scholarly journals In-Depth Genetic Diversity and Population Structure of Endangered Peruvian Amazon Rosewood Germplasm Using Genotyping by Sequencing (GBS) Technology

Forests ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 197
Author(s):  
Muhammad Azhar Nadeem ◽  
Stalin Juan Vasquez Guizado ◽  
Muhammad Qasim Shahid ◽  
Muhammad Amjad Nawaz ◽  
Ephrem Habyarimana ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Molecular Characterization ◽  
Clustering Algorithms ◽  
Genotyping By Sequencing ◽  
Diversity Indices ◽  
Peruvian Amazon ◽  
Mean Values ◽  
Management Plans

Research studies on conservative genetics of endangered plants are very important to establish the management plans for the conservation of biodiversity. Rosewood is an evergreen tree of the Amazon region and its essential oil has great acceptance in the medical and cosmetic industry. The present study aimed to explore the genetic diversity and population structure of 90 rosewood accessions collected from eight localities of Peruvian Amazon territory through DArTseq markers. A total of 7485 informative markers resulted from genotyping by sequencing (GBS) analysis were used for the molecular characterization of rosewood germplasm. Mean values of various calculated diversity parameters like observed number of alleles (1.962), the effective number of alleles (1.669), unbiased expected heterozygosity (0.411), and percent polymorphism (93.51%) over the entire germplasm showed the existence of a good level of genetic variations. Our results showed that the Mairiricay population was more diverse compared to the rest of the populations. Tamshiyacu-2 and Mairiricay-15 accessions were found genetically distinct accessions. The analysis of molecular variance (AMOVA) reflected maximum variations (75%) are due to differences within populations. The implemented clustering algorithms, i.e., STRUCTURE, neighbor-joining analysis and principal coordinate analysis (PCoA) separated the studied germplasm on the basis of their geographical locations. Diversity indices for STRUCTURE-based populations showed that subpopulation A is more diverse population than the rest of the populations, for such reason, individuals belonging to this subpopulation should be used for reintroduction or reinforcement plans of rosewood conservation. We envisage that molecular characterization of Peruvian rosewood germplasm with DArTseq markers will provide a platform for the conservation, management and restoration of endangered rosewood in upcoming years.

scholarly journals Genetic diversity and population structure of endangered rosewood from the Peruvian Amazon using ISSR markers

2020 ◽  
Vol 50 (3) ◽  
pp. 204-212
Author(s):  
Stalin Juan Vasquez GUIZADO ◽  
Muhammad Azhar NADEEM ◽  
Fawad ALI ◽  
Muzaffer BARUT ◽  
Ephrem HABYARIMANA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Diversity ◽  
Population Level ◽  
Diversity Indices ◽  
Issr Markers ◽  
Neighbor Joining ◽  
Peruvian Amazon ◽  
Over Exploitation ◽  
Issr Primers

ABSTRACT Rosewood, Aniba rosaeodora is an endangered species in Amazon forests and its natural stands have been heavily depleted due to over-exploitation for the cosmetic industry. This study aimed to investigate the genetic diversity and population structure of 90 rosewood accessions from eight localities in the Peruvian Amazon through 11 Inter Simple Sequence Repeats (ISSR) primers. The ISSR primers produced a sum of 378 bands, of which 375 (99.2%) were polymorphic, with an average polymorphism information content (PIC) value of 0.774. The mean effective number of alleles (Ne), Shannon informative index (I), gene diversity (He) and total gene diversity (Ht) were 1.485, 0.294, 0.453 and 0.252, respectively. Analysis of molecular variance (AMOVA) showed the presence of maximum variability within populations (88%). The Structure algorithm, neighbor joining and principal coordinate analysis (PCoA) grouped the 90 rosewood accessions into three main populations (A, B and C). Diversity indices at the inter-population level revealed a greater genetic diversity in population A, due to higher gene flow. The neighbor-joining analysis grouped populations A and B, while population C was found to be divergent at the inter population level. We concluded that population A reflects higher genetic diversity and should be prioritized for future management and conservation plans.

