings suggested a shift in S. frugiperda dynamics in Thailand that was possibly influenced by factors, such as competitive exclusion principle, pesticide usage in rice cultivation, and preferences for corn over rice. Our study suggests a need to reexamine the previous reports of rice-strain dominance in various countries in the eastern hemisphere after the initial invasion.

First report of resistance in Spodoptera frugiperda (Lepidoptera: Noctuidae) to lambda-cyhalothrin from Pakistan: baseline susceptibility, selection, occurrence of cross-resistance, realized heritability, and inheritance mode of resistance

Fall armyworm (FAW) Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), is a global pest causing damage to several crops. However, its management using chemical control is a challenge due to its capacity to evolve resistance to insecticides. After 6 generations of selection with lambda-cyhalothrin, the LC50 for the insecticide-resistant strain (Lambda-Sel) was 486 ppm, higher than that of the field strain (FAW-MUL) (7.5 ppm), susceptible laboratory strain (Lab-PK) (0.46 ppm), and laboratory unselected strain (UNSEL) (5.26 ppm). Laboratory selection with lambda-cyhalothrin increased resistance from 16.3- to 1056.52-fold and 1.43- to 92.4-fold to lambda-cyhalothrin compared to Lab-PK and UNSEL strains, respectively. The selected strain of S. frugiperda (Lambda-Sel) presented low cross-resistance to chlorpyrifos, moderate to deltamethrin and indoxacarb, very low to spinosad, and no cross-resistance to emamectin benzoate. The realized heritability (h2) of lambda-cyhalothrin resistance in the Lambda-Sel strain was very high (0.88). The reciprocal cross progenies of F1 (Lambda-Sel ♀ × Lab-PK ♂), F1' (Lambda-Sel ♂ × Lab-PK ♀), BC1 (F1 ♀ × Lambda-Sel ♂), and BC2 (F1 ♀ × Lab-PK ♂) showed high resistance ratios of 545.64-, 396.52-, 181.18-, and 146.54-fold, respectively compared to Lab-PK. The degree of dominance values for lambda-cyhalothrin in F1 and F1' indicates incompletely dominant resistance. The difference between observed and expected mortality in backcross populations (BC1 and BC2) revealed a polygenic resistance. In conclusion, the resistance to lambda-cyhalothrin was autosomal, incompletely dominant, and polygenic. These findings provide new insights for insect resistance management strategies to mitigate the occurrence of resistance in this global pest.

Genetic variation in the triosephosphate isomerase gene of the fall armyworm and its distribution across China

The fall armyworm (FAW), Spodoptera frugiperda, has colonized and caused consistent damage in the Eastern hemisphere. The identification of various FAW strains is essential for developing precise prevention and control measures. The triosephosphate isomerase (Tpi) gene is recognized as an effective marker closely linked to FAW subpopulations. However, most current studies primarily focus on the comparison of variations in specific gene sites of this gene. In this study, we conducted full-length sequencing of the Tpi genes from 5 representative FAW groups. Our findings revealed that the Tpi genes varied in length from 1220 to 1420 bp, with the primary variation occurring within 4 introns. Notably, the exon lengths remained consistent, at 747 bp, with 37 observed base variations; however, no amino acid variations were detected. Through sequence alignment, we identified 8 stable variation sites that can be used to distinguish FAW strains in the Eastern hemisphere. Additionally, we performed strain identification on 1569 FAW samples collected from 19 provinces in China between 2020 and 2021. The extensive analysis indicated the absence of the rice strain in the samples. Instead, we only detected the presence of the corn strain and the Zambia strain, with the Zambia strain being distributed in a very low proportion (3.44%). Furthermore, the corn strain could be further categorized into 2 subgroups. This comprehensive study provides a valuable reference for enhancing our understanding of FAW population differentiation and for improving monitoring and early warning efforts.

CRISPR/Cas9 mediated mutagenesis of the major sex pheromone gene, acyl-CoA delta-9 desaturase (DES9) in Fall armyworm Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae)

The Fall armyworm, Spodoptera frugiperda is a significant global pest causing serious yield loss on several staple crops. In this regard, this pest defies several management approaches based on chemicals, Bt transgenics etc., requiring effective alternatives. Recently CRISPR/Cas9 mediated genome editing has opened up newer avenues to establish functions of various target genes before employing them for further application. The virgin female moths of S. frugiperda emit sex pheromones to draw conspecific males. Therefore, we have edited the key pheromone synthesis gene, fatty acyl-CoA Delta-9 desaturase (DES9) of the Indian population of S. frugiperda. In order to achieve a larger deletion of the DES9, we have designed two single guide RNA (sgRNA) in sense and antisense direction targeting the first exon instead of a single guide RNA. The sgRNA caused site-specific knockout with a larger deletion which impacted the mating. Crossing studies between wild male and mutant female resulted in no fecundity, while fecundity was normal when mutant male crossed with the wild female. This indicates that mating disruption is stronger in females where DES9 is mutated. The current work is the first of its kind to show that DES9 gene editing impacted the likelihood of mating in S. frugiperda.

