scholarly journals KIR2DL4 genetic diversity in a Brazilian population sample: implications for transcription regulation and protein diversity in samples with different ancestry backgrounds

2020 ◽  
Author(s):  
Emiliana Weiss ◽  
Heloisa S. Andrade ◽  
Juliana Rodrigues Lara ◽  
Andreia S. Souza ◽  
Michelle A. Paz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Massively Parallel Sequencing ◽  
Gene Diversity ◽  
Association Studies ◽  
Population Sample ◽  
Gene Families ◽  
High Linkage Disequilibrium ◽  
Brazilian Population ◽  
Southeastern Brazil ◽  
Mapping Bias

AbstractKIR2DL4 is an important immune modulator expressed in Natural Killer cells, being HLA-G its main ligand. We characterize KIR2DL4 gene diversity considering the promoter, all exons, and all introns, in a highly admixed Brazilian population sample using massively parallel sequencing. We also introduce a molecular method to amplify and sequence the complete KIR2DL4 gene. To avoid mapping bias and genotype errors commonly observed in gene families, we have developed a bioinformatic pipeline designed to minimize mapping, genotyping, and haplotyping errors. We have applied this method to survey the variability of 220 samples from the State of São Paulo, southeastern Brazil. We have also compared the KIR2DL4 genetic diversity in Brazilian samples with the previously reported by the 1000Genomes consortium. KIR2DL4 presents high linkage disequilibrium throughout the gene, with coding sequences associated with specific promoters. There were few, but divergent, promoter haplotypes. We have also detected many new KIR2DL4 sequences, all with nucleotide exchanges in introns and encoding previously described proteins. Exons 3 and 4, which encode the external domains, were the most variable ones. The ancestry background influences KIR2DL4 allele frequencies and must be considered for association studies regarding KIR2DL4.

scholarly journals HLA-F coding and regulatory segments variability determined by massively parallel sequencing procedures in a Brazilian population sample

2016 ◽  
Vol 77 (10) ◽  
pp. 841-853 ◽  
Author(s):  
Thálitta Hetamaro Ayala Lima ◽  
Renato Vidal Buttura ◽  
Eduardo Antônio Donadi ◽  
Luciana Caricati Veiga-Castelli ◽  
Celso Teixeira Mendes-Junior ◽  
...  
Keyword(s):  
Massively Parallel Sequencing ◽  
Population Sample ◽  
Brazilian Population ◽  
Massively Parallel ◽  
Parallel Sequencing

scholarly journals Características epidemiológicas da população brasileira e implicações à condução de pesquisas clínicas / Epidemiological characteristics of the Brazilian population and implications for the conduction of clinical research

2019 ◽  
Vol 64 (2) ◽  
pp. 142
Author(s):  
Marina De Carvalho Souza Ferreira ◽  
Luis Lopez Martinez
Keyword(s):  
Genetic Diversity ◽  
Clinical Trials ◽  
Clinical Research ◽  
Large Population ◽  
Population Sample ◽  
Target Population ◽  
Brazilian Population ◽  
Diverse Groups ◽  
Epidemiological Characteristics ◽  
Burden Of Diseases

Objetivo: A Pesquisa Clínica (PC) é um meio fundamental para a redução da carga de doenças mundialmente, proporcionando o desenvolvimento de terapias inovadoras, seguras e eficazes. Para tanto, necessita-se considerar que os participantes nela incluídos sejam representativos da população alvo do produto estudado, garantindo a confiabilidade e a capacidade de generalização dos resultados obtidos. Logo, a inclusão de grupos diversificados resulta, futuramente, em uma maior qualidade na prestação de assistência à saúde. Com isso, buscou-se caracterizar a população brasileira, gerando informações que possam ser relevantes e atrativas para a realização de PC no país, destacando-se a importância da diversidade genética na amostra populacional a ser alocada em PC. Material e Método: Levantamento através de bases de dados científicas e governamentais.  Resultados e Conclusão: A realização de PC no Brasil, além de representar oportunidades de benefícios econômicos, técnicos e estruturais para o país, possui a qualidade de incluir uma população numerosa, composta por uma grande variedade étnico-racial, podendo representar uma vantagem competitiva e estratégica na escolha de países para realização de estudos multicêntricos internacionais.Descritores: Pesquisa Clínica, Estudo Clínico, Epidemiologia, População, BrasilABSTRACTObjective: Clinical Research (CR) is a fundamental path to reduce the burden of diseases worldwide by providing the development of innovative, safe and effective therapies, mainly through clinical trials. Therefore, the design of a CR needs to consider that the participants included are representative of the target population of the studied product, guaranteeing the reliability and generalization of the results. Thus, the inclusion of diverse groups results in a higher quality in the provision of healthcare. Thereby, we sought to characterize the Brazilian population, generating information that may be relevant and attractive to the development of CR in that country, highlighting the importance of genetic diversity in the population sample to be allocated in CR. Material and Methods: Survey through scientific and governmental databases. Results and Conclusion: Brazil, in addition to providing economic, technical and structural benefits for the development of clinical research, has a large population and comprises a large ethnic-racial variety, which may represent a competitive and strategic advantage in the choice of countries to perform multicenter and international studies.Keywords:, Clinical Research, Clinical Study, Epidemiology, Population, Brazil

