scholarly journals Mining of Simple Sequence Repeats Loci, Genetic Relationship And Population Structure of Bottle Gourd (Lagenaria Siceraria (Molina) Standl.) Accessions With Different Geographical Origin Using Single Nucleotide Polymorphism (SNPs) Markers

2021 ◽  
Author(s):  
Rodrigo Iván Contreras-Soto ◽  
Ariel Salvatierra ◽  
Carlos Maldonado ◽  
Jacob Mashilo
Keyword(s):  
South Africa ◽  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Simple Sequence Repeats ◽  
Bottle Gourd ◽  
Lagenaria Siceraria ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Ssr Loci ◽  
Simple Sequence

Abstract Lagenaria siceraria (Molina) Standl. (2n = 2x = 22) is an important horticultural and medicinal crop grown worldwide serving for food and pharmaceutical industries. The crop exhibit extensive phenotypic and genetic variation useful for cultivar obtention targeting economic traits, however limited genomic resources are available for effective germplasm characterization into breeding and conservation strategies. This study determined the genetic relationships and population structure in a collection of different accessions of bottle gourd prevenient from Chile, Asia, and South Africa by using single nucleotide polymorphism (SNPs) markers and mining of simple sequence repeats (SSR) loci derived from genotyping-by-sequencing (GBS) data. The GBS resulted in 12,766 SNPs molecular markers classified as moderate to highly informative with mean polymorphic information content of 0.29. The mean gene diversity of 0.16, indicated low genetic differentiation of the accessions. Analysis of molecular variance revealed lower differentiation between (36%) than within (48%) bottle gourd accessions suggesting that random mating system dominates inbreeding. Population structure revealed two genetically differentiated groups comprising of South Africa accessions and an admixed group with genotypes of Asian and Chilean origin. The results of SSR loci mining from GBS data should be developed and validated before being used in diverse bottle gourd accessions. The SNPs markers developed in the present study are useful genomic resources in bottle gourd breeding programs for assessing the extent of genetic diversity for effective parental selection and breeding.

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.

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 Identification and Validation of a Core Single-Nucleotide Polymorphism Marker Set for Genetic Diversity Assessment, Fingerprinting Identification, and Core Collection Development in Bottle Gourd

2021 ◽  
Vol 12 ◽  
Author(s):  
Ying Wang ◽  
Xiaohua Wu ◽  
Yanwei Li ◽  
Zishan Feng ◽  
Zihan Mu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Snp Markers ◽  
Bottle Gourd ◽  
Snp Marker ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
The Core ◽  
Germplasm Collections ◽  
Diversity Assessment

Germplasm collections are indispensable resources for the mining of important genes and variety improvement. To preserve and utilize germplasm collections in bottle gourd, we identified and validated a highly informative core single-nucleotide polymorphism (SNP) marker set from 1,100 SNPs. This marker set consisted of 22 uniformly distributed core SNPs with abundant polymorphisms, which were established to have strong representativeness and discriminatory power based on analyses of 206 bottle gourd germplasm collections and a multiparent advanced generation inter-cross (MAGIC) population. The core SNP markers were used to assess genetic diversity and population structure, and to fingerprint important accessions, which could provide an optimized procedure for seed authentication. Furthermore, using the core SNP marker set, we developed an accessible core population of 150 accessions that represents 100% of the genetic variation in bottle gourds. This core population will make an important contribution to the preservation and utilization of bottle gourd germplasm collections, cultivar identification, and marker-assisted breeding.

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.

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