ddRAD Sequencing: A Novel Arsenal Added to the Biosecurity Toolbox to Trace the Origin of Brown Marmorated Stink Bug, Halyomorpha Halys (Hemiptera: Pentatomidae)

Abstract BackgroundBrown marmorated stink bug (BMSB), Halyomorpha halys (Hemiptera: Pentatomidae) is native to East Asia but has invaded many countries in the world. It is a polyphagous insect pest and causing 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 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.ResultA total of 1775 high confidence single nucleotide polymorphisms (SNPs) were identified from ddRAD sequencing data collected from 389 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. ConclusionThe 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 separated 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 from multiple invasions. Furthermore, this study has produced novel set of SNP markers to enhance knowledge of genetic diversity among BMSB populations and demonstrate a great potential to trace the origin of BMSB individuals for future invasion events.

Download Full-text

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

BMC Genomics ◽

10.1186/s12864-021-07678-z ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Juncong Yan ◽

Gábor Vétek ◽

Chandan Pal ◽

Jinping Zhang ◽

Rania Gmati ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Structure Analysis ◽

Dna Sequences ◽

Economic Losses ◽

Halyomorpha Halys ◽

Invasion History ◽

Brown Marmorated Stink Bug ◽

Stink Bug ◽

Genetic Clusters

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.

Download Full-text

Conservation genetics of the threatened plant species Physaria filiformis (Missouri bladderpod) reveals strong genetic structure and a possible cryptic species

PLoS ONE ◽

10.1371/journal.pone.0247586 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0247586

Author(s):

Christine E. Edwards ◽

Brooke C. Tessier ◽

Joel F. Swift ◽

Burgund Bassüner ◽

Alexander G. Linan ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Structure ◽

Plant Species ◽

Genetic Drift ◽

Rare Species ◽

Ex Situ ◽

Ouachita Mountains ◽

Genetic Diversity And Structure ◽

Genetic Clusters

Understanding genetic diversity and structure in a rare species is critical for prioritizing both in situ and ex situ conservation efforts. One such rare species is Physaria filiformis (Brassicaceae), a threatened, winter annual plant species. The species has a naturally fragmented distribution, occupying three different soil types spread across four disjunct geographical locations in Missouri and Arkansas. The goals of this study were to understand: (1) whether factors associated with fragmentation and small population size (i.e., inbreeding, genetic drift or genetic bottlenecks) have reduced levels of genetic diversity, (2) how genetic variation is structured and which factors have influenced genetic structure, and (3) how much extant genetic variation of P. filiformis is currently publicly protected and the implications for the development of conservation strategies to protect its genetic diversity. Using 16 microsatellite markers, we genotyped individuals from 20 populations of P. filiformis from across its geographical range and one population of Physaria gracilis for comparison and analyzed genetic diversity and structure. Populations of P. filiformis showed comparable levels of genetic diversity to its congener, except a single population in northwest Arkansas showed evidence of a genetic bottleneck and two populations in the Ouachita Mountains of Arkansas showed lower genetic variation, consistent with genetic drift. Populations showed isolation by distance, indicating that migration is geographically limited, and analyses of genetic structure grouped individuals into seven geographically structured genetic clusters, with geographic location/spatial separation showing a strong influence on genetic structure. At least one population is protected for all genetic clusters except one in north-central Arkansas, which should therefore be prioritized for protection. Populations in the Ouachita Mountains were genetically divergent from the rest of P. filiformis; future morphological analyses are needed to identify whether it merits recognition as a new, extremely rare species.

Download Full-text

Assemblage of the Egg Parasitoids of the Invasive Stink Bug Halyomorpha halys: Insights on Plant Host Associations

Insects ◽

10.3390/insects11090588 ◽

2020 ◽

Vol 11 (9) ◽

pp. 588

Author(s):

Livia Zapponi ◽

Marie Claude Bon ◽

Jalal Melhem Fouani ◽

Gianfranco Anfora ◽

Silvia Schmidt ◽

...

Keyword(s):

