Genome-Wide SNP Analysis Reveals Multiple Paternity in Burmese Pythons Invasive to the Greater Florida Everglades

2021 ◽  
Vol 55 (4) ◽  
Author(s):  
James Skelton ◽  
Ian Bartoszek ◽  
Caitlin E. Beaver ◽  
Kristen M. Hart ◽  
Margaret E. Hunter
Keyword(s):  
Multiple Paternity ◽  
Florida Everglades ◽  
Snp Analysis ◽  
Genome Wide

Genome-wide SNP analysis suggests male heterogamety in bighead catfish (Clarias macrocephalus, )

Aquaculture ◽  
2021 ◽  
pp. 737005
Author(s):  
Dung Ho My Nguyen ◽  
Jatupong Ponjarat ◽  
Nararat Laopichienpong ◽  
Ekaphan Kraichak ◽  
Thitipong Panthum ◽  
...  
Keyword(s):  
Snp Analysis ◽  
Genome Wide ◽  
Clarias Macrocephalus ◽  
Male Heterogamety

SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napusThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 948-956 ◽  
Author(s):  
G. Durstewitz ◽  
A. Polley ◽  
J. Plieske ◽  
H. Luerssen ◽  
E. M. Graner ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Oilseed Rape ◽  
Expressed Sequence Tag ◽  
Diploid Species ◽  
Amplicon Sequencing ◽  
Snp Markers ◽  
Snp Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Illumina Goldengate

Oilseed rape ( Brassica napus ) is an allotetraploid species consisting of two genomes, derived from B. rapa (A genome) and B. oleracea (C genome). The presence of these two genomes makes single nucleotide polymorphism (SNP) marker identification and SNP analysis more challenging than in diploid species, as for a given locus usually two versions of a DNA sequence (based on the two ancestral genomes) have to be analyzed simultaneously during SNP identification and analysis. One hundred amplicons derived from expressed sequence tag (ESTs) were analyzed to identify SNPs in a panel of oilseed rape varieties and within two sister species representing the ancestral genomes. A total of 604 SNPs were identified, averaging one SNP in every 42 bp. It was possible to clearly discriminate SNPs that are polymorphic between different plant varieties from SNPs differentiating the two ancestral genomes. To validate the identified SNPs for their use in genetic analysis, we have developed Illumina GoldenGate assays for some of the identified SNPs. Through the analysis of a number of oilseed rape varieties and mapping populations with GoldenGate assays, we were able to identify a number of different segregation patterns in allotetraploid oilseed rape. The majority of the identified SNP markers can be readily used for genetic mapping, showing that amplicon sequencing and Illumina GoldenGate assays can be used to reliably identify SNP markers in tetraploid oilseed rape and to convert them into successful SNP assays that can be used for genetic analysis.

Genome‐wide SNP analysis clearly distinguished the Belarusian Red cattle from other European cattle breeds

2021 ◽  
Author(s):  
N. A. Zinovieva ◽  
I. P. Sheiko ◽  
A. V. Dotsev ◽  
R. I. Sheiko ◽  
M. E. Mikhailova ◽  
...  
Keyword(s):  
Snp Analysis ◽  
Cattle Breeds ◽  
Genome Wide ◽  
European Cattle

Pregnancy following exclusion testing for SCA3 on polar bodies in a fresh cycle: a comparison of STR-based targeted haplotyping and genome-wide SNP analysis and meiomapping

2019 ◽  
Vol 38 ◽  
pp. e14
Author(s):  
P.J. Laitinen-Forsblom ◽  
B. Poost ◽  
D. Noss ◽  
A.H. Handyside ◽  
C. Nevinny-Stickel-Hinzpeter
Keyword(s):  
Snp Analysis ◽  
Polar Bodies ◽  
Genome Wide

scholarly journals Genetic characterization of wild barley populations (Hordeum vulgare ssp. spontaneum) from Kazakhstan based on genome wide SNP analysis

2014 ◽  
Vol 64 (4) ◽  
pp. 399-403 ◽  
Author(s):  
Yerlan Turuspekov ◽  
Saule Abugalieva ◽  
Kanat Ermekbayev ◽  
Kazuhiro Sato
Keyword(s):  
Hordeum Vulgare ◽  
Wild Barley ◽  
Genetic Characterization ◽  
Snp Analysis ◽  
Genome Wide ◽  
Hordeum Vulgare Ssp

scholarly journals Insights into the genetic history of G reen‐legged P artridgelike fowl: mt DNA and genome‐wide SNP analysis

