Genetic comparisons of fall armyworm populations from 11 countries spanning sub-Saharan Africa provide insights into strain composition and migratory behaviors

Abstract

The recent discovery of fall armyworm ( Spodoptera frugiperda , J.E. Smith) in Africa presents a significant threat to that continent’s food security. The species exhibits several traits in the Western Hemisphere that if transferred to Africa would significantly complicate control efforts. These include a broad host range, long-distance migratory behavior, and resistance to multiple pesticides that varies by regional population. Therefore, determining which fall armyworm subpopulations are present in Africa could have important implications for risk assessments and mitigation efforts. The current study is an extension of earlier surveys that together combine the collections from 11 nations to produce the first genetic description of fall armyworm populations spanning the sub-Saharan region. Comparisons of haplotype frequencies indicate significant differences between geographically distant populations. The haplotype profile from all locations continue to identify Florida and the Caribbean regions as the most likely Western Hemisphere origins of the African infestations. The current data confirm the uncertainty of fall armyworm strain identification in Africa by genetic methods, with the possibility discussed that the African infestation may represent a novel interstrain hybrid population of potentially uncertain behavioral characteristics.

Chromosome level draft genomes of the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), an alien invasive pest in China

“…There are three strain-specific sites (E4165, E4168 and E4183) in the fourth exon of the Tpi gene that can identify the C strain from the R strain for Western Hemisphere populations 57 . Especially, the E4183 is an effective diagnostic marker for Tpi gene to define the C or R strain.…”

“…We identified the Tpi gene fragments from four FAWs, including two from Yunnan province (sequences were retrieved from the whole genome sequencing data) and two from Guangdong province (sequences were retrieved from the RNA-seq data). Eight sites (TpiE4-129, TpiE4-144, TpiE4-165, TpiE4-168, TpiE4-180, TpiE4-183, TpiE4-192, TpiE4-198) in the fourth exon of the Tpi gene were used for determining the strains and a possible source of the invaded FAW 57 . The fourth intron of the Tpi gene 57 was used for constructing the phylogenetic tree using the PhyML (v3.0) 58 software with the Maximum-Likelihood methods to assist in identifying the strains.…”

High-depth resequencing reveals hybrid population and insecticide resistance characteristics of fall armyworm (Spodoptera frugiperda) invading China

“…Because of their hybridization, identification based on the maternally-inherited mitochondrial genotype is inaccurate and the insertion of two C-strain mitochondrial fragments in this study further confirms this inaccuracy. Therefore, it is not possible to accurately infer fall armyworm strain status based on the complete mitochondrial genome or the single COI mitochondrial gene, as suggested previously [40][41] . The Tpi gene, located in the nuclear genome, is more suitable for strain identification and 10 SNPs in this gene can distinguish between R-or C-strains fall armyworm in the Americas 37 .…”

“…Recent studies have indicated that the molecular identification of the two strains of fall armyworm is dependent on which markers are used [35][36][37] . The early molecular markers based on mitochondrial Cytochrome Oxidase Subunit I (COI) and Z-chromosome-linked Triosephosphate isomerase (Tpi) genes failed to accurately assign strain identification [38][39][40][41] . The dominant population of fall armyworm invading Africa and Asia were speculated to be hybrid populations of the female R-strain and male C-strain, based on these two molecular markers 42 .…”

“…The dominant population of fall armyworm invading Africa and Asia were speculated to be hybrid populations of the female R-strain and male C-strain, based on these two molecular markers 42 . In addition, an Africa-specific haplotype, different from those of native Americas, was also reported in African and Chinese samples based on the Tpi gene 18,40 , which makes strain identification and population genetic structure more complicated. Therefore, a genome-wide analysis of the genetic characteristics of invasive fall armyworm is becoming imperative.…”