scholarly journals Use of High Density Single Nucleotide Polymorphism (SNP) Arrays to Assess Genetic Diversity and Population Structure of Dairy Cattle in Smallholder Dairy Systems: The Case of Girinka Programme in Rwanda

2018 ◽  
Vol 9 ◽  
Author(s):  
Mizeck G. G. Chagunda ◽  
Fidalis D. N. Mujibi ◽  
Theogene Dusingizimana ◽  
Olivier Kamana ◽  
Evans Cheruiyot ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Dairy Cattle ◽  
High Density ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Snp Arrays ◽  
Smallholder Dairy ◽  
Dairy Systems

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 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.

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