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 Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep

2014 ◽  
Vol 37 (2) ◽  
pp. 389-395 ◽  
Author(s):  
Andrés N Grasso ◽  
Virginia Goldberg ◽  
Elly A Navajas ◽  
Wanda Iriarte ◽  
Diego Gimeno ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Genomic Variation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Molecular genetic diversity and population structure analyses of rutabaga accessions from Nordic countries as revealed by single nucleotide polymorphism markers

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhiyu Yu ◽  
Rudolph Fredua-Agyeman ◽  
Sheau-Fang Hwang ◽  
Stephen E. Strelkov
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Seed Quality ◽  
Leaf Shape ◽  
Crop Improvement ◽  
Geographic Origin ◽  
Nordic Countries ◽  
Group Method ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Abstract Background Rutabaga or swede (Brassica napus ssp. napobrassica (L.) Hanelt) varies in root and leaf shape and colour, flesh colour, foliage growth habits, maturity date, seed quality parameters, disease resistance and other traits. Despite these morphological differences, no in-depth molecular analyses of genetic diversity have been conducted in this crop. Understanding this diversity is important for conservation and broadening the use of this resource. Results This study investigated the genetic diversity within and among 124 rutabaga accessions from five Nordic countries (Norway, Sweden, Finland, Denmark and Iceland) using a 15 K single nucleotide polymorphism (SNP) Brassica array. After excluding markers that did not amplify genomic DNA, monomorphic and low coverage site markers, the accessions were analyzedwith 6861 SNP markers. Allelic frequency statistics, including polymorphism information content (PIC), minor allele frequency (MAF) and mean expected heterozygosity ($$ \overline{H} $$ H ¯ e) and population differentiation statistics such as Wright’s F-statistics (FST) and analysis of molecular variance (AMOVA) indicated that the rutabaga accessions from Norway, Sweden, Finland and Denmark were not genetically different from each other. In contrast, accessions from these countries were significantly different from the accessions from Iceland (P < 0.05). Bayesian analysis with the software STRUCTURE placed 66.9% of the rutabaga accessions into three to four clusters, while the remaining 33.1% constituted admixtures. Three multivariate analyses: principal coordinate analysis (PCoA), the unweighted pair group method with arithmetic mean (UPGMA) and neighbour-joining (NJ) clustering methods grouped the 124 accessions into four to six subgroups. Conclusion Overall, the correlation of the accessions with their geographic origin was very low, except for the accessions from Iceland. Thus, Icelandic rutabaga accessions can offer valuable germplasm for crop improvement.

scholarly journals Genetic Diversity and Population Structure Analysis of Citrus Germplasm with Single Nucleotide Polymorphism Markers

2018 ◽  
Vol 143 (6) ◽  
pp. 399-408
Author(s):  
Yuan Yu ◽  
Chunxian Chen ◽  
Ming Huang ◽  
Qibin Yu ◽  
Dongliang Du ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Phylogenetic Relationships ◽  
Snp Array ◽  
Poncirus Trifoliata ◽  
Citrus Paradisi ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Population Structure Analysis

Citrus (Citrus sp.) germplasm collections are a valuable resource for citrus genetic breeding studies, and further utilization of the resource requires knowledge of their genotypic and phylogenetic relationships. Diverse citrus accessions, including citron (Citrus medica), mandarin (Citrus reticulata), pummelo (Citrus maxima), papeda (Papeda sp.), trifoliate orange (Poncirus trifoliata), kumquat (Fortunella sp.), and related species, have been housed at the Florida Citrus Arboretum, Winter Haven, FL, but the accessions in the collection have not been genotyped. In this study, a collection of 80 citrus accessions were genotyped using 1536 sweet orange–derived single nucleotide polymorphism (SNP) markers, to determine their SNP fingerprints and to assess genetic diversity, population structure, and phylogenetic relationships, and thereby to test the efficiency of using the single genotype-derived SNP chip with relatively low cost for these analyses. Phylogenetic relationships among the 80 accessions were determined by multivariate analysis. A model-based clustering program detected five basic groups and revealed that C. maxima introgressions varied among mandarin cultivars and segregated in mandarin F1 progeny. In addition, reciprocal differences in C. maxima contributions were observed among citranges (Citrus sinensis × P. trifoliata vs. P. trifoliata × C. sinensis) and may be caused by the influence of cytoplasmic DNA and its effect on selection of cultivars. Inferred admixture structures of many secondary citrus species and important cultivars were confirmed or revealed, including ‘Bergamot’ sour orange (Citrus aurantium), ‘Kinkoji’ (C. reticulata × Citrus paradisi), ‘Hyuganatsu’ orange (Citrus tamurana), and palestine sweet lime (Citrus aurantifolia). The relatively inexpensive SNP array used in this study generated informative genotyping data and led to good consensus and correlations with previously published observations based on whole genome sequencing (WGS) data. The genotyping data and the phylogenetic results may facilitate further exploitation of interesting genotypes in the collection and additional understanding of phylogenetic relationships in citrus.

scholarly journals Genetic Diversity and Population Structure of Soybean Lines Adapted to Sub-Saharan Africa Using Single Nucleotide Polymorphism (SNP) Markers

Agronomy ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 604
Author(s):  
Subhash Chander ◽  
Ana Luísa Garcia-Oliveira ◽  
Melaku Gedil ◽  
Trushar Shah ◽  
Gbemisola Oluwayemisi Otusanya ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Polymorphic Information Content ◽  
Snp Markers ◽  
Sub Saharan Africa ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Or Groups ◽  
Sub Saharan

Soybean productivity in sub-Saharan Africa (SSA) is less than half of the global average yield. To plug the productivity gap, further improvement in grain yield must be attained by enhancing the genetic potential of new cultivars that depends on the genetic diversity of the parents. Hence, our aim was to assess genetic diversity and population structure of elite soybean genotypes, mainly released cultivars and advanced selections in SSA. In this study, a set of 165 lines was genotyped with high-throughput single nucleotide polymorphism (SNP) markers covering the complete genome of soybean. The genetic diversity (0.414) was high considering the bi-allelic nature of SNP markers. The polymorphic information content (PIC) varied from 0.079 to 0.375, with an average of 0.324 and about 49% of the markers had a PIC value above 0.350. Cluster analysis grouped all the genotypes into three major clusters. The model-based STRUCTURE and discriminant analysis of principal components (DAPC) exhibited high consistency in the allocation of lines in subpopulations or groups. Nonetheless, they presented some discrepancy and identified the presence of six and five subpopulations or groups, respectively. Principal coordinate analysis revealed more consistency with subgroups suggested by DAPC analysis. Our results clearly revealed the broad genetic base of TGx (Tropical Glycine max) lines that soybean breeders may select parents for crossing, testing and selection of future cultivars with desirable traits for SSA.

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