scholarly journals Genome-wide SNP discovery in field and laboratory colonies of Australian Plutella species

2017 ◽  
Author(s):  
K.D. Perry ◽  
S.M. Pederson ◽  
S.W. Baxter
Keyword(s):  
Population Structure ◽  
Insecticide Resistance ◽  
Population Genetic ◽  
Diamondback Moth ◽  
Snp Markers ◽  
Pest Species ◽  
Genetic Studies ◽  
High Dispersal ◽  
Wild Host ◽  
Wide Range

ABSTRACTUnderstanding dispersal and gene flow is an important focus of evolutionary biology, conservation biology and pest management. The diamondback moth, Plutella xylostella, is a worldwide pest of Brassica vegetable and oilseed cropping systems. This insect has high dispersal ability, which has important consequences for population dynamics and the potential spread of insecticide resistance genes. Population genetic studies of the diamondback moth have found little evidence of population structure, suggesting that frequent intermixing occurs within regions, however the patterns of local and regional dispersal remain to be identified. For this and many other pest species, understanding dispersal is crucial for developing integrated management tactics such as forecasting systems and insecticide resistance management plans. In recent years, next generation sequencing (NGS) methods have provided previously unparalleled resolution for population genetic studies in a wide range of species. Here, we assessed the potential of NGS-derived molecular markers to provide new insights about population structure in the diamondback moth. We use restriction-site-associated DNA sequencing (RAD-Seq) to discover hundreds to thousands of single nucleotide polymorphism (SNP) markers in nine field and laboratory-reared populations collected from Australia. Genotypic data from RAD-Seq markers identified a cryptic species, P. australiana, among individuals collected from a wild host, Diplotaxis sp., indicating strong divergence in the nuclear genomes of two Australian Plutella lineages. Significant genetic differentiation was detected among populations of P. xylostella used in our study, however this could be explained by reduced heterozogosity and genetic drift in laboratory-reared populations founded by relatively few individuals. This study demonstrates that RAD-Seq is a powerful method for generating SNP markers for population genetic studies in this species.

scholarly journals Development of nuclear SNP markers for Mahogany (Swietenia spp.)

2020 ◽  
Vol 12 (4) ◽  
pp. 585-587
Author(s):  
Birte Pakull ◽  
Lasse Schindler ◽  
Malte Mader ◽  
Birgit Kersten ◽  
Celine Blanc-Jolivet ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Population Genetic ◽  
Snp Markers ◽  
Genetic Studies ◽  
Timber Tracking

Abstract Swietenia species are the most valuable American tropical timbers and have been heavily overexploited for decades. The three species are listed as either vulnerable or endangered by IUCN and are included on Appendix II of CITES, yet illegal exploitation continues. Here, we used restriction associated DNA sequencing to develop a new set of 120 SNP markers for Swietenia sp., suitable for MassARRAY®iPLEX™ genotyping. These markers can be used for population genetic studies and timber tracking purposes.

Conservation and Management of Salmon in the Age of Genomics

2020 ◽  
Vol 8 (1) ◽  
pp. 117-143 ◽  
Author(s):  
Robin S. Waples ◽  
Kerry A. Naish ◽  
Craig R. Primmer
Keyword(s):  
Population Structure ◽  
Population Genetic ◽  
Evolutionary Ecology ◽  
Natural Populations ◽  
Structure And Function ◽  
Population Assignment ◽  
Genetic Studies ◽  
And Function ◽  
Management And Conservation ◽  
Conservation And Management

Salmon were among the first nonmodel species for which systematic population genetic studies of natural populations were conducted, often to support management and conservation. The genomics revolution has improved our understanding of the evolutionary ecology of salmon in two major ways: ( a) Large increases in the numbers of genetic markers (from dozens to 104–106) provide greater power for traditional analyses, such as the delineation of population structure, hybridization, and population assignment, and ( b) qualitatively new insights that were not possible with traditional genetic methods can be achieved by leveraging detailed information about the structure and function of the genome. Studies of the first type have been more common to date, largely because it has taken time for the necessary tools to be developed to fully understand the complex salmon genome. We expect that the next decade will witness many new studies that take full advantage of salmonid genomic resources.

