Micro-epidemiological structuring of Plasmodium falciparum parasite populations in regions with varying transmission intensities in Africa.

Background: The first models of malaria transmission assumed a completely mixed and homogeneous population of parasites. Recent models include spatial heterogeneity and variably mixed populations. However, there are few empiric estimates of parasite mixing with which to parametize such models. Methods: Here we genotype 276 single nucleotide polymorphisms (SNPs) in 5199 P. falciparum isolates from two Kenyan sites (Kilifi county and Rachuonyo South district) and one Gambian site (Kombo coastal districts) to determine the spatio-temporal extent of parasite mixing, and use Principal Component Analysis (PCA) and linear regression to examine the relationship between genetic relatedness and distance in space and time for parasite pairs. Results: Using 107, 177 and 82 SNPs that were successfully genotyped in 133, 1602, and 1034 parasite isolates from The Gambia, Kilifi and Rachuonyo South district, respectively, we show that there are no discrete geographically restricted parasite sub-populations, but instead we see a diffuse spatio-temporal structure to parasite genotypes. Genetic relatedness of sample pairs is predicted by relatedness in space and time. Conclusions: Our findings suggest that targeted malaria control will benefit the surrounding community, but unfortunately also that emerging drug resistance will spread rapidly through the population.

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Genetic analysis reveals unique characteristics of Plasmodium falciparum parasite populations in Haiti

Malaria Journal ◽

10.1186/s12936-020-03439-7 ◽

2020 ◽

Vol 19 (1) ◽

Author(s):

Rachel F. Daniels ◽

Stella Chenet ◽

Eric Rogier ◽

Naomi Lucchi ◽

Camelia Herman ◽

...

Keyword(s):

Plasmodium Falciparum ◽

Genetic Relatedness ◽

Dried Blood Spots ◽

Caribbean Region ◽

Nucleotide Polymorphisms ◽

Single Genome ◽

Plasmodium Falciparum Parasite ◽

Genetic Signatures ◽

Parasite Populations

Abstract Background With increasing interest in eliminating malaria from the Caribbean region, Haiti is one of the two countries on the island of Hispaniola with continued malaria transmission. While the Haitian population remains at risk for malaria, there are a limited number of cases annually, making conventional epidemiological measures such as case incidence and prevalence of potentially limited value for fine-scale resolution of transmission patterns and trends. In this context, genetic signatures may be useful for the identification and characterization of the Plasmodium falciparum parasite population in order to identify foci of transmission, detect outbreaks, and track parasite movement to potentially inform malaria control and elimination strategies. Methods This study evaluated the genetic signals based on analysis of 21 single-nucleotide polymorphisms (SNPs) from 462 monogenomic (single-genome) P. falciparum DNA samples extracted from dried blood spots collected from malaria-positive patients reporting to health facilities in three southwestern Haitian departments (Nippes, Grand’Anse, and Sud) in 2016. Results Assessment of the parasite genetic relatedness revealed evidence of clonal expansion within Nippes and the exchange of parasite lineages between Nippes, Sud, and Grand'Anse. Furthermore, 437 of the 462 samples shared high levels of genetic similarity–at least 20 of 21 SNPS–with at least one other sample in the dataset. Conclusions These results revealed patterns of relatedness suggestive of the repeated recombination of a limited number of founding parasite types without significant outcrossing. These genetic signals offer clues to the underlying relatedness of parasite populations and may be useful for the identification of the foci of transmission and tracking of parasite movement in Haiti for malaria elimination.

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Genetic analysis reveals unique characteristics of Plasmodium falciparum parasite populations in Haiti

10.21203/rs.3.rs-37125/v2 ◽

2020 ◽

Author(s):

Rachel Daniels ◽

Stella Chenet ◽

Eric Rogier ◽

Naomi Lucchi ◽

Camelia Herman ◽

...

Keyword(s):

