scholarly journals Simulasi Metode Statistik untuk Seleksi Single Nucleotide Polymorphism pada Populasi Plasmodium

Life Science ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 54-64
Author(s):  
Mohamad Ikhsan Nurulloh ◽  
Yustinus Ulung Anggraito ◽  
Hidayat Trimarsanto ◽  
Endah Peniati ◽  
R. Susanti
Keyword(s):  
Principal Component Analysis ◽  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Principal Component ◽  
Selection Method ◽  
Principal Coordinate Analysis ◽  
Neighbor Joining ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Informative Snps

Plasmodium is a pathogen that causes malaria which has high genetic diversity and resistance to antimalarial drugs. Information on the population structure of Plasmodium can be used as molecular markers, one of which is Single Nucleotide Polymorphism (SNP). SNP markers are in large numbers and not entirely informative. The existing method has not been effective in producing informative SNPs, therefore it is necessary to develop an effective SNP selection method. The SNP selection method is developed using FST as the main filter (filter) and combines Linkage Disequilibrium (LD). The population structure of the SNP is known to use Principal Component Analysis (PCA), Principal Coordinate Analysis (PCoA), pairwise FST, and neighbor-joining population trees. Informative SNP criteria known by calculating FST and Minor Allele Frequency (MAF). Statistical methods were tested to determine their effectiveness in producing informative SNPs. The method testing was carried out using genetic data simulation of the Plasmodium population. The results of the study show that the statistical method is effective in producing informative SNPs. The informative SNP criteria are SNPs with MAF 0.2-0.4 and FST 0.1-0.4 and 0.8-1.0.   Plasmodium merupakan patogen penyebab malaria dengan keanekaragaman genetik tinggi dan memiliki resistensi terhadap obat antimalaria. Informasi sturuktur populasi Plasmodium dapat dimanfaatkan sebagai marka molekuler seperti Single Nucleotide Polymorphism (SNP). Marka SNP terdapat dalam jumlah yang banyak dan tidak seluruhnya informatif. Metode yang telah ada belum efektif dalam menghasilkan SNP informatif sehingga perlu dilakukan pengembangan metode seleksi SNP yang efektif. Metode seleksi SNP dikembangkan menggunakan FST sebagai filter (penyaring) utamanya dan gabungkan Linkage Disequilibrium (LD). Struktur populasi dari SNP diketahui menggunakan Principal Component Analysis (PCA), Principal Coordinate Analysis (PCoA), pairwise FST, dan neighbor-joining population tree. Kriteria SNP informatif yang diketahui dengan menghitung FST dan Minor Allele Frequency (MAF). Metode statistika diuji untuk mengetahui keefektifannya dalam menghasilkan SNP informatif. Pengujian metode dilakukan menggunakan simulasi data genetik populasi Plasmodium. Hasil penelitian menunjukkan metode statistika efektif dalam menghasilkan SNP informatif. Kriteria SNP informatif adalah SNP dengan MAF 0.2-0.4 serta FST 0.1-0.4 dan 0.8-1.0.

scholarly journals Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping Data

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2025
Author(s):  
Shyryn Almerekova ◽  
Yuliya Genievskaya ◽  
Saule Abugalieva ◽  
Kazuhiro Sato ◽  
Yerlan Turuspekov
Keyword(s):  
Population Structure ◽  
Heading Date ◽  
Snp Markers ◽  
Principal Coordinate Analysis ◽  
Neighbor Joining ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Polymorphic Snps ◽  
Ancestral Node

The genetic relationship and population structure of two-rowed barley accessions from Kazakhstan were assessed using single-nucleotide polymorphism (SNP) markers. Two different approaches were employed in the analysis: (1) the accessions from Kazakhstan were compared with barley samples from six different regions around the world using 1955 polymorphic SNPs, and (2) 94 accessions collected from six breeding programs from Kazakhstan were studied using 5636 polymorphic SNPs using a 9K Illumina Infinium assay. In the first approach, the neighbor-joining tree showed that the majority of the accessions from Kazakhstan were grouped in a separate subcluster with a common ancestral node; there was a sister subcluster that comprised mainly barley samples that originated in Europe. The Pearson’s correlation analysis suggested that Kazakh accessions were genetically close to samples from Africa and Europe. In the second approach, the application of the STRUCTURE package using 5636 polymorphic SNPs suggested that Kazakh barley samples consisted of five subclusters in three major clusters. The principal coordinate analysis plot showed that, among six breeding origins in Kazakhstan, the Krasnovodopad (KV) and Karaganda (KA) samples were the most distant groups. The assessment of the pedigrees in the KV and KA samples showed that the hybridization schemes in these breeding stations heavily used accessions from Ethiopia and Ukraine, respectively. The comparative analysis of the KV and KA samples allowed us to identify 214 SNPs with opposite allele frequencies that were tightly linked to 60 genes/gene blocks associated with plant adaptation traits, such as the heading date and plant height. The identified SNP markers can be efficiently used in studies of barley adaptation and deployed in breeding projects to develop new competitive cultivars.