Molecular characterization of echovirus 13 uncovering high genetic diversity and identification of new genotypes in Pakistan

2017 ◽  
Vol 48 ◽  
pp. 102-108
Author(s):  
Shahzad Shaukat ◽  
Mehar Angez ◽  
Tariq Mahmood ◽  
Muhammad Masroor Alam ◽  
Salmaan Sharif ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Characterization ◽  
High Genetic Diversity

scholarly journals Molecular Characterization of Pathogenicity Locus (PaLoc) and tcdC Genetic Diversity Among tcdA+B+ Clostridioides Difficile Clinical Isolates in Tehran, Iran

2020 ◽  
Author(s):  
Mansoor Kodori ◽  
Zohreh Ghalavand ◽  
Abbas Yadegar ◽  
Gita Eslami ◽  
Masoumeh Azimirad ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Characterization ◽  
Disease Severity ◽  
Genetic Variants ◽  
Rflp Analysis ◽  
Clostridioides Difficile ◽  
Pcr Rflp ◽  
The Common ◽  
Healthcare Associated

Abstract Background: Clostridioides difficile is the main cause of healthcare-associated diarrhea worldwide. It is proposed that certain C. difficile toxinotypes with distinct pathogenicity locus (PaLoc) variants are associated with disease severity and outcomes. Additionally, few studies have described the common C. difficile toxinotypes, and also little is known about the tcdC variants in Iranian isolates. We characterized the toxinotypes and the tcdC genotypes from a collection of Iranian clinical C. difficile tcdA+B+ isolates with known ribotypes (RTs).Methods: Fifty C. difficile isolates with known RTs and carrying the tcdA and tcdB toxin genes were analyzed. Toxinotyping was carried out based on a PCR-RFLP analysis of a 19.6 kb region encompassing the PaLoc. Genetic diversity of the tcdC gene was determined by the sequencing of the gene.Results: Of the 50 C. difficile isolates investigated, five distinct toxinotypes were recognized. Toxinotypes 0 (33/50, 66%) and V (11/50, 22%) were the most frequently found. C. difficile isolates of the toxinotype 0 mostly belonged to RT 001 (12/33, 36.4%), whereas toxinotype V consisted of RT 126 (9/11, 81.8%). The tcdC sequencing showed six variants (35/50, 70%); tcdC-sc3 (24%), tcdC-A (22%), tcdC-sc9 (18%), tcdC-B (2%), tcdC-sc14 (2%), and tcdC-sc15 (2%). The remaining isolates were wild-types (15/50, 30%) in the tcdC gene.Conclusions: The present study demonstrates that the majority of clinical tcdA+B+ isolates of C. difficile frequently harbor tcdC genetic variants. We also found that the RT 001/ toxinotype 0 and the RT 126/ toxinotype V are the most common types among Iranian isolates. Further studies are needed to investigate the putative association of various tcdC genotypes with CDI severity and its recurrence.

scholarly journals Phenotypic and molecular characterization of a set of tropical maize inbred lines from a public breeding program in Brazil

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Sirlene Viana de Faria ◽  
Leandro Tonello Zuffo ◽  
Wemerson Mendonça Rezende ◽  
Diego Gonçalves Caixeta ◽  
Hélcio Duarte Pereira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Inbred Lines ◽  
Breeding Program ◽  
Tropical Maize ◽  
Maize Breeding ◽  
Breeding Programs ◽  
The Public ◽  
Maize Inbred Lines

Abstract Background The characterization of genetic diversity and population differentiation for maize inbred lines from breeding programs is of great value in assisting breeders in maintaining and potentially increasing the rate of genetic gain. In our study, we characterized a set of 187 tropical maize inbred lines from the public breeding program of the Universidade Federal de Viçosa (UFV) in Brazil based on 18 agronomic traits and 3,083 single nucleotide polymorphisms (SNP) markers to evaluate whether this set of inbred lines represents a panel of tropical maize inbred lines for association mapping analysis and investigate the population structure and patterns of relationships among the inbred lines from UFV for better exploitation in our maize breeding program. Results Our results showed that there was large phenotypic and genotypic variation in the set of tropical maize inbred lines from the UFV maize breeding program. We also found high genetic diversity (GD = 0.34) and low pairwise kinship coefficients among the maize inbred lines (only approximately 4.00 % of the pairwise relative kinship was above 0.50) in the set of inbred lines. The LD decay distance over all ten chromosomes in the entire set of maize lines with r2 = 0.1 was 276,237 kb. Concerning the population structure, our results from the model-based STRUCTURE and principal component analysis methods distinguished the inbred lines into three subpopulations, with high consistency maintained between both results. Additionally, the clustering analysis based on phenotypic and molecular data grouped the inbred lines into 14 and 22 genetic divergence clusters, respectively. Conclusions Our results indicate that the set of tropical maize inbred lines from UFV maize breeding programs can comprise a panel of tropical maize inbred lines suitable for a genome-wide association study to dissect the variation of complex quantitative traits in maize, mainly in tropical environments. In addition, our results will be very useful for assisting us in the assignment of heterotic groups and the selection of the best parental combinations for new breeding crosses, mapping populations, mapping synthetic populations, guiding crosses that target highly heterotic and yielding hybrids, and predicting untested hybrids in the public breeding program UFV.