Plasmodium Falciparum ◽

Genetic Relatedness ◽

Dried Blood Spots ◽

Caribbean Region ◽

Nucleotide Polymorphisms ◽

Single Genome ◽

Plasmodium Falciparum Parasite ◽

Genetic Signatures ◽

Parasite Populations

Abstract Background: With increasing interest in eliminating malaria from the Caribbean region, Haiti is one of the two countries on the island of Hispaniola with continued malaria transmission. While the Haitian populace remains at risk for malaria, there are a limited number of cases annually, making conventional epidemiological measures such as case incidence and prevalence of potentially limited value for fine-scale resolution of transmission patterns and trends. In this context, genetic signatures may be useful for the identification and characterization of the Plasmodium falciparum parasite population in order to identify foci of transmission, detect outbreaks, and track parasite movement to potentially inform malaria control and elimination strategies. Methods: This study evaluated the genetic signals based on analysis of 21 single-nucleotide polymorphisms (SNPs) from 462 monogenomic (single-genome) P. falciparum DNA samples extracted from dried blood spots collected from malaria-positive patients reporting to health facilities in three southwestern Haitian departments (Nippes, Grand’Anse, and Sud) in 2016. Results: Assessment of the parasite genetic relatedness revealed evidence of clonal expansion within Nippes and the exchange of parasite lineages between Nippes, Sud, and Grand'Anse. Furthermore, 437 of the 462 samples shared high levels of genetic similarity—at least 20 of 21 SNPS—with at least one other sample in the dataset. Conclusions: These results revealed patterns of relatedness suggestive of the repeated recombination of a limited number of founding parasite types without significant outcrossing. These genetic signals offer clues to the underlying relatedness of parasite populations and may be useful for the identification of the foci of transmission and tracking of parasite movement in Haiti for malaria elimination.

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Genetic Analysis Reveals Unique Characteristics of Plasmodium Falciparum Parasite Populations in Haiti

10.21203/rs.3.rs-37125/v1 ◽

2020 ◽

Author(s):

Rachel Daniels ◽

Stella Chenet ◽

Eric Rogier ◽

Naomi Lucchi ◽

Camelia Herman ◽

...

Keyword(s):

Plasmodium Falciparum ◽

Genetic Relatedness ◽

Dried Blood Spots ◽

Caribbean Region ◽

Nucleotide Polymorphisms ◽

Single Genome ◽

Plasmodium Falciparum Parasite ◽

Genetic Signatures ◽

Parasite Populations

Abstract Background: With increasing interest in eliminating malaria from the Caribbean region, Haiti is one of the two countries on the island of Hispaniola with continued malaria transmission. While the Haitian populace remains at risk for malaria, there are a limited number of cases annually, making conventional epidemiological measures such as case incidence and prevalence of potentially limited value for fine-scale resolution of transmission patterns and trends. In this context, genetic signatures may be useful for the identification and characterization of the Plasmodium falciparum parasite population in order to identify foci of transmission, detect outbreaks, and track parasite movement to potentially inform malaria control and elimination strategies. Methods: This study evaluated the genetic signals based on analysis of 21 single-nucleotide polymorphisms (SNPs) from 462 monogenomic (single-genome) P. falciparum DNA samples extracted from dried blood spots collected from malaria-positive patients reporting to health facilities in three southwestern Haitian departments (Nippes, Grand’Anse, and Sud) in 2016. Results: Assessment of the parasite genetic relatedness revealed evidence of clonal expansion within Nippes and the exchange of parasite lineages between Nippes, Sud, and Grand'Anse. Furthermore, 437 of the 462 samples shared high levels of genetic similarity—at least 20 of 21 SNPS—with at least one other sample in the dataset. Conclusions: These results revealed patterns of relatedness suggestive of the repeated recombination of a limited number of founding parasite types without significant outcrossing. These genetic signals offer clues to the underlying relatedness of parasite populations and may be useful for the identification of the foci of transmission and tracking of parasite movement in Haiti for malaria elimination.

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Genetic analysis reveals unique characteristics of Plasmodium falciparum parasite populations in Haiti

10.21203/rs.3.rs-37125/v3 ◽

2020 ◽

Author(s):

Rachel Daniels ◽

Stella Chenet ◽

Eric Rogier ◽

Naomi Lucchi ◽

Camelia Herman ◽

...

Keyword(s):

Plasmodium Falciparum ◽

Genetic Relatedness ◽

Dried Blood Spots ◽

Caribbean Region ◽

Nucleotide Polymorphisms ◽

Single Genome ◽

Plasmodium Falciparum Parasite ◽

Genetic Signatures ◽

Parasite Populations

Abstract Background With increasing interest in eliminating malaria from the Caribbean region, Haiti is one of the two countries on the island of Hispaniola with continued malaria transmission. While the Haitian population remains at risk for malaria, there are a limited number of cases annually, making conventional epidemiological measures such as case incidence and prevalence of potentially limited value for fine-scale resolution of transmission patterns and trends. In this context, genetic signatures may be useful for the identification and characterization of the Plasmodium falciparum parasite population in order to identify foci of transmission, detect outbreaks, and track parasite movement to potentially inform malaria control and elimination strategies. Methods This study evaluated the genetic signals based on analysis of 21 single-nucleotide polymorphisms (SNPs) from 462 monogenomic (single-genome) P. falciparum DNA samples extracted from dried blood spots collected from malaria-positive patients reporting to health facilities in three southwestern Haitian departments (Nippes, Grand’Anse, and Sud) in 2016. Results Assessment of the parasite genetic relatedness revealed evidence of clonal expansion within Nippes and the exchange of parasite lineages between Nippes, Sud, and Grand'Anse. Furthermore, 437 of the 462 samples shared high levels of genetic similarity–at least 20 of 21 SNPS–with at least one other sample in the dataset. Conclusions These results revealed patterns of relatedness suggestive of the repeated recombination of a limited number of founding parasite types without significant outcrossing. These genetic signals offer clues to the underlying relatedness of parasite populations and may be useful for the identification of the foci of transmission and tracking of parasite movement in Haiti for malaria elimination.