Microbiome analysis of Spodoptera frugiperda (Lepidoptera, Noctuidae) larvae exposed to Bacillus thuringiensis (Bt) endotoxins

Background

Spodoptera frugiperda (or fall armyworm, FAW) is a polyphagous pest native to Western Hemisphere and recently discovered in the Eastern Hemisphere. In Colombia, S. frugiperda is recognized as a pest of economic importance in corn. The species has genetically differentiated into two host populations named "corn" and "rice" strains. In 2012, a study made in central Colombia demonstrated that the corn strain is less susceptible to Bacillus thuringiensis (Bt) endotoxins (Cry1Ac and Cry 1Ab) than the rice strain. In this country, Bt transgenic corn has been extensively produced over the last 15 years. Since gut microbiota plays a role in the physiology and immunity of insects, and has been implicated in promoting the insecticidal activity of Bt, in this study an analysis of the interaction between Bt endotoxins and FAW gut microbiota was made. Also, the detection of endosymbionts was performed here, as they might have important implications in the biological control of a pest.

Methods

The composition and diversity of microbiomes associated with larval specimens of S. frugiperda(corn strain) was investigated in a bioassay based on six treatments in the presence/absence of Bt toxins and antibiotics (Ab) through bacterial isolate analyses and by high throughput sequencing of the bacterial 16S rRNA gene. Additionally, species specific primers were used, to detect endosymbionts from gonads in S. frugiperda corn strain.

Results

Firmicutes, Proteobacteria and Bacteroidota were the most dominant bacterial phyla found in S. frugiperda corn strain. No significant differences in bacteria species diversity and richness among the six treatments were found. Two species of Enterococcus spp., E. mundtii and E. casseliflavus were detected in treatments with Bt and antibiotics, suggesting that they are less susceptible to both of them. Additionally, the endosymbiont Arsenophonus was also identified on treatments in presence of Bt and antibiotics. The results obtained here are important since little knowledge exists about the gut microbiota on this pest and its interaction with Bt endotoxins. Previous studies made in Lepidoptera suggest that alteration of gut microbiota can be used to improve the management of pest populations, demonstrating the relevance of the results obtained in this work.

Invasion, Distribution, Monitoring and Farmers Perception of Fall Armyworm (Spodoptera frugiperda) and Farm-Level Management Practices in Bangladesh

Fall armyworm (FAW), Spodoptera frugiperda, is a major pest of maize that was first detected in Bangladesh in 2018 and rapidly spread throughout the maize-growing areas. The presence of FAW was monitored using sex pheromone traps. Farmers' pest management practices were assessed through a questionnaire. The damage is most apparent in the early and late whorl stages. As the crop is grown mostly from November to April, both vegetative and reproductive growth stages remain vulnerable to extensive damage. The survey results showed that 100% of the farmers used pesticides for FAW control, 40.4% handpicked and crushed egg masses, 75.8% handpicked and crushed caterpillars, and only 5.4% used other techniques like applying ash/sand in the funnel of maize. Commonly used pesticides included Spinosad, Emamectin benzoate, Imidacloprid, and others. Thirty-four percent of farmers applied pesticides twice in a season and 48% applied pesticides three times in a season and 54% and 39% of farmers sprayed chemicals at 7-day and 15-day intervals, respectively. FAW causes an average economic loss of 37.7% in maize production without pesticides. Increased use of pesticides to control FAW poses hazards to human health, wildlife, and the environment, and is expensive. Therefore, well-tested agroecological practices and bio-control agents are needed for sustainable FAW management.

Genetic analyses and detection of point mutations in the acetylcholinesterase-1 gene associated with organophosphate insecticide resistance in fall armyworm (Spodoptera frugiperda) populations from Uganda

BACKGROUND

The fall armyworm (FAW), Spodoptera frugiperda; J.E. Smith (Lepidoptera: Noctuidae), is now an economically important pest that causes huge losses to maize productivity in sub-Saharan Africa. Variations in sub-population genetics and the processes of rapid adaptation underpinning the invasion remain unclear. For this, the genetic identity and diversity of FAW populations in Uganda were revealed by sequencing 87 samples (collected across the country). Based on the partial mitochondrial cytochrome oxidase I (COI) gene polymorphisms, we further examined the mitochondrial haplotype configuration and compared the FAW in Uganda with sequences from other parts of the world. The molecular target for organophosphate and carbamate resistance, acetylcholinesterase, was also investigated.

