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 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.

scholarly journals Uncovering phylogenetic relationships and genetic diversity of water dropwort using phenotypic traits and SNP markers

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0249825
Author(s):  
Qun Ji ◽  
Honglian Zhu ◽  
Xinfang Huang ◽  
Kai Zhou ◽  
Zhengwei Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Phylogenetic Tree ◽  
Phylogenetic Relationships ◽  
Morphological Characteristics ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Linear Leaf ◽  
Water Dropwort

The water dropworts Oenanthe linearis Wall. ex DC. and O. javanica (Blume) DC. are aquatic perennial herbs that have been used in China as vegetables and traditional medicines. However, their phylogenetic relationships and genetic diversity are poorly understood. Here, we presented the phenotypic traits and genome-wide DNA marker-based analysis of 158 water dropwort accessions representing both species. The analysis revealed that Oenanthe linearis was readily segregated into linear-leaf and deep-cleft leaf water dropworts according to their leaf shapes at flowering. Oenanthe javanica was classified by clustering analysis into two clusters based mainly on the morphological characteristics of their ultimate segments (leaflets). A set of 11 493 high-quality single-nucleotide polymorphisms was identified and used to construct a phylogenetic tree. There was strong discrimination between O. linearis and O. javanica, which was consistent with their phenotype diversification. The population structure and phylogenetic tree analyses suggested that the O. linearis accessions formed two major groups, corresponding to the linear-leaf and deep-cleft leaf types. The most obvious phenotypic differences between them were fully expressed at the reproductive growth stage. A single-nucleotide polymorphism-based analysis revealed that the O. javanica accessions could be categorized into groups I andII. However, this finding did not entirely align with the clusters revealed by morphological classification. Landraces were clustered into one group along with the remaining wild accessions. Hence, water dropwort domestication was short in duration. The level of genetic diversity for O. linearis (π = 0.1902) was slightly lower than that which was estimated for O. javanica (π = 0.2174). There was a low level of genetic differentiation between O. linearis and O. javanica (Fst = 0.0471). The mean genetic diversity among accessions ranged from 0.1818 for the linear-leaf types to 0.2318 for the groupII accessions. The phenotypic traits and the single-nucleotide polymorphism markers identified here lay empirical foundation for future genomic studies on water dropwort.

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 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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