scholarly journals Correction to: Genome-wide assessment of population structure and genetic diversity of Eucalyptus urophylla based on a multi-species single-nucleotide polymorphism chip analysis

2020 ◽  
Vol 16 (3) ◽  
Author(s):  
Huixiao Yang ◽  
Fang Xu ◽  
Huanqin Liao ◽  
Weihua Zhang ◽  
XiaoHui Yang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Eucalyptus Urophylla ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Single Nucleotide Polymorphism Chip ◽  
Genome Wide ◽  
Chip Analysis

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.

Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphism markers

2006 ◽  
Vol 112 (6) ◽  
pp. 1104-1114 ◽  
Author(s):  
Karl J. Schmid ◽  
Ottó Törjék ◽  
Rhonda Meyer ◽  
Heike Schmuths ◽  
Matthias H. Hoffmann ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Large Scale ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Scale Population

scholarly journals Genome-wide Single Nucleotide Polymorphism Analyses Reveal Genetic Diversity and Structure of Wild and Domestic Cattle in Bangladesh

2014 ◽  
Vol 27 (10) ◽  
pp. 1381-1386 ◽  
Author(s):  
Md. Rasel Uzzaman ◽  
Zewdu Edea ◽  
Md. Shamsul Alam Bhuiyan ◽  
Jeremy Walker ◽  
A. K. F. H. Bhuiyan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Genetic Diversity And Structure

scholarly journals Putative Variants, Genetic Diversity and Population Structure among Soybean Cultivars Bred at Different Ages in Huang-Huai-Hai Region

2021 ◽  
Author(s):  
Jialin Liu ◽  
Huimin Xie ◽  
Ting Lin ◽  
Congxiao Tie ◽  
Huolin Luo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variants ◽  
Pedigree Information ◽  
Biological Processes ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Soybean Cultivars ◽  
Genome Wide

Abstract Soybean cultivars bred in the Huang-Huai-Hai region (HR) are rich in pedigree information. To data, few reports have exposed the genetic variants, population structure and genetic diversity of cultivars in this region by making use of genome-wide resequencing data. To depict genetic variation, population structure and composition characteristics of genetic diversity, a sample of soybean population that composed all by cultivars was constructed. We re-sequenced 181 soybean cultivar genomes with an average depth of 10.38x. In total, 11185589 single nucleotide polymorphisms (SNPs) and 2520208 insertion-deletions (InDels) were identified on all 20 chromosomes. A considerable number of putative variants existed in important genome regions that may have an incalculable influence on genes, which participated in momentous biological processes. PCA and population structure figured out that there was no obvious grouping trend. The LD semi-decay distances of the five sub-populations were 290kb, 380kb, 753kb, 182kb, and 227kb, respectively. Sub-population A (SA) had the highest value of nucleotide polymorphism (π). With the passage of time, the nucleotide polymorphism of SB and SC decreased gradually, however that of SD and SE, opposite to SB and SC, gave a rapid up-climbing trend, which meant a sharp increasing in genetic diversity during the latest 20 years, hinting that breeders may have different breeding goals in different breeding periods in HR. Analysis of the PIC statistics exhibited very similar results with π. The current study was to analyze the genetic variants and characterize the structure and genetic diversity of soybean cultivars bred in different decades in HR, and in the hope of providing a theoretical reference for other identical studies.

scholarly journals Genome-Wide Single-Nucleotide Polymorphism Data Unveil Admixture of Chinese Indigenous Chicken Breeds with Commercial Breeds

2019 ◽  
Vol 11 (7) ◽  
pp. 1847-1856
Author(s):  
Changsheng Nie ◽  
Pedro Almeida ◽  
Yaxiong Jia ◽  
Haigang Bao ◽  
Zhonghua Ning ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Isolation By Distance ◽  
Critical Role ◽  
Geographic Origin ◽  
Genomic Variation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Chicken Breeds

Abstract The conservation and development of chicken have received considerable attention, but the admixture history of chicken breeds, especially Chinese indigenous breeds, has been poorly demonstrated. In this study, we aimed to evaluate the genetic diversity and population structure of eight chicken breeds (including conserved chicken breeds) from different geographic origin and to identify admixture within these breeds using a 600-K single-nucleotide polymorphism panel for genotyping. Using the genotype of 580,961 single-nucleotide polymorphism markers scored in 1,200 animals, we evaluated the genetic diversity (heterozygosity and proportion of polymorphic markers), linkage disequilibrium decay, population structure (principal component analysis and neighbor-joining tree), genetic differentiation (FST and genetic distance), and migration events (TreeMix and f-statistics) of the eight domesticated chicken breeds. The results of population analytical methods revealed patterns of hybridization that occurred after divergence in Tibetan chicken. We argue that chicken migration and admixture, followed by trade, have been important forces in shaping the genomic variation in modern Chinese chicken. Moreover, isolation by distance might play a critical role in shaping the genomic variation within Eurasia continent chicken breeds. Moreover, genetic information provided in this study is valuable resources for production applications (genomic prediction, and breeding strategy) and scientific research (genetic basis detection, studying evolution, or domestication).

scholarly journals Population structure and breed composition prediction in a multi-breed sheep population using genome-wide single nucleotide polymorphism genotypes

animal ◽  
2020 ◽  
Vol 14 (3) ◽  
pp. 464-474
Author(s):  
A.C. O’Brien ◽  
D.C. Purfield ◽  
M.M. Judge ◽  
C. Long ◽  
S. Fair ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Sheep Population ◽  
Genome Wide ◽  
Breed Sheep
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