RESULTS

Analysis of the partial COI gene sequences showed the presence of both rice (predominant) and corn strain haplotypes, with a haplotype diversity of 0.382. Based on the COI marker, pairwise difference distribution analyses, and neutrality tests, showed that the FAW populations in Uganda and the rest of Africa are evolving neutrally, but those in America and Asia are undergoing expansion. Our findings support observations that invasive FAW populations throughout the rest of Africa and Asia share a common origin. Sequencing of the S. frugiperda ace-1 gene revealed four amino acid substitutions, two of which (A201S and F290V) were previously shown to confer organophosphate resistance in both S. frugiperda and several other insect species. The other two previously reported new variations in positions g-396 and g-768, are presumed to be related to the development of insecticide resistance.

CONCLUSIONS

This research has increased our knowledge of the genetics of FAW in Uganda, which is critical for pest surveillance and the detection of resistance. However, due to the low gene polymorphism of COI, more evolutionary studies incorporating the Spodoptera frugiperda whole-genome sequence are required to precisely understand the FAW population dynamics, introduction paths, origin, and subsequent spread.

Polymorphisms in the hypervariable control region of the mitochondrial DNA differentiate BPH populations

The brown planthopper (BPH; Nilaparvata lugens) is one of India's most destructive pests of rice. BPH, a monophagous migratory insect, reported from all major rice-growing ecosystems of the country, is capable of traversing large distances and causing massive crop loss. A crucial step for developing viable management strategies is understanding its population dynamics. Very few reliable markers are currently available to screen BPH populations for their diversity. In the current investigation, we developed a combinatorial approach using the polymorphism present within the mitochondrial Control Region of BPH and in the nuclear genome (genomic simple sequence repeats; gSSRs) to unravel the diversity present in BPH populations collected from various rice-growing regions of India. Using two specific primer pairs, the complete Control Region (1112 to 2612 bp) was PCR amplified as two overlapping fragments, cloned and sequenced from BPH individuals representing nine different populations. Results revealed extensive polymorphism within this region due to a variable number of tandem repeats. The three selected gSSR markers also exhibited population-specific amplification patterns. Overall genetic diversity between the nine populations was high (>5%). Further, in silico double-digestion of the consensus sequences of the Control Region, with HpyCH4IV and Tsp45I restriction enzymes, revealed unique restriction fragment length polymorphisms (digital-RFLPs; dRFLPs) that differentiated all the nine BPH populations. To the best of our knowledge, this is the first report of markers developed from the Control Region of the BPH mitogenome that can differentiate populations. Eventually, such reliable and rapid marker-based identification of BPH populations will pave the way for an efficient pest management strategy.

Two Microsatellite Types Within NAD6 Gene Help to Distinguish Populations and Infer the Migratory Route of the Invasive Fall Armyworm, Spodoptera frugiperda, (Lepidoptera, Noctuidae) in China

Spodoptera frugiperda is a major agricultural pest that has invaded China since January 2019. Given that most of the individuals present in China carried the diagnostic rice-strain mtDNA (COI-RS), there was no efficient method to distinguish populations of S. frugiperda. In this study, we identified and characterized two variant microsatellite alleles in the mitochondrial NAD6 gene of S. frugiperda retrieved from the National Center for Biotechnology Center GenBank. We then sequenced partial NAD6 genes containing the microsatellite region and the diagnostic COI barcoding gene (used to distinguish the corn-strain and the rice-strain) of 429 invasive S. frugiperda individuals that were collected from the main infested regions in China during 2019-2020. Our data indicates that two kinds of interrupted repeat sequences, (ATA)4T(ATA)3 and (ATA)5T(ATA)3, exist in the microsatellite region which we defined as the deletion type (NAD6-D), and the insertion type (NAD6-I) based on the repeat units' differentiation, respectively. The presence of these two microsatellite types in the mtDNA genome of S. frugiperda was further confirmed with the sequencing results in 429 samples. Moreover, NAD6-I and NAD6-D types were both present in individuals with COI-RS, while only NAD6-D type was detected in the COI-CS individuals. Interestingly, the two microsatellite types suggested a possible geographic distribution: the western migratory route (Yunan and Chongqing) was comprised exclusively of NAD6-I type, while both NAD6-I and NAD6-D types were identified in the predicted eastern migration trajectories (Hainan, Guangxi, Shandong, etc.). These results suggested that NAD6-D and NAD6-I types may be useful in distinguishing between populations, analyzing the evolutionary mechanism of mtDNA microsatellite polymorphism, inferring the migratory route of S. frugiperda in China, and developing precise and integrated control strategies for S. frugiperda.