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Spatio-Temporal Dynamic of Malaria Incidence: A Comparison of Two Ecological Zones in Mali

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph17134698 ◽

2020 ◽

Vol 17 (13) ◽

pp. 4698 ◽

Cited By ~ 1

Author(s):

François Freddy Ateba ◽

Issaka Sagara ◽

Nafomon Sogoba ◽

Mahamoudou Touré ◽

Drissa Konaté ◽

...

Keyword(s):

Malaria Transmission ◽

Malaria Incidence ◽

Additive Model ◽

Principal Component ◽

Environmental Data ◽

Ecological Zones ◽

Time Period ◽

Passive Case Detection ◽

Spatio Temporal ◽

The Relationship

Malaria transmission largely depends on environmental, climatic, and hydrological conditions. In Mali, malaria epidemiological patterns are nested within three ecological zones. This study aimed at assessing the relationship between those conditions and the incidence of malaria in Dangassa and Koila, Mali. Malaria data was collected through passive case detection at community health facilities of each study site from June 2015 to January 2017. Climate and environmental data were obtained over the same time period from the Goddard Earth Sciences (Giovanni) platform and hydrological data from Mali hydraulic services. A generalized additive model was used to determine the lagged time between each principal component analysis derived component and the incidence of malaria cases, and also used to analyze the relationship between malaria and the lagged components in a multivariate approach. Malaria transmission patterns were bimodal at both sites, but peak and lull periods were longer lasting for Koila study site. Temperatures were associated with malaria incidence in both sites. In Dangassa, the wind speed (p = 0.005) and river heights (p = 0.010) contributed to increasing malaria incidence, in contrast to Koila, where it was humidity (p < 0.001) and vegetation (p = 0.004). The relationships between environmental factors and malaria incidence differed between the two settings, implying different malaria dynamics and adjustments in the conception and plan of interventions.

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Admixture Analysis Using Genotyping-by-Sequencing Reveals Genetic Relatedness and Parental Lineage Distribution in Highbush Blueberry Genotypes and Cross Derivatives

10.20944/preprints202011.0577.v1 ◽

2020 ◽

Author(s):

Krishnanand P. Kulkarni ◽

Nicholi Vorsa ◽

Purushothaman Natarajan ◽

Sathya Elavarthi ◽

Massimo Iorizzo ◽

...

Keyword(s):

Genetic Relatedness ◽

Principal Component ◽

Genotyping By Sequencing ◽

Vaccinium Corymbosum ◽

Snp Markers ◽

Fixation Index ◽

Nucleotide Polymorphisms ◽

Admixture Analysis ◽

Cross Derivatives ◽

Southern Highbush

Blueberries (Vaccinium section Cyanococcus) are perennial shrubs widely cultivated for their edible fruits. In this study, we used admixture and genetic relatedness analysis of northern highbush (NHB, V. corymbosum) and southern highbush (SHB, V. darrowii) blueberry genotypes and F2 progenies of the V. corymbosum × V. darrowii cross. Using genotyping-by-sequencing (GBS), we generated ~3.34 billion reads (75 bp). The GBS reads were aligned to the Vaccinium corymbosum cv. Draper v1.0 reference genome sequence, and ~2.8 million reads were successfully mapped. From the alignments, we identified 2,244,039 single nucleotide polymorphisms (SNPs), which were used for principal component, haplotype, and admixture analysis. PCA formed three main groups: 1) NHB cultivars, 2) SHB cultivars, and 3) BNJ16-5 progenies. The overall fixation index (FST) and nucleotide diversity for NHB and SHB, indicated wide genetic differentiation, and haplotype analysis revealed that SHB cultivars are more genetically diverse than NHB cultivars. The admixture analysis identified a mix of various lineages of parental genomic introgression. This study demonstrated the effectiveness of GBS-derived SNP markers in genetic and admixture analyses to reveal genetic relatedness and to examine parental lineages in blueberry, which may be useful for future breeding plans.