Biological Control ◽

Mitochondrial Gene ◽

Strong Support ◽

Egg Parasitoids ◽

Economic Losses ◽

Halyomorpha Halys ◽

Stink Bug ◽

Plant Host ◽

Egg Masses ◽

Host Associations

Halyomorpha halys (Stål) (Hemiptera: Pentatomidae) is an invasive alien species and a key agricultural pest. Its native parasitoids (Trissolcus japonicus Ashmead and Tr. mitsukurii Ashmead) have been registered in several countries where H. halys brought dramatic economic losses and where biological control is considered to be the most effective long-term solution. By searching for stink bug egg masses and exposing sentinel egg masses, we monitored the distribution of native and exotic egg parasitoids in Trentino-Alto Adige (Italy), an area where both the host and parasitoids are in expansion. We recorded ten pentatomids, seven parasitoid species, with the first report of Tr. japonicus in this area and a hyperparasitoid. In the assemblage, Anastatus bifasciatus (Geoffroy) and Tr. mitsukurii were the dominant parasitoids, with a different distribution in terms of context and host plants. Sycamore was the host plant where the highest number of naturally laid parasitized egg masses (26%) were recorded. Trissolcus mitsukurii showed the highest parasitism rate, and was often found in apple orchards. The emergence of exotic parasitoids showed a temporal delay compared to native ones. Sequence analysis of 823 bp of the CO1 mitochondrial gene revealed that the recovered Tr. japonicus and Tr. mitsukurii harbored one single haplotype each. These haplotypes were previously found in 2018 in Northern Italy. While sentinel egg masses proved to be very effective in tracking the arrival of exotic Trissolcus species, the collection of stink bug egg masses provided fundamental data on the plant host species. The results lend strong support to the adaptation of exotic Trissolcus species to the environmental conditions of the range of introduction, providing new information on plant host-associations, fundamental for the development of biological control programs.

Download Full-text

Genetic Diversity and Genetic Structure Analysis of the Natural Populations of Lilium brownii from Guangdong, China

Biochemical Genetics ◽

10.1007/s10528-009-9258-y ◽

2009 ◽

Vol 47 (7-8) ◽

pp. 503-510 ◽

Cited By ~ 7

Author(s):

Yong-fang Huang ◽

Mao-xun Yang ◽

Hao Zhang ◽

Xue-ying Zhuang ◽

Xue-hui Wu ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Structure Analysis ◽

Natural Populations

Download Full-text

Genetic structure and diversity of the endangered growling grass frog in a rapidly urbanizing region

Royal Society Open Science ◽

10.1098/rsos.140255 ◽

2015 ◽

Vol 2 (8) ◽

pp. 140255 ◽

Cited By ~ 7

Author(s):

Claire C. Keely ◽

Joshua M. Hale ◽

Geoffrey W. Heard ◽

Kirsten M. Parris ◽

Joanna Sumner ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Dna Sequences ◽

Nuclear Dna ◽

Urban Expansion ◽

Nuclear Gene ◽

Management Approach ◽

Natural Habitats ◽

High Genetic Diversity ◽

Genetic Structure And Diversity

Two pervasive and fundamental impacts of urbanization are the loss and fragmentation of natural habitats. From a genetic perspective, these impacts manifest as reduced genetic diversity and ultimately reduced genetic viability. The growling grass frog ( Litoria raniformis ) is listed as vulnerable to extinction in Australia, and endangered in the state of Victoria. Remaining populations of this species in and around the city of Melbourne are threatened by habitat loss, degradation and fragmentation due to urban expansion. We used mitochondrial DNA (mtDNA) and microsatellites to study the genetic structure and diversity of L. raniformis across Melbourne's urban fringe, and also screened four nuclear gene regions (POMC, RAG-1, Rhod and CRYBA1). The mtDNA and nuclear DNA sequences revealed low levels of genetic diversity throughout remnant populations of L. raniformis . However, one of the four regions studied, Cardinia, exhibited relatively high genetic diversity and several unique haplotypes, suggesting this region should be recognized as a separate Management Unit. We discuss the implications of these results for the conservation of L. raniformis in urbanizing landscapes, particularly the potential risks and benefits of translocation, which remains a contentious management approach for this species.

Download Full-text

First regional evaluation of nuclear genetic diversity and population structure in northeastern coyotes (Canis latrans)

F1000Research ◽

10.12688/f1000research.3567.1 ◽

2014 ◽

Vol 3 ◽

pp. 66 ◽

Cited By ~ 3

Author(s):

Javier Monzón

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Markers ◽

Genetic Structure ◽

Dna Sequences ◽

Canis Latrans ◽

Regional Analysis ◽

Model Organism ◽

Nucleotide Polymorphisms ◽

Genomic Markers

Previous genetic studies of eastern coyotes (Canis latrans) are based on one of two strategies: sampling many individuals using one or very few molecular markers, or sampling very few individuals using many genomic markers. Thus, a regional analysis of genetic diversity and population structure in eastern coyotes using many samples and several molecular markers is lacking. I evaluated genetic diversity and population structure in 385 northeastern coyotes using 16 common single nucleotide polymorphisms (SNPs). A region-wide analysis of population structure revealed three primary genetic populations, but these do not correspond to the same three subdivisions inferred in a previous analysis of mitochondrial DNA sequences. More focused geographic analyses of population structure indicated that ample genetic structure occurs in coyotes from an intermediate contact zone where two range expansion fronts meet. These results demonstrate that genotyping several highly heterozygous SNPs in a large, geographically dense sample is an effective way to detect cryptic population genetic structure. The importance of SNPs in studies of population and wildlife genomics is rapidly increasing; this study adds to the growing body of recent literature that demonstrates the utility of SNPs ascertained from a model organism for evolutionary inference in closely related species.