Genetic Structure and Colonization of North America by Depressaria depressana (Fabricius 1775) (Lepidoptera: Depressariidae) over 15 Years; Contrasts with Westward Expansion of Depressaria radiella (Goeze, 1783) over 160 Years

Depressaria depressana, the purple carrot seed moth, is a Eurasian species first reported in North America in 2008 and currently undergoing range expansion. This invasion follows that of its Eurasion congener Depressaria radiella (parsnip webworm), first documented in North America 160 years ago. Unlike D. depressana, which utilizes hostplants across multiple tribes of Apiaceae, Depressaria radiella is a "superspecialist" effectively restricted in its native and non-indigenous ranges to two closely related apiaceous genera. We investigated the genetic structure of D. depressana populations across latitudinal and longitudinal gradients in the eastern United States by constructing COI haplotype networks and then comparing these with haplotype networks constructed from available COI sequence data from contemporary European D. depressana populations and from European and North American D. radiella populations. Haplotype data revealed higher genetic diversity in D. depressana, indicating high dispersal capacity, multiple introductions, and/or a genetically diverse founding population. Museum and literature records of D. radiella date back to 1862 and indicate that range expansion to the West Coast required more than 50 years. Higher levels of genetic diversity observed in D. depressana compared to its congener may indicate a greater propensity for dispersal, colonization and establishment in its non-indigenous range.

Adipokinetic hormone signaling regulates cytochrome P450-mediated chlorantraniliprole sensitivity in Spodoptera frugiperda (Lepidoptera: Noctuidae)

BACKGROUND

Fall armyworm (FAW, Spodoptera frugiperda) is one of the most destructive and invasive pests worldwide and causes significant economic losses. Intensive and frequent use of insecticides has led to the development of resistance in FAW. Adipokinetic hormone (AKH) have been proven to be involved in insecticide resistance in insects. However, the molecular mechanism underlying chlorantraniliprole resistance mediated by AKH signaling in FAW remains unclear.

RESULTS

The expression of SpfAKHR was highest in male adults and lowest in 1st instar larvae. SpfAKH was expressed the highest in eggs and the lowest in 6th instar larvae. AKH signaling was involved in the sensitivity of FAW to chlorantraniliprole through a toxicological bioassay, and the combination of chlorantraniliprole and bithionol (an inhibitor of key enzymes in the AKH pathway) significantly increased the mortality of FAW. Chlorantraniliprole significantly induced the expression of ten P450s, SpfAKH and SpfAKHR in FAW. RNA interference against SpfAKHR significantly decreased the P450 content, downregulated the expression of three P450 genes (SpfCYP6B50, SpfCYP321A9 and SpfCYP9A58) and inhibited the resistance of FAW to chlorantraniliprole. The topical application of AKH peptide significantly increased the P450 content, upregulated the expression of five P450 genes (SpfCYP321A9, SpfCY321A8, SpfCYP321A10, SpfCYP321A7 and SpfCYP6AB12), and enhanced the survival of FAW against chlorantraniliprole.

CONCLUSIONS

AKH plays an important role in enhancing chlorantraniliprole resistance in FAW by exerting a positive influence on P450 gene expression and P450 content. These results provide valuable insights into insecticide resistance regulation and FAW control strategies. © 2022 Society of Chemical Industry.

Microsatellites reveal that genetic mixing commonly occurs between invasive fall armyworm populations in Africa

Understanding the population structure and movements of the invasive fall armyworm (FAW, Spodoptera frugiperda) is important as it can help mitigate crop damage, and highlight areas at risk of outbreaks or evolving insecticide resistance. Determining population structure in invasive FAW has been a challenge due to genetic mutations affecting the markers traditionally used for strain and haplotype identification; mitochondrial cytochrome oxidase I (COIB) and the Z-chromosome-linked Triosephosphate isomerase (Tpi). Here, we compare the results from COIB and Tpi markers with highly variable repeat regions (microsatellites) to improve our understanding of FAW population structure in Africa. There was very limited genetic diversity using the COIB marker, whereas using the TpiI4 marker there was greater diversity that showed very little evidence of genetic structuring between FAW populations across Africa. There was greater genetic diversity identified using microsatellites, and this revealed a largely panmictic population of FAW alongside some evidence of genetic structuring between countries. It is hypothesised here that FAW are using long-distance flight and prevailing winds to frequently move throughout Africa leading to population mixing. These approaches combined provide important evidence that genetic mixing between invasive FAW populations may be more common than previously reported.

