scholarly journals Development of a Multilocus Sequence Typing Scheme for Giardia intestinalis

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 764
Author(s):  
Adriana Higuera ◽  
Marina Muñoz ◽  
Myriam Consuelo López ◽  
Patricia Reyes ◽  
Plutarco Urbano ◽  
...  
Keyword(s):  
Population Structure ◽  
Allelic Diversity ◽  
Giardia Intestinalis ◽  
Genome Sequences ◽  
Intestinal Protozoan ◽  
Valuable Alternative ◽  
Phylogenetic Reconstructions ◽  
Population Structure Analysis ◽  
Dehydrogenase Gene ◽  
Stool Samples

Giardia intestinalis is an intestinal protozoan most commonly found in humans. It has been grouped into 8 assemblages (A-H). Markers such as the glutamate dehydrogenase gene, triose phosphate isomerase and beta-giardin (β-giardin) have been widely used for genotyping. In addition, different genetic targets have been proposed as a valuable alternative to assess diversity and genetics of this microorganism. Thus, our objective was to evaluate new markers for the study of the diversity and intra-taxa genetic structure of G. intestinalis in silico and in DNA obtained from stool samples. We analysed nine constitutive genes in 80 complete genome sequences and in a group of 24 stool samples from Colombia. Allelic diversity was evaluated by locus and for the concatenated sequence of nine loci that could discriminate up to 53 alleles. Phylogenetic reconstructions allowed us to identify AI, AII and B assemblages. We found evidence of intra- and inter-assemblage recombination events. Population structure analysis showed genetic differentiation among the assemblages analysed.

scholarly journals Investigation of Giardia intestinalis Genotypes among the Food Handlers of Qazvin, Iran

2019 ◽  
Author(s):  
Mojtaba SHAHNAZI ◽  
Farzaneh NAGHIZADEH ◽  
Elham HAJIALILO ◽  
Safar Ali ALIZADEH ◽  
Mehrzad SARAEI ◽  
...  
Keyword(s):  
Giardia Intestinalis ◽  
P Value ◽  
Giardia Cyst ◽  
Food Handlers ◽  
Dehydrogenase Gene ◽  
Stool Samples ◽  
Stool Specimens ◽  
The Impact ◽  
Concentration Methods

Background: We aimed to investigate the genotypes of Giardia intestinalis among the food handlers in Qazvin, Iran. Methods: Overall, 1530 stool specimens were collected from the food handlers who visited Shahid Bolandian Health Center, Qazvin, Iran during 2016. Specimens were evaluated by microscopic and concentration methods. Twenty specimens with appropriate number of giardia cysts were selected followed by DNA extraction. Determination of giardia genotypes was achieved through PCR and sequencing the glutamate dehydrogenase gene. The phylogenetic tree was drawn using the MEGA7 software. Finally, the data were analyzed statistically with a P-value<0.05 was considered as significant. Results: Twenty stool samples (1.3%) were positive for Giardia cyst. All positive specimens were obtained from male participants with abdominal cramp being their most common symptoms. The mean age for infected individuals was 32 yr. Molecular characterization was successfully performed for 17 isolates and two genotypes A (AII, 65%) and B (BIII, 35%) were identified. Conclusion: The most prevalent giardia genotypes among the food handlers in Qazvin were A (AII) and B (BIII) genotypes with A (AII) genotype as the dominant one in the region. Considering the direct association between the food handlers and public health as well as the impact of geographical and host conditions on dispersion and pathogenicity of various genotypes and their zoonotic aspects, further investigations are necessary.

scholarly journals POPULATION STRUCTURE AND GENETIC DIVERSITY OF THE PEE DEE COTTON BREEDING PROGRAM

2021 ◽  
Author(s):  
Grant T Billings ◽  
Michael A Jones ◽  
Sachin Rustgi ◽  
Amanda M Hulse-Kemp ◽  
B Todd Campbell
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Upland Cotton ◽  
Fiber Quality ◽  
Allelic Diversity ◽  
Breeding Systems ◽  
Pairwise Distance ◽  
Population Structure Analysis ◽  
Pee Dee ◽  
Breeding Cycles

Abstract Accelerated marker-assisted selection and genomic selection breeding systems require genotyping data to select the best parents for combining beneficial traits. Since 1935, the Pee Dee cotton germplasm enhancement program has developed an important genetic resource for upland cotton (Gossypium hirsutum L.), contributing alleles for improved fiber quality, agronomic performance, and genetic diversity. To date, a detailed genetic survey of the program’s eight historical breeding cycles has yet to be undertaken. The objectives of this study were to evaluate genetic diversity across and within breeding groups, examine population structure, and contextualize these findings relative to the global upland cotton gene pool. The CottonSNP63K array was used to identify 17,441 polymorphic markers in a panel of 114 diverse Pee Dee genotypes. A subset of 4,597 markers was selected to decrease marker density bias. Identity by state (IBS) pairwise distance varied substantially, ranging from 0.55 to 0.97. Pedigree-based estimates of relatedness were not very predictive of observed genetic similarities. Few rare alleles were present, with 99.1% of SNP alleles appearing within the first four breeding cycles. Population structure analysis with principal component analysis, discriminant analysis of principal components, fastSTRUCTURE, and a phylogenetic approach revealed an admixed population with moderate substructure. A small core collection (n &lt; 20) captured 99% of the program’s allelic diversity. Allele frequency analysis indicated potential selection signatures associated with stress resistance and fiber cell growth. The results of this study will steer future utilization of the program’s germplasm resources and aid in combining program-specific beneficial alleles and maintaining genetic diversity.

scholarly journals Phylogenetic structure of Salmonella Enteritidis provides context for a foodborne outbreak in Peru

