Genetic variation and population genetic structure of the large yellow croaker (Larimichthys crocea) based on genome‐wide single nucleotide polymorphisms in farmed and wild populations

In the present research, I used an open access data set (Medicinal Genomics) consisting of nearly 200'000 genome-wide single nucleotide polymorphisms (SNPs) typed in 28 cannabis accessions to shed light on the plant's underlying genetic structure. Genome-wide loadings were used to sequentially cull less informative markers. The process involved reducing the number of SNPs to 100K, 10K, 1K, 100 until I identified a set of 42 highly informative SNPs that I present here. The two first principal components, encompass over 3/4 of the genetic variation present in the dataset (PCA1 = 48.6%, PCA2= 26.3%). This set of diagnostic SNPs is then used to identify clusters into which cannabis accession segregate. I identified three clear and consistent clusters; reflective of the ancient domestication trilogy of the genus Cannabis.

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Genome-wide analyses reveal clustering in Cannabis cultivars: the ancient domestication trilogy of a panacea

10.7287/peerj.preprints.1553 ◽

2015 ◽

Cited By ~ 1

Author(s):

Philippe Henry

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Open Access ◽

Nucleotide Polymorphisms ◽

Data Set ◽

Single Nucleotide ◽

Genome Wide ◽

Access Data ◽

Diagnostic Snps ◽

Shed Light

In the present research, I used an open access data set (Medicinal Genomics) consisting of nearly 200'000 genome-wide single nucleotide polymorphisms (SNPs) typed in 28 cannabis accessions to shed light on the plant's underlying genetic structure. Genome-wide loadings were used to sequentially cull less informative markers. The process involved reducing the number of SNPs to 100K, 10K, 1K, 100 until I identified a set of 42 highly informative SNPs that I present here. The two first principal components, encompass over 3/4 of the genetic variation present in the dataset (PCA1 = 48.6%, PCA2= 26.3%). This set of diagnostic SNPs is then used to identify clusters into which cannabis accession segregate. I identified three clear and consistent clusters; reflective of the ancient domestication trilogy of the genus Cannabis.

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Genome-wide analyses reveal clustering in Cannabis cultivars: the ancient trilogy of a panacea

10.7287/peerj.preprints.1553v1 ◽

2015 ◽

Author(s):

Philippe Henry

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Open Access ◽

Nucleotide Polymorphisms ◽

Data Set ◽

Single Nucleotide ◽

Genome Wide ◽

Access Data ◽

Diagnostic Snps ◽

Shed Light

In the present research, I used an open access data set (Medicinal Genomics) consisting of nearly 200'000 genome-wide single nucleotide polymorphisms (SNPs) typed in 28 cannabis accessions to shed light on the plant's underlying genetic structure. Genome-wide loadings were used to sequentially cull less informative markers. The process involved reducing the number of SNPs to 100K, 10K, 1K, 100 until I identified a set of 42 highly informative SNPs that I present here. The two first principal components, encompass over 3/4 of the genetic variation present in the dataset (PCA1 = 48.6%, PCA2= 26.3%). This set of diagnostic SNPs is then used to identify clusters into which cannabis accession segregate. I identified three clear and consistent clusters; reflective of the ancient trilogy of the genus Cannabis.

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

Journal of Economic Entomology ◽

10.1093/jee/toz145 ◽

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.

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Genomic Analyses of Globodera pallida, A Quarantine Agricultural Pathogen in Idaho

Pathogens ◽

10.3390/pathogens10030363 ◽

2021 ◽

Vol 10 (3) ◽

pp. 363

Author(s):

Sulochana K. Wasala ◽

Dana K. Howe ◽

Louise-Marie Dandurand ◽

Inga A. Zasada ◽

Dee R. Denver

Keyword(s):

Genetic Variation ◽

Potato Production ◽

Globodera Pallida ◽

Fixation Index ◽

Parasitic Nematodes ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide ◽

Field Samples ◽

Multiple Introduction

Globodera pallida is among the most significant plant-parasitic nematodes worldwide, causing major damage to potato production. Since it was discovered in Idaho in 2006, eradication efforts have aimed to contain and eradicate G. pallida through phytosanitary action and soil fumigation. In this study, we investigated genome-wide patterns of G. pallida genetic variation across Idaho fields to evaluate whether the infestation resulted from a single or multiple introduction(s) and to investigate potential evolutionary responses since the time of infestation. A total of 53 G. pallida samples (~1,042,000 individuals) were collected and analyzed, representing five different fields in Idaho, a greenhouse population, and a field in Scotland that was used for external comparison. According to genome-wide allele frequency and fixation index (Fst) analyses, most of the genetic variation was shared among the G. pallida populations in Idaho fields pre-fumigation, indicating that the infestation likely resulted from a single introduction. Temporal patterns of genome-wide polymorphisms involving (1) pre-fumigation field samples collected in 2007 and 2014 and (2) pre- and post-fumigation samples revealed nucleotide variants (SNPs, single-nucleotide polymorphisms) with significantly differentiated allele frequencies indicating genetic differentiation. This study provides insights into the genetic origins and adaptive potential of G. pallida invading new environments.