2013 ◽  
Vol 44 (5) ◽  
pp. 522-532 ◽  
Author(s):  
M. Siwek ◽  
D. Wragg ◽  
A. Sławińska ◽  
M. Malek ◽  
O. Hanotte ◽  
...  
Keyword(s):  
Snp Analysis ◽  
Mt Dna ◽  
Genetic History ◽  
Genome Wide ◽  
History Of

scholarly journals Genome-wide scan in Hispanics highlights candidate loci for brain white matter hyperintensities

2017 ◽  
Vol 3 (5) ◽  
pp. e185 ◽  
Author(s):  
Ashley Beecham ◽  
Chuanhui Dong ◽  
Clinton B. Wright ◽  
Nicole Dueker ◽  
Adam M. Brickman ◽  
...  
Keyword(s):  
White Matter ◽  
Genetic Variants ◽  
White Matter Hyperintensities ◽  
Brain Mri ◽  
Intracranial Volume ◽  
Snp Analysis ◽  
Community Based ◽  
Brain White Matter ◽  
Genome Wide ◽  
A Genome

Objective:To investigate genetic variants influencing white matter hyperintensities (WMHs) in the understudied Hispanic population.Methods:Using 6.8 million single nucleotide polymorphisms (SNPs), we conducted a genome-wide association study (GWAS) to identify SNPs associated with WMH volume (WMHV) in 922 Hispanics who underwent brain MRI as a cross-section of 2 community-based cohorts in the Northern Manhattan Study and the Washington Heights–Inwood Columbia Aging Project. Multiple linear modeling with PLINK was performed to examine the additive genetic effects on ln(WMHV) after controlling for age, sex, total intracranial volume, and principal components of ancestry. Gene-based tests of association were performed using VEGAS. Replication was performed in independent samples of Europeans, African Americans, and Asians.Results:From the SNP analysis, a total of 17 independent SNPs in 7 genes had suggestive evidence of association with WMHV in Hispanics (p < 1 × 10−5) and 5 genes from the gene-based analysis with p < 1 × 10−3. One SNP (rs9957475 in GATA6) and 1 gene (UBE2C) demonstrated evidence of association (p < 0.05) in the African American sample. Four SNPs with p < 1 × 10−5 were shown to affect binding of SPI1 using RegulomeDB.Conclusions:This GWAS of 2 community-based Hispanic cohorts revealed several novel WMH-associated genetic variants. Further replication is needed in independent Hispanic samples to validate these suggestive associations, and fine mapping is needed to pinpoint causal variants.

scholarly journals COPHYLOGENETIC ANALYSES OF TRACHYMYRMEX ANT-FUNGAL SPECIFICITY: ‘ONE TO ONE WITH SOME EXCEPTIONS’

2021 ◽  
Author(s):  
Katherine Beigel ◽  
Alix Matthews ◽  
Katrin Kellner ◽  
Christine Pawlik ◽  
Matthew Greenwold ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Marker Genes ◽  
Snp Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Native Populations ◽  
Symbiotic Fungi ◽  
Fungal Specificity

Over the past few decades, large-scale phylogenetic analyses of fungus-gardening ants and their symbiotic fungi have depicted strong concordance among major clades of ants and their symbiotic fungi, yet within clades, fungus sharing is somewhat widespread among unrelated ant lineages. These symbioses are thought to be explained by a diffuse coevolution model within major clades. Understanding horizontal exchange within clades has been limited by conventional genetic markers that lack both interspecific and geographic variation. To examine whether reports of horizontal exchange was indeed symbiont sharing or an issue of employing relatively uninformative molecular markers, samples of Trachymyrmex arizonensis and Trachymyrmex pomonae and their fungi were collected from native populations in Arizona and genotyped using conventional marker genes and genome-wide single nucleotide polymorphisms (SNPs). Conventional markers of the fungal symbionts generally exhibited cophylogenetic patterns that were consistent with some symbiont sharing, but most fungal clades had low support. SNP analysis, in contrast, indicated that each ant species exhibited fidelity to its own fungal subclade with only one instance of a colony growing a fungus that was otherwise associated with a different ant species. This evidence supports a pattern of codivergence between Trachymyrmex species and their fungi, and thus a diffuse coevolutionary model may not accurately predict symbiont exchange. These results suggest that fungal sharing across host species in these symbioses may be less extensive than previously thought.

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