Spread and global population structure of the diamondback moth Plutella xylostella (Lepidoptera: Plutellidae) and its larval parasitoids Diadegma semiclausum and Diadegma fenestrale (Hymenoptera: Ichneumonidae) based on mtDNA

2016 ◽  
Vol 107 (2) ◽  
pp. 155-164 ◽  
Author(s):  
I. Juric ◽  
W. Salzburger ◽  
O. Balmer
Keyword(s):  
Population Structure ◽  
Genetic Variability ◽  
Dna Sequences ◽  
Plutella Xylostella ◽  
Diamondback Moth ◽  
Parasitic Wasps ◽  
Diadegma Semiclausum ◽  
Wasp Species ◽  
Wide Range ◽  
Diadegma Fenestrale

AbstractThe diamondback moth (DBM) (Plutella xylostella) is one of the main pests of brassicaceous crops worldwide and shows resistance against a wide range of synthetic insecticides incurring millions of dollars in control costs every year. The DBM is a prime example of the introduction of an exotic species as a consequence of globalization. In this study we analyzed the genetic population structure of the DBM and two of its parasitic wasps, Diadegma semiclausum and Diadegma fenestrale, based on mitochondrial DNA sequences. We analyzed DBM samples from 13 regions worldwide (n = 278), and samples of the two wasp species from six European and African countries (n = 131), in an attempt to reconstruct the geographic origin and phylogeography of the DBM and its two parasitic wasps. We found high variability in COI sequences in the diamondback moth. Haplotype analysis showed three distinct genetic clusters, one of which could represent a cryptic species. Mismatch analysis confirmed the hypothesized recent spread of diamondback moths in North America, Australia and New Zealand. The highest genetic variability was found in African DBM samples. Our data corroborate prior claims of Africa as the most probable origin of the species but cannot preclude Asia as an alternative. No genetic variability was found in the two Diadegma species. The lack of variability in both wasp species suggests a very recent spread of bottlenecked populations, possibly facilitated by their use as biocontrol agents. Our data thus also contain no signals of host-parasitoid co-evolution.

scholarly journals Genotyping-By-Sequencing Reveals Population Structure and Genetic Diversity of a Buffelgrass (Cenchrus ciliaris L.) Collection

Diversity ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 88
Author(s):  
Alemayehu Teressa Negawo ◽  
Yilikal Assefa ◽  
Jean Hanson ◽  
Asebe Abdena ◽  
Meki S. Muktar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Core Collection ◽  
Reference Genome ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Soil Conditions ◽  
Cenchrus Ciliaris ◽  
Population Structure Analysis ◽  
Wide Range

Buffelgrass (Cenchrus ciliaris L.) is an important forage grass widely grown across the world with many good characteristics including high biomass yield, drought tolerance, and adaptability to a wide range of soil conditions and agro-ecologies. Two hundred and five buffelgrass accessions from diverse origins, conserved as part of the in-trust collection in the ILRI genebank, were analyzed by genotyping-by-sequencing using the DArTseq platform. The genotyping generated 234,581 single nucleotide polymorphism (SNP) markers, with polymorphic information content (PIC) values ranging from 0.005 to 0.5, and the short sequences of the markers were aligned with foxtail millet (Setaria italica) as a reference genome to generate genomic map positions of the markers. One thousand informative SNP markers, representing a broad coverage of the reference genome and with an average PIC value of 0.35, were selected for population structure and diversity analyses. The population structure analysis suggested two main groups, while the hierarchical clustering showed up to eight clusters in the collection. A representative core collection containing 20% of the accessions in the collection, with germplasm from 10 African countries and Oman, was developed. In general, the study revealed the presence of considerable genetic diversity and richness in the collection and a core collection that could be used for further analysis for specific traits of interest.

scholarly journals PSIII-15 Genetic diversity and population structure in nine beef cattle sub-populations using whole genome SNP markers

2019 ◽  
Vol 97 (Supplement_2) ◽  
pp. 169-170 ◽  
Author(s):  
Nayan Bhowmik ◽  
Kris A Ringwall ◽  
Carl R Dahlen ◽  
Kendall C Swanson ◽  
Lauren L Hulsman Hanna
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Beef Cattle ◽  
Genetic Improvement ◽  
Snp Markers ◽  
Total Variance ◽  
Fixation Index ◽  
Genetic Studies ◽  
Improvement Programs