Download Full-text

Association Mapping for Yield Attributing Traits and Yellow Mosaic Disease Resistance in Mung Bean [Vigna radiata (L.) Wilczek]

Frontiers in Plant Science ◽

10.3389/fpls.2021.749439 ◽

2022 ◽

Vol 12 ◽

Author(s):

Versha Rohilla ◽

Rajesh Kumar Yadav ◽

Atman Poonia ◽

Ravika Sheoran ◽

Gita Kumari ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Association Mapping ◽

Structure Analysis ◽

Population Genetic Structure ◽

Vigna Radiata ◽

Mung Bean ◽

Population Genetic ◽

Mosaic Disease ◽

Yellow Mosaic Disease

Mung bean [Vigna radiata (L.) Wilczek] is an important short-duration grain legume widely known for its nutritional, soil ameliorative, and cropping system intensification properties. This study aims at evaluating genetic diversity among mung bean genotypes and detecting genomic regions associated with various yield attributing traits and yellow mosaic disease (YMD) resistance by association mapping. A panel of 80 cultivars and advanced breeding lines was evaluated for 10 yield-related and YMD resistance traits during kharif (monsoon) and summer seasons of 2018–2019 and 2019–2020. A total of 164 genome-wide simple sequence repeat (SSR) markers were initially screened, out of which 89 were found polymorphic which generated 317 polymorphic alleles with an average of 3.56 alleles per SSR locus. The number of alleles at each locus varied from 2 to 7. The population genetic structure analysis grouped different genotypes in three major clusters and three genetically distinct subpopulations (SPs) (i.e., SP-1, SP-2, and SP-3) with one admixture subpopulation (SP-4). Both cluster and population genetic structure analysis categorized the advanced mung bean genotypes in a single group/SP and the released varieties in other groups/SPs, suggesting that the studied genotypes may have common ancestral history at some level. The population genetic structure was also in agreement with the genetic diversity analysis. The estimate of the average degree of linkage disequilibrium (LD) present at the genome level in 80 mung bean genotypes unveiled significant LD blocks. Over the four seasons, 10 marker-trait associations were observed significant for YMD and four seed yield (SY)-related traits viz., days to flowering, days to maturity, plant height, and number of pods per plant using the mixed linear model (MLM) method. These associations may be useful for marker-assisted mung bean yield improvement programs and YMD resistance.

Download Full-text

Comparing the genetic structure of codling moth Cydia pomonella (L.) from Greece and France: long distance gene-flow in a sedentary pest species

Bulletin of Entomological Research ◽

10.1017/s0007485311000563 ◽

2011 ◽

Vol 102 (2) ◽

pp. 185-198 ◽

Cited By ~ 15

Author(s):

C.Ch. Voudouris ◽

P. Franck ◽

J. Olivares ◽

B. Sauphanor ◽

Z. Mamuris ◽

...

Keyword(s):

Gene Flow ◽

Genetic Structure ◽

Genetic Differentiation ◽

Insect Pest ◽

Cydia Pomonella ◽

Codling Moth ◽

Pest Species ◽

Long Distance ◽

Control Programs ◽

Genetic Clusters

AbstractCodling moth Cydia pomonella L. (Lepidoptera: Tortricidae) is the most important insect pest of apple production in Europe. Despite the economic importance of this pest, there is not information about the genetic structure of its population in Greece and the patterns of gene-flow which might affect the success of control programs. In this study, we analysed nine samples from apple, pear and walnut from various regions of mainland Greece using 11 microsatellite loci. Six samples from the aforementioned hosts from southern France were also examined for comparison. Bayesian clustering and genetic distance analyses separated the codling moth samples in two genetic clusters. The first cluster consisted mainly of the individuals from Greece, and the second of those from France, although admixture and miss-classified individuals were also observed. The low genetic differentiation among samples within each country was also revealed by FST statistics (0.009 among Greek samples and 0.0150 among French samples compared to 0.050 global value among all samples and 0.032 the mean of the pair-wise values between the two countries). These FST values suggest little structuring at large geographical scales in agreement with previous published studies. The host species and local factors (climatic conditions, topography, pest control programs) did not affect the genetic structure of codling moth populations within each country. The results are discussed in relation to human-made activities that promote gene-flow even at large geographic distances. Possible factors for the genetic differentiation between the two genetic clusters are also discussed.

Download Full-text