scholarly journals Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1298
Author(s):  
Caléo Panhoca de Almeida ◽  
Jean Fausto de Carvalho Paulino ◽  
Sérgio Augusto Morais Carbonell ◽  
Alisson Fernando Chiorato ◽  
Qijian Song ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Common Bean ◽  
Gene Diversity ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Association Mapping Approach

Brazil is the largest consumer and third highest producer of common beans (Phaseolus vulgaris L.) worldwide. Since the 1980s, the commercial Carioca variety has been the most consumed in Brazil, followed by Black and Special beans. The present study evaluates genetic diversity and population structure of 185 Brazilian common bean cultivars using 2827 high-quality single-nucleotide polymorphisms (SNPs). The Andean allelic introgression in the Mesoamerican accessions was investigated, and a Carioca panel was tested using an association mapping approach. The results distinguish the Mesoamerican from the Andean accessions, with a prevalence of Mesoamerican accessions (94.6%). When considering the commercial classes, low levels of genetic differentiation were seen, and the Carioca group showed the lowest genetic diversity. However, gain in gene diversity and allelic richness was seen for the modern Carioca cultivars. A set of 1060 ‘diagnostic SNPs’ that show alternative alleles between the pure Mesoamerican and Andean accessions were identified, which allowed the identification of Andean allelic introgression events and shows that there are putative introgression segments in regions enriched with resistance genes. Finally, genome-wide association studies revealed SNPs significantly associated with flowering time, pod maturation, and growth habit, showing that the Carioca Association Panel represents a powerful tool for crop improvements.

scholarly journals Genetic associations in the detection of QTLs for wheat spike-related traits

2015 ◽  
Vol 50 (2) ◽  
pp. 149-159 ◽  
Author(s):  
Ljiljana Brbaklić ◽  
Dragana Trkulja ◽  
Ankica Kondić-Špika ◽  
Nikola Hristov ◽  
Srbislav Denčić ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Linear Model ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Association Studies ◽  
Mixed Linear Model ◽  
General Linear ◽  
Genetic Associations ◽  
Trait Associations

The objective of this work was to assess the genetic diversity and population structure of wheat genotypes, to detect significant and stable genetic associations, as well as to evaluate the efficiency of statistical models to identify chromosome regions responsible for the expression of spike-related traits. Eight important spike characteristics were measured during five growing seasons in Serbia. A set of 30 microsatellite markers positioned near important agronomic loci was used to evaluate genetic diversity, resulting in a total of 349 alleles. The marker-trait associations were analyzed using the general linear and mixed linear models. The results obtained for number of allelic variants per locus (11.5), average polymorphic information content value (0.68), and average gene diversity (0.722) showed that the exceptional level of polymorphism in the genotypes is the main requirement for association studies. The population structure estimated by model-based clustering distributed the genotypes into six subpopulations according to log probability of data. Significant and stable associations were detected on chromosomes 1B, 2A, 2B, 2D, and 6D, which explained from 4.7 to 40.7% of total phenotypic variations. The general linear model identified a significantly larger number of marker-trait associations (192) than the mixed linear model (76). The mixed linear model identified nine markers associated to six traits.

scholarly journals Genetic Diversity, Population Structure, and Formation of a Core Collection of 1197 Citrullus Accessions