scholarly journals Global range expansion history of pepper (Capsicum spp.) revealed by over 10,000 genebank accessions

2021 ◽  
Vol 118 (34) ◽  
pp. e2104315118
Author(s):  
Pasquale Tripodi ◽  
Mark Timothy Rabanus-Wallace ◽  
Lorenzo Barchi ◽  
Sandip Kale ◽  
Salvatore Esposito ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genotyping By Sequencing ◽  
Focal Region ◽  
Nucleotide Polymorphisms ◽  
Trade Routes ◽  
Genebank Management ◽  
Capsicum Spp ◽  
History Of ◽  
Cultural Commodity

Genebanks collect and preserve vast collections of plants and detailed passport information, with the aim of preserving genetic diversity for conservation and breeding. Genetic characterization of such collections has the potential to elucidate the genetic histories of important crops, use marker–trait associations to identify loci controlling traits of interest, search for loci undergoing selection, and contribute to genebank management by identifying taxonomic misassignments and duplicates. We conducted a genomic scan with genotyping by sequencing (GBS) derived single nucleotide polymorphisms (SNPs) of 10,038 pepper (Capsicum spp.) accessions from worldwide genebanks and investigated the recent history of this iconic staple. Genomic data detected up to 1,618 duplicate accessions within and between genebanks and showed that taxonomic ambiguity and misclassification often involve interspecific hybrids that are difficult to classify morphologically. We deeply interrogated the genetic diversity of the commonly consumed Capsicum annuum to investigate its history, finding that the kinds of peppers collected in broad regions across the globe overlap considerably. The method ReMIXTURE—using genetic data to quantify the similarity between the complement of peppers from a focal region and those from other regions—was developed to supplement traditional population genetic analyses. The results reflect a vision of pepper as a highly desirable and tradable cultural commodity, spreading rapidly throughout the globe along major maritime and terrestrial trade routes. Marker associations and possible selective sweeps affecting traits such as pungency were observed, and these traits were shown to be distributed nonuniformly across the globe, suggesting that human preferences exerted a primary influence over domesticated pepper genetic structure.

Prevalence and Molecular Characterization of Microbial Contaminants in Raw Cow Milk of Tangail District in Bangladesh

2021 ◽  
Vol 17 ◽  
Author(s):  
Shahin Mahmud ◽  
Md. Firoz Ali ◽  
Md. Omar Faruque ◽  
Muhammad Wasim ◽  
Fatematuz Zuhura Evamoni ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Raw Milk ◽  
Health Impact ◽  
Cow Milk ◽  
Milk Consumption ◽  
Salmonella Spp ◽  
Mean Values ◽  
The Mean ◽  
Quality Of Milk

Objectives: The aim of this study is to evaluate the microbial quality and associated health Methodology: An intensive study was carried out from January¬ to October 2019 at the Tangail district of Bangladesh to assess bacterial contamination of raw milk. A total of 60 samples were examined by following the standard bacteriological methods and the health impact was evaluated with the help of a semi-structured-based questionnaire. Molecular characterization of isolated bacteria was carried out by PCR. Results: Results revealed the mean values of TVC and TCC in raw milk, udder, oil, and utensil samples were 7.6×106, 8.8×106, 4.6×106, and 1.3×106 cfu/ml and 3.7×105, 1.4×106, 4.4×105, and 8.9×104 cfu/ml, respectively. The yeast and mold in raw milk, udder, and oil were 1.5×103, 1.8×103, and 1.3×102cfu/ml, respectively, and the mean values of E. coli in the above-mentioned samples were 1.9×103, 1.8×104, 2.1×103, and 1.6×103cfu/ml, respectively. On the other hand, the mean values of Salmonella spp. in raw milk, udder, oil, and utensil samples were 2.4×102, 7.9×102, 1.5×102, and 1.1×102cfu/ml, respectively. Some selected isolates confirmed by molecular identification were tested for their sensitivity against some common antibiotics used in Bangladesh. Escherichia coli showed 70% resistance to Amoxicillin and 90% sensitivity to Ciprofloxacin whereas Salmonella spp. And Staphylococcus aureus showed 90% resistance to Ampicillin and both were 80% and 90% sensitive to Ciprofloxacin, respectively. Conclusion, Significance, and Impact of Study: Milk producers should be appropriately trained to monitor the overall hygienic conditions surrounding the production and handling of milk until it reaches the consumer. Frequent monitoring of the milk production facility, occasional testing of raw milk, and minimal use of antibiotics will ensure the quality of milk. Consumption of quality milk and avoidance of raw milk consumption will reduce the health risk of the consumers.

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