Abstract Commercial beef cattle populations are rarely purebred. Understanding genetic diversity and population structure of crossbreds is important for future genetic improvement programs. Currently, an admixed beef cattle population comprised of British, Continental and Australian origin is being used for long-term research goals in understanding longevity, efficiency (reproductive and nutritional), and their interaction. This experiment aimed to assess the levels of genetic diversity and population structure among purebred (n = 6) and admixed (n = 3) sub-populations. A total of 727 animals were genotyped using the GeneSeek Genomic Profiler 150K. After quality checking, expected heterozygosity (HE) and polymorphism were calculated using 108,249 markers by sub-population. After LD-pruning, the remaining 19,316 SNP were used for pairwise fixation index (FST), analysis of molecular variance (AMOVA), and principle component analysis. The call rate for each sub-population ranged from 0.9866 ± 0.0351 to 0.9994 ± 0.0006. The lowest proportion (0.8527) of polymorphism was in the American Aberdeen (AA) and the highest proportion (1) was in the admixed populations. By sub-population, HE ranged from 0.3490 ± 0.1482 in AA to 0.3935 ± 0.1315 in Angus. The average nucleotide diversity over loci varied from 0.2976 ± 0.1444 in AA to 0.3872 ± 0.1879 in unknown parentage sub-population. The highest genetic differentiation was observed between AA and Continental breeds (Gelbvieh and Simmental) as FST estimates ranged from 0.1757 to 0.1789, respectively. Differences within individuals explained 98.15% of the total variance, whereas only -2.33% was due to differences among individuals within sub-populations. The first and second principal components (PC) explained 37.77% and 24.29% of the total variance, respectively. These PC show that admixed individuals clustered with animals of their primary breed. Therefore, this study suggests that clustering individuals according to their primary breed will assist in future genetic studies with this population and potentially future commercial genetic improvement programs.

Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2362-2368
Author(s):  
Yan Liu ◽  
Lei Chen ◽  
Xing-Zhi Duan ◽  
Dian-Shu Zhao ◽  
Jing-Tao Sun ◽  
...  
Keyword(s):  
Population Structure ◽  
Discriminant Analysis ◽  
Genetic Structure ◽  
Population Genetic ◽  
Brown Planthopper ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Brown Planthopper ◽  
Scale Population

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

Allozyme variation and an estimate of the inbreeding coefficient in the coffee berry borer, Hypothenemus hampei (Coleoptera: Scolytidae)

1995 ◽  
Vol 85 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Philippe Borsa ◽  
D. Pierre Gingerich
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Genetic ◽  
New Caledonia ◽  
Allozyme Variation ◽  
Inbreeding Coefficient ◽  
Hypothenemus Hampei ◽  
Coffee Berry ◽  
Biological Features ◽  
High Degree

AbstractSeven presumed Mendelian enzyme loci (Est-2, Est-3, Gpi, Idh-l, Idh-2, Mdh-2 and Mpi) were characterized and tested for polymorphism in coffee berry borers, Hypothenemus hampei (Ferrari), sampled in Côte d′Ivoire, Mexico and New Caledonia. The average genetic diversity was H = 0.080. Two loci, Mdh-2 and Mpi were polymorphic, and thus usable as genetic markers. The population structure of H. hampei was analysed using Weir & Cockerham's estimators of Wright's F-statistics. A high degree of inbreeding (f = 0.298) characterized the elementary geographic sampling unit, the coffee field. The estimate of gene flow between fields within a country was Nm = 10.6 and that between countries was Nm = 2. The population genetic structure in H. hampei could be related to its known population biological features and history.

scholarly journals mtDNAcombine: tools to combine sequences from multiple studies

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Eleanor F. Miller ◽  
Andrea Manica
Keyword(s):  
Sequence Data ◽  
Data Extraction ◽  
Bayesian Skyline Plot ◽  
Model Organisms ◽  
Data Sets ◽  
Data Handling ◽  
Online Database ◽  
Genetic Studies ◽  
Wide Range ◽  
Existing Data

Abstract Background Today an unprecedented amount of genetic sequence data is stored in publicly available repositories. For decades now, mitochondrial DNA (mtDNA) has been the workhorse of genetic studies, and as a result, there is a large volume of mtDNA data available in these repositories for a wide range of species. Indeed, whilst whole genome sequencing is an exciting prospect for the future, for most non-model organisms’ classical markers such as mtDNA remain widely used. By compiling existing data from multiple original studies, it is possible to build powerful new datasets capable of exploring many questions in ecology, evolution and conservation biology. One key question that these data can help inform is what happened in a species’ demographic past. However, compiling data in this manner is not trivial, there are many complexities associated with data extraction, data quality and data handling. Results Here we present the mtDNAcombine package, a collection of tools developed to manage some of the major decisions associated with handling multi-study sequence data with a particular focus on preparing sequence data for Bayesian skyline plot demographic reconstructions. Conclusions There is now more genetic information available than ever before and large meta-data sets offer great opportunities to explore new and exciting avenues of research. However, compiling multi-study datasets still remains a technically challenging prospect. The mtDNAcombine package provides a pipeline to streamline the process of downloading, curating, and analysing sequence data, guiding the process of compiling data sets from the online database GenBank.

scholarly journals Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Grimar Abdiel Perez ◽  
Pumipat Tongyoo ◽  
Julapark Chunwongse ◽  
Hans de Jong ◽  
Anucha Wongpraneekul ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Fixation Index ◽  
Breeding Programs ◽  
Total Fixation ◽  
Unrooted Phylogenetic Tree ◽  
Luffa Acutangula ◽  
Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS =  − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

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