HortScience ◽  
2016 ◽  
Vol 51 (1) ◽  
pp. 23-29 ◽  
Author(s):  
Haiying Zhang ◽  
Jianguang Fan ◽  
Shaogui Guo ◽  
Yi Ren ◽  
Guoyi Gong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Diversity Index ◽  
Gene Diversity ◽  
Association Studies ◽  
Economic Benefits ◽  
Genetic Distances ◽  
Genetic Variations ◽  
Average Value ◽  
Core Set

Watermelon belongs to the genus Citrullus. There have been continuing interests in breeding of watermelon for economic benefits, but information on the scope and utilization of genetic variations in Citrullus is still limited. The present study was conducted in 2012–13, to evaluate the genetic diversity and population structure of the 1197 line watermelon collection maintained by the Beijing Vegetable Research Center (BVRC), which belongs to seven Citrullus species including Citrullus naudinianus, Citrullus colocynthis, Citrullus rehmii, Citrullus ecirrhosus, Citrullus amarus, Citrullus mucosospermus, and Cirullus lanatus subsp. vulgaris. Twenty-three highly informative microsatellite markers evenly distributed in the watermelon genome were used to assess genetic diversity in this collection. The markers detected on an average of 6.05 alleles per locus with the average value of polymorphism information content (PIC) at 0.49. A high level of gene diversity [Nei’s gene diversity index (Nei) = 0.56] and a low observed heterozygosity (Ho = 0.10) were revealed within the collection. Structure analysis grouped the 1197 accessions into two main populations (Pop I and Pop II) and an admixture group. Pop I contained 450 accessions from C. lanatus subsp. vulgaris (446) and C. mucosospermus (4). Pop II comprised 465 accessions, 379 of which belonged to C. lanatus subsp. vulgaris and 86 to C. naudinianus (3), C. ecirrhosus (2), C. rehmii (2), C. colocynthis (11), C. amarus (58), and C. mucosospermus (10). The remaining 282 accessions were classified as an admixture group. The two main populations were further subdivided into four subgroups. The groupings were consistent with the estimation of F statistics (Fst) and Nei’s genetic distances in collections. We confirmed the distinct genetic backgrounds between American and East Asian ecotypes. Subsequently, we defined a core set consisting of 130 accessions including 47 from Pop I, 68 from Pop II, and 15 from the Admixture group. This core set was able to capture all 133 alleles detected by 23 simple sequence repeats (SSRs) in 1197 accessions. These results will facilitate efficient use of genetic variations in Citrullus in watermelon breeding and help optimization of accessions in genomewide association studies.

Population structure and core collection construction of apricot (Prunus armeniaca L.) in North Africa based on microsatellite markers

2015 ◽  
Vol 15 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Hedia Bourguiba ◽  
Mohamed-Amine Batnini ◽  
Lamia Krichen ◽  
Neila Trifi-Farah ◽  
Jean-Marc Audergon
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
North Africa ◽  
Core Collection ◽  
Diversity Index ◽  
Gene Diversity ◽  
Association Studies ◽  
Conservation Strategies ◽  
Phenotypic Data

North Africa enclosed original apricot genetic resources with the cohabitation of grafting and seed-propagated accessions. In this study, we assessed the genetic diversity and population structure of 183 apricot accessions using 24 microsatellite markers distributed evenly in the Prunus genome. A total of 192 alleles and a high level of gene diversity (0.593) were detected among the whole panel. Genetic structure analysis revealed the presence of four genetic clusters. We also found that both geographical origin and mode of propagation are important factors structuring genetic diversity in apricot species. Results confirmed the presence of gene exchange between the northern and southern countries of the Mediterranean Basin. Subsequently, a core collection of 98 accessions based on M (maximization) strategy showing 99.47% of allele retention ratio was constructed. No significant differences for Shannon's information index and Nei's diversity index were observed between the core and entire collections. Our results provide an effective aid for future germplasm preservation and conservation strategies as well as genetic association studies development in relation to phenotypic data.

