Identification of single nucleotide polymorphism markers for population genetic studies in Zizania palustris L.

AbstractWe used Double Digest Restriction site associated DNA sequencing (ddRAD) and Miseq to develop new geographically informative nuclear and plastid SNP and indel loci in Quercus robur and Q. petraea. Genotypes derived from sequence data of 95 individuals and two pools of 20 individuals each of Q. robur and Q. mongolica covering the distribution range of the species, were analysed to select geographically informative and polymorphic loci within Germany and Russia. We successfully screened a selected set of 431 nuclear single nucleotide polymorphism (nSNP), six nuclear Indel, six mitochondrial single nucleotide polymorphism (mtSNP) and ten chloroplast single nucleotide polymorphism (cpSNP) loci with a SeqSNP genotyping platform on 100 individuals Quercus petraea from 10 locations in Germany, 100 individuals Quercus robur from ten locations in Germany and 100 individuals Quercus robur from ten locations in Russia. The newly developed loci are useful for species identification and genetic studies on the genetic diversity and genetic differentiation of Quercus robur and Quercus petraea in Europe.

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You Can’t Unscramble an Egg: Population Genetic Structure of Oncorhynchus mykiss in the California Central Valley Inferred from Combined Microsatellite and Single Nucleotide Polymorphism Data

San Francisco Estuary and Watershed Science ◽

10.15447/sfews.2015v13iss4art3 ◽

2015 ◽

Vol 13 (4) ◽

Cited By ~ 8

Author(s):

Devon E. Pearse ◽

John Carlos Garza

Keyword(s):

Single Nucleotide Polymorphism ◽

Genetic Structure ◽

Oncorhynchus Mykiss ◽

Population Genetic Structure ◽

Population Genetic ◽

Central Valley ◽

Single Nucleotide Polymorphism Data ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Polymorphism Data

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Identification of sixteen single-nucleotide polymorphism markers in the pearl oyster, Pinctada fucata, for population genetic structure analysis

Journal of Genetics ◽

10.1007/s12041-014-0324-9 ◽

2014 ◽

Vol 94 (S1) ◽

pp. 1-4 ◽

Cited By ~ 1

Author(s):

XIANDE HUANG ◽

SHANZENG WU ◽

YUNYAN GUAN ◽

YAOGUO LI ◽

MAOXIAN HE

Keyword(s):

Single Nucleotide Polymorphism ◽

Genetic Structure ◽

Structure Analysis ◽

Population Genetic Structure ◽

Population Genetic ◽

Pearl Oyster ◽

Pinctada Fucata ◽

Nucleotide Polymorphism ◽

Single Nucleotide

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A Highly Polymorphic Panel Consisting of Microhaplotypes and Compound Markers with the NGS and Its Forensic Efficiency Evaluations in Chinese Two Groups

Genes ◽

10.3390/genes11091027 ◽

2020 ◽

Vol 11 (9) ◽

pp. 1027

Author(s):

Xiaoye Jin ◽

Xingru Zhang ◽

Chunmei Shen ◽

Yanfang Liu ◽

Wei Cui ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Genetic Markers ◽

Population Genetic ◽

Indel Polymorphism ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Forensic Research ◽

Expected Heterozygosity ◽

Forensic Efficiency ◽

Population Genetic Analyses

Novel genetic markers like microhaplotypes and compound markers show promising potential in forensic research. Based on previously reported single nucleotide polymorphism (SNP) and insertion/deletion (InDel) polymorphism loci, 29 genetic markers including 22 microhaplotypes and seven compound markers were identified. Genetic distributions of the 29 loci in five continental populations, Kazak and Mongolian groups in China were investigated. We found that the expected heterozygosity values of these 29 loci were >0.4 in these populations, indicating these loci were relatively high polymorphisms. Population genetic analyses of five continental populations showed that five loci displayed relatively high genetic variations among these continental populations and could be useful markers for ancestry analysis. In summary, the 29 loci displayed relatively high genetic diversities in continental populations and Chinese two groups and could be informative loci for forensic research.

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Genetic structure of Hucul and Anglo-Arabian horses at the Tert locus

Annals of Animal Science ◽

10.2478/v10220-012-0040-4 ◽

2012 ◽

Vol 12 (4) ◽

pp. 483-494 ◽

Cited By ~ 1

Author(s):

Tomas Z Ząbek ◽

Paweł Czapla ◽

Maciej Wnuk ◽

Anna Lewińska ◽

Bernadetta Oklejewicz ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Genetic Basis ◽

Gene Sequence ◽

Association Studies ◽

Snp Markers ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Genetic Studies ◽

Tert Gene ◽

Degree Of Differentiation

Abstract The objective of the study was to identify single nucleotide polymorphism (SNP) genetic markers in the equine TERT gene sequence, which were used to assess the degree of differentiation between Anglo-Arabian and Hucul horses. Polymorphisms were identified by sequencing 30 amplification products representing 18000 bp of TERT sequences. Twenty-seven SNP markers were investigated, which were at genetic equilibrium. Haplotypes and genotypes were determined, and usefulness of polymorphisms for genetic studies was assessed based on minor allele frequency (MAF). Alleles characteristic of both horse breeds were identified. SNP markers with MAF > 0.18 were considered suitable for genetic analyses concerning association studies and parentage testing. In total 26 haplotypes were identified, of which three were common to the investigated horse populations. Twelve haplotypes were found only in Anglo-Arabians and 11 in Hucul horses. Identified polymorphism of TERT gene might be useful in the search for genetic basis of aging in the Equus caballus species.

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