scholarly journals A comparative analysis of proximity measures to determine the Lithuanian population structure

2021 ◽  
Vol 62 ◽  
pp. 86-93
Author(s):  
Alma Molytė ◽  
Alina Urnikytė
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Comparative Analysis ◽  
Multidimensional Scaling ◽  
Principal Component ◽  
Genetic Data ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Proximity Measures

In this paper the multidimensional scaling, the principal coordinate and principal component methods for the Lithuanian population structure have investigated, taken that the proximity measures are Euclid, Gower, Bray-Curtis, Kulczynski, Jaccard and Morisita. The genome-wide single nucleotide polymorphism genetic data analyzed. A comparative analysis of proximity measures performed. The results of visualization are also presented.

scholarly journals Proportioning Whole-Genome Single-Nucleotide–Polymorphism Diversity for the Identification of Geographic Population Structure and Genetic Ancestry

2006 ◽  
Vol 78 (4) ◽  
pp. 680-690 ◽  
Author(s):  
Oscar Lao ◽  
Kate van Duijn ◽  
Paula Kersbergen ◽  
Peter de Knijff ◽  
Manfred Kayser
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Genetic Ancestry ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Geographic Population

Assessment of population structure in Pacific Lepeophtheirus salmonis (Krøyer) using single nucleotide polymorphism and microsatellite genetic markers

Aquaculture ◽  
2011 ◽  
Vol 320 (3-4) ◽  
pp. 183-192 ◽  
Author(s):  
Amber M. Messmer ◽  
Eric B. Rondeau ◽  
Stuart G. Jantzen ◽  
Krzysztof P. Lubieniecki ◽  
William S. Davidson ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Genetic Markers ◽  
Lepeophtheirus Salmonis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Genetic Characterization of Global Cultivated Potato Clones, Including Korean Potatoes, Using Genome-Wide Single Nucleotide Polymorphism Markers

2021 ◽  
Author(s):  
Kwang Ryong Jo ◽  
Seungho Cho ◽  
Ji-Hong Cho ◽  
Hyun-Jin Park ◽  
Jang-Gyu Choi ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Abiotic Stress Tolerance ◽  
The United States ◽  
Extended Haplotype Homozygosity ◽  
Biotic And Abiotic Stress ◽  
Nucleotide Polymorphism ◽  
Extended Haplotype ◽  
Single Nucleotide ◽  
Population Structure Analysis

Abstract Characterizing the genetic diversity and population structure of breeding materials is essential for breeding to improve crop plants. The potato is an important non-cereal food crop worldwide, but breeding potatoes remains challenging owing to their auto-tetraploidy and highly heterozygous genome. We evaluated the genetic structure of a 110-line Korean potato germplasm using the SolCAP 8303 single nucleotide polymorphism (SNP) Infinium array and compared it with potato clones from other countries to understand the genetic landscape of cultivated potatoes. Following the tetraploid model, we conducted population structure analysis, revealing three subpopulations represented by two Korean potato groups and one separate foreign potato group within 110 lines. When analyzing 393 global potato clones, country/region-specific genetic patterns were revealed. The Korean potato clones exhibited higher heterozygosity than those from Japan, the United States, and other potato landraces. We also employed integrated extended haplotype homozygosity (iHS) and cross-population extended haplotype homozygosity (XP-EHH) to identify selection signatures spanning candidate genes associated with biotic and abiotic stress tolerance. Based on the informativeness of SNPs for dosage genotyping calls, 10 highly informative SNPs discriminating all 393 potatoes were identified. Our results could help understanding a potato breeding history that reflects regional adaptations and distinct market demands.

Porcine Single Nucleotide Polymorphism (SNP) Development and Population Structure of Pigs Assessed by Validated SNPs

2011 ◽  
Vol 50 (5-6) ◽  
pp. 428-439
Author(s):  
Toshimi Matsumoto ◽  
Naohiko Okumura ◽  
Hirohide Uenishi ◽  
Takeshi Hayashi ◽  
Noriyuki Hamasima ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Snp Development
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