The status in Africa of fall armyworm expressing genetic markers related to infestations of pasture, millet, alfalfa, and rice in the Americas

Abstract

The establishment of the fall armyworm (FAW), Spodoptera frugiperda, in Africa is reported to have caused substantial agricultural losses since its detection in 2016 and subsequent spread into Asia and Australia by 2020. Based on the crops being infested, it appears that the population (C strain) primarily responsible for FAW infestations of corn in the Americas is widespread in Africa but there is uncertainty about the status of the R strain that targets pastures, alfalfa, millet, and rice in the United States. The two strains can only physically be distinguished by molecular markers, with single nucleotide polymorphisms (SNPs) in the mitochondrial Cytochrome oxidase subunit I (COI) and nuclear Z-chromosome-linked Triosephosphate isomerase (Tpi) gene demonstrated to consistently identify strains in both American continents. However, the COI and Tpi markers are generally in disagreement in the Eastern Hemisphere. This together with conflicting results from whole genome SNP studies creates uncertainty about the strain composition of this invasive population. In this paper the legitimacy of the Tpi markers is supported and used to not only confirm the existence of the R strain in Africa, but to also provide evidence for the introduction of new R strain variants in western Africa since 2017. These findings have implications on the crops at risk in the Eastern Hemisphere and for understanding how the invasion of Africa by FAW occurred.

Fig 1. Description of the COIB and TpiE4 haplotype markers.

A, molecular map of the COI gene. COIA is region frequently used for DNA barcoding. The locations of the m1164D and m1287R polymorphisms in COIB are indicated with the empirically observed nucleotides listed below. The T₁₁₆₄A₁₂₈₇ combination identifies the R-strain based on COI (R_COI) while the other combinations define the COIB-based C-strain haplotypes (CSh) that are designated CSh1-h4. B, molecular map of the TpiE4 and TpiI4a200 segments indicating the relative locations SNPs that define the African FAW TpiE4 haplotypes. TpiI4a200 variants are denoted by a lower-case letter added to the linked TpiE4 haplotype with the DNA sequence described in S1 Fig.

Fig 2. Distribution of the COIB-CSh haplotypes.

A, distribution of CSh haplotypes at different Western Hemisphere locations. B, distribution of CSh haplotypes in multiple locations and times in Africa. Text in red indicate new sequence data from this study. Geographical maps with Natural Earth using QGIS version 3.24 (Open Source Geospatial Foundation).

Fig 3. Distribution of the TpiI4a200 variants in Africa from 2016-2019.

The frequencies of the TpiI4a200 haplotypes observed in collections from 2016-2017 are shown for collections from 2016-2019. In addition, new variants found in 2018 are described. The locations of the collection sites are as mapped in Fig 2B. Capture numbers can be found in S1 Table.

Fig 4. Maximum-Likelihood phylogenetic trees produced using the TpiI4a200 segment from Florida, Brazil, and Argentina collections (midpoint rooting).

Clades were attributed to strains according to TpiE4, with C (green lines) and R (red lines) strain clades determined by the Tpi183Y SNP. Colored ovals identify the strain category of the host plant from which the sample was collected (red or green), while yellow ovals identify the African TpiI4a200 haplotypes. The scale bar represents 0.02 nucleotide substitutions per site.

Fig 5. TpiE4 sequences and chromatographs showing relevant SNPs.

The consensus Western Hemisphere TpiE4 sequences for two strains are WH C strain and WH R strain, with gTpi165Y, gTpi168Y, and gTpi183Y the strain specific SNPs. Polymorphic nomenclature follows IUPAC convention, M = A/C, R = A/G, Y = C/T. Number of samples analyzed (n) is given for the various African TpiE4 haplotypes and hybrids observed. The AfrRa3 sequence is extrapolated from heterozygotes.

Fig 6. Distribution of the C_TpiE4, R_TpiE4 and H_TpiE4 populations in the Eastern Hemisphere.

Pie charts show proportions of each strain and hybrids for each collection. The approximate locations of the collection sites are denoted by red circles. Capture numbers are available in S2 Table. The number of specimens examined in each collection is listed in the circle. Geographical map was made with Natural Earth using QGIS version 3.24 (Open Source Geospatial Foundation).

Fig 7. Bar graph describing the percentage of specimens from different countries and years carrying at least one R_TpiE4 chromosome.

Countries are differentiated by color with the number of specimens analyzed above each column. Raw data available in S3 Table.

Fig 8. Diagram of reciprocal crosses between strains and their resultant hybrid progeny showing their sex chromosome genotypes.

Autosomes are assumed to have no influence on strain identity and are not shown. Chromosomes marked with Z are the Z-chromosome, which carries the genes directing host specificity and the Tpi markers. Chromosome with a W is the W-chromosome.