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Willi Quino ◽  
Junior Caro-Castro ◽  
Orson Mestanza ◽  
Carmen V. Hurtado ◽  
Maria L. Zamudio ◽  
...  
Keyword(s):  
Population Structure ◽  
Structure Analysis ◽  
Salmonella Enteritidis ◽  
Foodborne Outbreak ◽  
Genome Sequences ◽  
Phylogenetic Structure ◽  
Population Structure Analysis ◽  
The World ◽  
Relationship Of ◽  
Microbiological Procedures

AbstractSalmonella Enteritidis, an important foodborne zoonosis, has a dramatically increased number of cases around the world. To explore the phylogenetic structure of Peruvian Salmonella Enteritidis strains and their relationship with an outbreak occurred in 2018, we analyzed a comprehensive strains of S. Enteritidis received by the National Institute of Health during the period 2000–2018. A total of 180 strains were characterized by microbiological procedures, serotyping and whole genome sequencing. Based on genome sequences annotated, virulence factors and accessory genes were identified. Phylogenetic and population structure analysis were also analyzed based on SNPs. The phylogenetic analysis grouped the genomes into two well-supported clades that were consistent with population structure analysis. The clinical and food strains corresponding to the outbreak were included in the same cluster, which presented the sdhA gene, related to the increase of the virulence of this pathogen. The phylogenetic relationship of Peruvian S. Enteritidis suggests the presence of four S. enteritidis population with high epidemiological importance.

scholarly journals Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaoting Xia ◽  
Shunjin Zhang ◽  
Huaju Zhang ◽  
Zijing Zhang ◽  
Ningbo Chen ◽  
...  
Keyword(s):  
Population Structure ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
System Response ◽  
Whole Genome ◽  
Population Structure Analysis ◽  
Native Cattle ◽  
Genomic Regions

Abstract Background Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle. Results The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6). Conclusion We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.

scholarly journals Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

2021 ◽  
Vol 134 (5) ◽  
pp. 1343-1362
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Lukas A. Mueller ◽  
Eder Jorge de Oliveira ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

scholarly journals Genetic diversity and population structure analysis of Lateolabrax maculatus from Chinese coastal waters using polymorphic microsatellite markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wei Wang ◽  
Chunyan Ma ◽  
Longling Ouyang ◽  
Wei Chen ◽  
Ming Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Structure Analysis ◽  
Principal Component ◽  
Genetic Constitution ◽  
Southern Group ◽  
Population Structure Analysis ◽  
Lateolabrax Maculatus ◽  
Geographic Populations ◽  
Geographic Separation

AbstractIn order to provide valuable guidelines for the conservation of germplasm of Lateolabrax maculatus, the genetic diversity and population structure analysis were evaluated for eight geographic populations along coastal regions of China, using 11 microsatellite DNA markers. The genetic parameters obtained showed that, eight populations can be clustered into two groups, the Northern group and the Southern group, concordant with their geographical positions. The UPGMA tree constructed according to the Nei’s genetic distance along with the structure analysis and discriminant analysis of principal component also supported this result. This might be explained by the geographic separation and the divergent environmental conditions among the populations. It's worth noting that, QD (Qingdao) population from northern area was assigned to the Southern group and showed a close genetic relationship and similar genetic constitution with the southern populations. We speculated that large scales of anthropogenic transportation of wild fries from QD populations to the southern aquaculture areas in history should be the primary cause. The populations from GY (Ganyu), RD (Rudong) and BH (Binhai) had higher genetic diversity and showed limited genetic exchange with other populations, indicating better conservation of the natural resources in these regions. All populations were indicated to have experienced bottleneck events in history.

scholarly journals Population structure of Chinese southwest wheat germplasms resistant to stripe rust and powdery mildew using the DArT-seq technique

2018 ◽  
Vol 48 (4) ◽  
Author(s):  
Tianqing Chen ◽  
Piyada Alisha Tantasawat ◽  
Wei Wang ◽  
Xu Gao ◽  
Liyi Zhang
Keyword(s):  
Population Structure ◽  
Disease Resistance ◽  
Polymorphic Information Content ◽  
Wheat Breeding ◽  
Wheat Varieties ◽  
Group I ◽  
Population Structure Analysis ◽  
Specific Allele ◽  
The Mean ◽  
Different Origins

ABSTRACT: Understanding genetic variability in existing wheat accessions is critical for collection, conservation and use of wheat germplasms. In this study, 138 Chinese southwest wheat accessions were investigated by genotyping using two resistance gene makers (Pm21 and Yr26) and DArT-seq technique. Finally, about 50% cultivars (lines) amplified the specific allele for the Yr26 gene (Gwm11) and 40.6% for the Pm21 gene (SCAR1265). By DArT-seq analysis, 30,485 markers (6486 SNPs and 23999 DArTs) were obtained with mean polymorphic information content (PIC) value 0.33 and 0.28 for DArT and SNP marker, respectively. The mean Dice genetic similarity coefficient (GS) was 0.72. Two consistent groups of wheat varieties were identified using principal coordinate analysis (PCoA) at the level of both the chromosome 6AS and the whole-genome, respectively. Group I was composed of non-6VS/6AL translocation lines of different origins, while Group II was composed of 6VS/6AL translocation (T6VS/6AL) lines, most of which carried the Yr26 and Pm21 genes and originated from Guizhou. Besides, a model-based population structure analysis revealed extensive admixture and further divided these wheat accessions into six subgroups (SG1, SG2, SG3, SG4, SG5 and SG6), based on their origin, pedigree or disease resistance. This information is useful for wheat breeding in southwestern China and association mapping for disease resistance using these wheat germplasms in future.

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