ddRAD sequencing: an emerging technology added to the biosecurity toolbox for tracing the origin of brown marmorated stink bug, Halyomorpha halys (Hemiptera: Pentatomidae)

Abstract

Background Brown marmorated stink bug (BMSB), Halyomorpha halys (Hemiptera: Pentatomidae) is native to East Asia but has invaded many countries in the world. BMSB is a polyphagous insect pest and causes significant economic losses to agriculture worldwide. Knowledge on the genetic diversity among BMSB populations is scarce but is essential to understand the patterns of colonization and invasion history of local populations. Efforts have been made to assess the genetic diversity of BMSB using partial mitochondrial DNA sequences but genetic divergence on mitochondria is not high enough to precisely accurately identify and distinguish various BMSB populations. Therefore, in this study, we applied a ddRAD (double digest restriction-site associated DNA) sequencing approach to ascertain the genetic diversity of BMSB populations collected from 12 countries (2 native and 10 invaded) across four continents with the ultimate aim to trace the origin of BMSBs intercepted during border inspections and post-border surveillance. Result A total of 1775 high confidence single nucleotide polymorphisms (SNPs) were identified from ddRAD sequencing data collected from 389 adult BMSB individuals. Principal component analysis (PCA) of the identified SNPs indicated the existence of two main distinct genetic clusters representing individuals sampled from regions where BMSB is native to, China and Japan, respectively, and one broad cluster comprised individuals sampled from countries which have been invaded by BMSB. The population genetic structure analysis further discriminated the genetic diversity among the BMSB populations at a higher resolution and distinguished them into five potential genetic clusters. Conclusion The study revealed hidden genetic diversity among the studied BMSB populations across the continents. The BMSB populations from Japan were genetically distant from the other studied populations. Similarly, the BMSB populations from China were also genetically differentiated from the Japanese and other populations. Further genetic structure analysis revealed the presence of at least three genetic clusters of BMSB in the invaded countries, possibly originating via multiple invasions. Furthermore, this study has produced novel set of SNP markers to enhance the knowledge of genetic diversity among BMSB populations and demonstrates the potential to trace the origin of BMSB individuals for future invasion events.

Brown marmorated stink bug (BMSB): Introduction, its potential invasion and impact in South Asia

“…It was also found in Kazakhstan which is a central Asian country [9] . This pest is also reported in Chile [10] . These all reports signify that this pest has the capacity to cause problems in agriculture globally [11] .…”

Population genomic insights into invasion success in a polyphagous agricultural pest, Halyomorpha halys

“…BMSB is a polyphagous fruit‐piercing bug, capable of feeding on >100 plant hosts, many of which are economically important crops (Lee et al, 2013 ). Gregarious in nature, it has a high dispersal capacity and high potential to compete with endemic species, making it a serious pest for agriculture and horticulture and a nuisance of households (Sparks et al, 2020 ; Yan et al, 2021 ). BMSB is an opportunistic hitchhiker on commodities and a large number of adults can aggregate in shipping containers and imported fruit and wood (Duthie, ; Gariepy et al, 2015 ; Wermelinger et al, 2007 ).…”

“…Single‐locus or genome‐wide single nucleotide polymorphism (SNP) data have revealed highly divergent lineages among native populations in east Asia. China is suggested as the most likely source of global spread, with evidence of multiple out‐of‐China invasions, while bridgehead events from the USA to Europe and Chile have also been identified (Valentin et al, 2017 ; Yan et al, 2021 ).…”

Genome‐wide SNPs of vegetable leafminer, Liriomyza sativae: Insights into the recent Australian invasion

“…With the increasing ease and speed of DNA sequencing, high‐resolution genomic SNP‐based methods like double digest restriction‐site‐associated DNA sequencing (ddRAD‐seq) provide a new dimension to population‐level studies (Peterson et al, 2012 ). These markers have been successfully applied to understand patterns of movement in insects that act as pests or disease vectors (Ryan et al, 2019 ; Schmidt et al, 2019 ; Yan et al, 2021 ). They provide a much higher level of resolution than other nuclear marker systems like DNA microsatellites given the sheer number of marker loci that can be scored (Morin et al, 2004 ).…”