Extended HLA-G genetic diversity and ancestry composition in a Brazilian admixed population sample: Implications for HLA-G transcriptional control and for case-control association studies

2018 ◽  
Vol 79 (11) ◽  
pp. 790-799 ◽  
Author(s):  
Maria Luiza Guimarães de Oliveira ◽  
Luciana Caricati Veiga-Castelli ◽  
Letícia Marcorin ◽  
Guilherme Debortoli ◽  
Alison Luis Eburneo Pereira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Transcriptional Control ◽  
Association Studies ◽  
Population Sample ◽  
Case Control ◽  
Admixed Population ◽  
Control Association

scholarly journals Genetic diversity, population structure and selection signature in Ethiopian Sorghum (Sorghum bicolor L. [Moench]) germplasm

2021 ◽  
Author(s):  
Zeleke Wondimu ◽  
Hongxu Dong ◽  
Andrew H. Paterson ◽  
Walelign Worku ◽  
Kassahun Bantte
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Sorghum Bicolor ◽  
Large Scale ◽  
Gene Diversity ◽  
Association Studies ◽  
Abiotic Stress Tolerance ◽  
Genome Wide Association Studies ◽  
Selection Signature ◽  
Center Of Origin

Ethiopia, the probable center of origin and diversity for sorghum (Sorghum bicolor L. [Moench]) and with unique eco-geographic features, possesses a large number of sorghum landraces that have not been well studied. Increased knowledge of this diverse germplasm through large-scale genomic characterization may contribute for understanding of evolutionary biology, and adequate use of these valuable resources from the center of origin. In this study, we characterized genetic diversity, population structure and selection signature in 304 sorghum accessions collected from diverse sorghum growing regions of Ethiopia using genotyping-by-sequencing (GBS). We identified a total of 108,107 high-quality single nucleotide polymorphism (SNPs) markers that were evenly distributed across the sorghum genome. The average gene diversity among accessions was high(He = 0.29). We detected a relatively low frequency of rare alleles (26%), highlighting the potential of this germplasm for subsequent allele mining studies through genome wide association studies (GWAS). While we found no evidence of genetic differentiation among administrative regions (FST = 0.02, p = 0.12), population structure and cluster analyses showed clear differentiation among six Ethiopian sorghum populations (FST = 0.28, p = 0.01) adapting to different environments. Analysis of SNP differentiation between the identified genetic groups revealed a total of 40 genomic regions carrying signatures of selection. These regions harbored candidate genes potentially involved in a variety of biological processes, including abiotic stress tolerance, pathogen defense and reproduction. Overall, a high level of untapped diversity for sorghum improvement remains available in Ethiopia, with patterns of diversity consistent with divergent selection on a range of adaptive characteristics.

scholarly journals Genetic diversity, population structure and selection signature in Ethiopian Sorghum (Sorghum bicolor L. [Moench]) germplasm

2021 ◽  
Author(s):  
Zeleke Wondimu ◽  
Hongxu Dong ◽  
Andrew H Paterson ◽  
Walelign Worku ◽  
Kassahun Bantte
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Sorghum Bicolor ◽  
Large Scale ◽  
Gene Diversity ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Selection Signature ◽  
Center Of Origin ◽  
Sorghum Bicolor L

Abstract Ethiopia, the probable center of origin and diversity for sorghum (Sorghum bicolor L. [Moench]) and with unique eco-geographic features, possesses a large number of sorghum landraces that have not been well studied. Increased knowledge of this diverse germplasm through large-scale genomic characterization may contribute for understanding of evolutionary biology, and adequate use of these valuable resources from the center of origin. In this study, we characterized genetic diversity, population structure and selection signature in 304 sorghum accessions collected from diverse sorghum growing regions of Ethiopia using genotyping-by-sequencing (GBS). We identified a total of 108,107 high-quality single nucleotide polymorphism (SNPs) markers that were evenly distributed across the sorghum genome. The average gene diversity among accessions was high (He = 0.29). We detected a relatively low frequency of rare alleles (26%), highlighting the potential of this germplasm for subsequent allele mining studies through genome wide association studies (GWAS). While we found no evidence of genetic differentiation among administrative regions (FST = 0.02, p = 0.12), population structure and cluster analyses showed clear differentiation among six Ethiopian sorghum populations (FST = 0.28, p = 0.01) adapting to different environments. Analysis of SNP differentiation between the identified genetic groups revealed a total of 40 genomic regions carrying signatures of selection. These regions harbored candidate genes potentially involved in a variety of biological processes, including abiotic stress tolerance, pathogen defense and reproduction. Overall, a high level of untapped diversity for sorghum improvement remains available in Ethiopia, with patterns of diversity consistent with divergent selection on a range of adaptive characteristics.

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