Baseline Susceptibility of Spodoptera frugiperda Populations Collected in India towards Different Chemical Classes of Insecticides

Simple Summary

Fall armyworm (FAW) is a highly destructive moth pest and its larvae feed on many different host plants, including major crops such as maize. This pest is native to the Americas but invaded the Eastern hemisphere in 2016. It is highly migratory and was first detected in India in 2018, where it rapidly became a major threat to maize production across India. FAW control mostly relies on the application of chemical insecticides and transgenic crop plants expressing insecticidal proteins of bacterial origin. FAW has developed resistance against insecticides, and for management purposes, it is important to assess its sensitivity status against different chemical classes of insecticides, particularly in invaded regions. In this study, we conducted more than 400 bioassays with nine different insecticides from seven mode-of-action groups on 47 FAW populations collected in 2019 and 2020 across different geographical areas in India. The baseline susceptibility determined for all these insecticides will help to set-up appropriate resistance management strategies to keep FAW infestations in India below economic damage thresholds.

Abstract

Fall armyworm (FAW), Spodoptera frugiperda, is a major pest of maize in the Americas and recently invaded the Eastern hemisphere. It was first detected in India in 2018 and is considered a major threat to maize production. FAW control largely relies on the application of chemical insecticides and transgenic crops expressing Bacillus thuringiensis insecticidal proteins. Assessing FAW resistance and insecticide susceptibility is a cornerstone to develop sustainable resistance management strategies. In this study, we conducted more than 400 bioassays to assess the efficacy of nine insecticides from seven mode-of-action classes against 47 FAW populations collected in 2019 and 2020 across various geographical areas in India. The resistance status of the field-collected populations was compared to an Indian population sampled in 2018, and an insecticide susceptible reference population collected in 2005 in Brazil. Low to moderate resistance levels were observed for thiodicarb, chlorpyriphos, deltamethrin, chlorantraniliprole and flubendiamide in several populations (including the reference population collected in 2018). The highest resistance ratios were observed for deltamethrin which likely compromises recommended label rates for pyrethroid insecticides in general. Our data provide a useful baseline for future FAW resistance monitoring initiatives and highlight the need to implement insecticide resistance management strategies.

Genetic Relationship of Fall Armyworm (Spodoptera frugiperda) Populations That Invaded Africa and Asia

Simple Summary

Since 2016, the fall armyworm, an important economic pest native to tropical and subtropical regions of the Western Hemisphere, has invaded Africa and further spread rapidly into most Asian countries. The fall armyworm is highly polyphagous, but two of its major strains, the corn and the rice strains, cause severe damage in the Western Hemisphere. However, the invaded populations in Africa and Asia mostly infested the corn fields. Studies on the genetic identity of the species using two molecular markers, one nuclear gene and one mitochondrial gene, showed that the major genetic group is a heterogeneous hybrid of males from the corn strain and females from the rice strain. Moreover, a minor group of homogenous individuals from the corn strain but no homogenous individuals from the rice strain were also detected. A geographic distribution analysis at the subpopulation level indicated similar genetic diversity in Africa and Asia, suggesting fall armyworm in Africa spread into Asia without significant genetic change.

Abstract

The fall armyworm, Spodoptera frugiperda, is an important agricultural pest native to tropical and subtropical regions of the Western Hemisphere, and has invaded Africa and further spread into most countries of Asia within two years. Here, we analyzed the genetic variation of invaded populations by comparing the nucleotide sequences of two genes: the nuclear Z-chromosome linked gene triose phosphate isomerase (Tpi) and the mitochondrial gene cytochrome oxidase subunit I (COI) of 27 specimens collected in Africa (DR Congo, Tanzania, Uganda, and Zimbabwe) and Asia (Bangladesh, Korea, Nepal, and Vietnam). The results revealed that 25 specimens were from a heterogeneous hybrid (Tpi-corn strain and COI-rice strain; Tpi-C/COI-R) of the corn strain male and rice strain female, but two specimens were from a homogenous corn strain (Tpi-corn strain and COI-corn strain; Tpi-C/COI-C). The further analysis of the fourth exon and the fourth intron sequences of the Tpi gene identified at least four subgroups of the corn strain. These four genetic subgroups were identified in Africa and Asia, suggesting no significant genetic change due to the rapid migration within two years. Our study provides essential information for understanding the genetic diversity of fall armyworm in new habitats.