Development of Single Nucleotide Polymorphism (SNP) Markers for Analysis of Population Structure and Invasion Pathway in the Coconut Leaf Beetle Brontispa longissima (Gestro) Using Restriction Site-Associated DNA (RAD) Genotyping in Southern China

To determine population genomic structure through high-throughput sequencing techniques has revolutionized research on non-model organisms. The coconut leaf beetle, Brontispa longissima (Gestro), is a widely distributed pest in Southern China. Here, we used restriction site-associated DNA (RAD) genotyping to assess the invasion pathway by detecting and estimating the degree of genetic differentiation among 51 B. longissima accessions collected from Southern China. A total of 10,127 SNPs were obtained, the screened single nucleotide polymorphism (SNP) information was used to construct the phylogenetic tree, FST analysis, principal component analysis, and population structure analysis. Genetic structure analysis was used to infer the population structure; the result showed that all accessions were divided into Hainan population and non-Hainan population. The Hainan population remained stable, only the Sansha population differentiated, and the non-Hainan populations have gradually differentiated into smaller sub-populations. We concluded that there are two sources of invasion of B. longissima into mainland China: Taiwan and Hainan. With the increase of the invasion time, the Hainan population was relatively stable, and the Taiwan population was differentiated into three sub-populations. Based on the unrooted phylogenetic tree, we infer that Taiwan and Hainan are the two invasive base points. The Taiwan population invaded Fujian, Guangdong, and Guangxi, while the Hainan population invaded Yunnan and Sansha. Our results provide strong evidence for the utility of RAD sequencing (RAD-seq) in population genetics studies, and our generated SNP resource could provide a valuable tool for population genomics studies of B. longissima in the future.

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Simulasi Metode Statistik untuk Seleksi Single Nucleotide Polymorphism pada Populasi Plasmodium

Life Science ◽

10.15294/lifesci.v8i1.29990 ◽

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.

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

The American Journal of Human Genetics ◽

10.1086/501531 ◽

2006 ◽

Vol 78 (4) ◽

pp. 680-690 ◽

Cited By ~ 117

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

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P4064 Genetic diversity and population structure of wild and semi-domesticated reindeer (Rangifer tarandus) inhabited in northeastern Siberia based on single nucleotide polymorphism markers

Journal of Animal Science ◽

10.2527/jas2016.94supplement4110b ◽

2016 ◽

Vol 94 (suppl_4) ◽

pp. 110-111 ◽

Cited By ~ 1

Author(s):

V. R. Kharzinova ◽

A. V. Dotsev ◽

I. M. Okhlopkov ◽

E. A. Gladyr ◽

V. I. Fedorov ◽

...

Keyword(s):

Genetic Diversity ◽

Single Nucleotide Polymorphism ◽

Population Structure ◽

Rangifer Tarandus ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Northeastern Siberia

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

Aquaculture ◽

10.1016/j.aquaculture.2010.09.033 ◽

2011 ◽

Vol 320 (3-4) ◽

pp. 183-192 ◽

Cited By ~ 19

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

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

10.21203/rs.3.rs-1074016/v1 ◽

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.

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

Lietuvos matematikos rinkinys ◽

10.15388/lmr.2021.25232 ◽

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.

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