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Significant genetic differences among Heterodera schachtii populations within and among sugar beet production areas

Nematology ◽

10.1163/15685411-00003297 ◽

2020 ◽

Vol 22 (2) ◽

pp. 165-177 ◽

Cited By ~ 1

Author(s):

Rasha Haj Nuaima ◽

Johannes Roeb ◽

Johannes Hallmann ◽

Matthias Daub ◽

Holger Heuer

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Population Genetic Structure ◽

Population Genetic ◽

Spatial Scales ◽

Geographic Distance ◽

Heterodera Schachtii ◽

Parasitic Nematodes ◽

Neutral Genetic Variation ◽

Production Areas

Summary Characterising the non-neutral genetic variation within and among populations of plant-parasitic nematodes is essential to determine factors shaping the population genetic structure. This study describes the genetic variation of the parasitism gene vap1 within and among geographic populations of the beet cyst nematode Heterodera schachtii. Forty populations of H. schachtii were sampled at four spatial scales: 695 km, 49 km, 3.1 km and 0.24 km. DGGE fingerprinting showed significant differences in vap1 patterns among populations. High similarity of vap1 patterns appeared between geographically close populations, and occasionally among distant populations. Analysis of spatially sampled populations within fields revealed an effect of tillage direction on the vap1 similarity for two of four studied fields. Overall, geographic distance and similarity of vap1 patterns of H. schachtii populations were negatively correlated. In conclusion, the population genetic structure was shaped by the interplay between the genetic adaptation and the passive transport of this nematode.

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Absence of Population Genetic Structure Among Breeding Colonies of the Waved Albatross

The Condor ◽

10.1093/condor/108.2.440 ◽

2006 ◽

Vol 108 (2) ◽

pp. 440-445 ◽

Cited By ~ 1

Author(s):

Kathryn P. Huyvaert ◽

Patricia G. Parker

Keyword(s):

Genetic Variation ◽

Gene Flow ◽

Genetic Structure ◽

Population Genetic Structure ◽

Population Genetic ◽

Breeding Population ◽

Genetic Structuring ◽

Galapagos Archipelago ◽

Phoebastria Irrorata ◽

Waved Albatrosses

Abstract We used four variable microsatellite loci to examine the distribution of genetic variation and degree of genetic structuring among three subcolonies of Waved Albatrosses (Phoebastria irrorata). The breeding population of this species is almost entirely limited to the island of Española in the Galápagos Archipelago. Such strong philopatry could lead to population genetic structure among subcolonies on the island. Pairwise values of the FST analog, θ, calculated from microsatellite genotypes, were all less than 0.012, indicating little genetic differentiation and the presence of gene flow throughout the population.

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Effects of habitat fragmentation on population genetic structure in the white-footed mouse (Peromyscus leucopus)

Canadian Journal of Zoology ◽

10.1139/z00-201 ◽

2001 ◽

Vol 79 (2) ◽

pp. 285-295 ◽

Cited By ~ 33

Author(s):

Catherine A Mossman ◽

Peter M Waser

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Habitat Fragmentation ◽

Genetic Differentiation ◽

Population Genetic Structure ◽

Population Genetic ◽

Peromyscus Leucopus ◽

Marginal Effect ◽

Geographic Scale ◽

White Footed Mouse

Habitat fragmentation may have significant consequences for population genetic structure because geographic distance and physical barriers may impede gene flow. In this study, we investigated whether habitat fragmentation affects fine-scale genetic structure of populations of the white-footed mouse (Peromyscus leucopus). We studied 27 populations of P. leucopus, 17 in continuous forest and 10 in isolated woodlots. Populations were trapped in pairs that were either 500 or 2000 m apart. We estimated genetic variation at eight P. leucopus specific microsatellite DNA loci. We discovered significant genetic variation within all populations, but no significant differences in numbers of alleles or heterozygosity between populations. For given population pairs, we found significant genetic differentiation even at very short distances, based on multilocus FST estimates. The amount of genetic differentiation between population pairs was similar in the two habitats. Distance had a marginal effect on genetic differentiation when comparing paired populations separated by 2000 m with those separated by 500 m. However, at a larger geographic scale, there was no evidence of isolation by distance. This study confirms that microsatellite-based studies have the potential to detect interpopulation differentiation at an extremely local scale, and suggests that habitat fragmentation has surprisingly few effects on P. leucopus genetic structure.

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