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Target sequencing reveals genetic diversity, population structure, core-SNP markers, and fruit shape-associated loci in pepper varieties

BMC Plant Biology ◽

10.1186/s12870-019-2122-2 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 2

Author(s):

Heshan Du ◽

Jingjing Yang ◽

Bin Chen ◽

Xiaofen Zhang ◽

Jian Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Relatedness ◽

Principal Component ◽

Shape Index ◽

Fruit Shape ◽

Snp Markers ◽

Variety Identification ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Multiplex Amplification

Abstract Background The widely cultivated pepper (Capsicum spp.) is one of the most diverse vegetables; however, little research has focused on characterizing the genetic diversity and relatedness of commercial varieties grown in China. In this study, a panel of 92 perfect single-nucleotide polymorphisms (SNPs) was identified using re-sequencing data from 35 different C. annuum lines. Based on this panel, a Target SNP-seq genotyping method was designed, which combined multiplex amplification of perfect SNPs with Illumina sequencing, to detect polymorphisms across 271 commercial pepper varieties. Results The perfect SNPs panel had a high discriminating capacity due to the average value of polymorphism information content, observed heterozygosity, expected heterozygosity, and minor allele frequency, which were 0.31, 0.28, 0.4, and 0.31, respectively. Notably, the studied pepper varieties were morphologically categorized based on fruit shape as blocky-, long horn-, short horn-, and linear-fruited. The long horn-fruited population exhibited the most genetic diversity followed by the short horn-, linear-, and blocky-fruited populations. A set of 35 core SNPs were then used as kompetitive allele-specific PCR (KASPar) markers, another robust genotyping technique for variety identification. Analysis of genetic relatedness using principal component analysis and phylogenetic tree construction indicated that the four fruit shape populations clustered separately with limited overlaps. Based on STRUCTURE clustering, it was possible to divide the varieties into five subpopulations, which correlated with fruit shape. Further, the subpopulations were statistically different according to a randomization test and Fst statistics. Nine loci, located on chromosomes 1, 2, 3, 4, 6, and 12, were identified to be significantly associated with the fruit shape index (p < 0.0001). Conclusions Target SNP-seq developed in this study appears as an efficient power tool to detect the genetic diversity, population relatedness and molecular breeding in pepper. Moreover, this study demonstrates that the genetic structure of Chinese pepper varieties is significantly influenced by breeding programs focused on fruit shape.

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Genotyping pepper varieties using Target SNP-seq reveals that population structure clusters according to fruit shape

10.21203/rs.2.10821/v1 ◽

2019 ◽

Author(s):

Heshan Du ◽

Jingjing Yang ◽

Bin Chen ◽

Xiaofen Zhang ◽

Jian Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Relatedness ◽

Principal Component ◽

Randomization Test ◽

Fruit Shape ◽

Variety Identification ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Chromosome 11 ◽

Multiplex Amplification

Abstract Background The widely cultivated pepper (Capsicum spp.) is one of the most diverse vegetables; however, little research has characterized the genetic diversity and relatedness of commercial varieties grown in China. In this study, a panel of single-nucleotide polymorphisms (SNPs) was created that consisted of 97 perfect SNPs, which were identified using re-sequencing data from 35 diverse C. annuum lines. Based on this panel, a Target SNP-seq was designed that combined the multiplex amplification of the perfect SNPs with Illumina sequencing to detect polymorphisms across 271 commercial pepper varieties. Results The perfect SNPs panel had a high discriminating capacity due to the average value of polymorphism information content (PIC), observed heterozygosity (Ho), expected heterozygosity (He), and minor allele frequency (MAF), which were 0.31, 0.28, 0.4, and 0.31, respectively. Notably, the studied pepper varieties were morphologically categorized based on fruit shape; blocky, long horn, short horn, and linear-fruited. The long horn-fruited population exhibited the most genetic diversity followed by the short horn, linear, and blocky-fruited populations. A set of 35 core SNPs were then used as KASPar markers, another robust genotyping technique for variety identification. Analysis of genetic relatedness using principal component analysis (PCA) and phylogenetic tree construction indicated that the four fruit shape populations clustered separately with limited overlaps. Based on STRUCTURE clustering, it was possible to divide the varieties into five subpopulations, which correlated with fruit shape. Further, the subpopulations were statistically different according to a randomization test and Fst statistics. Notably, two SNP loci, CaSNP118 and CaSNP053, which are located on chromosome 11 and 6 were significantly associated with fruit shape (p < 1.0 × 10 -4) Conclusions Target SNP-seq developed in this study appears as an efficient power tool to detect the genetic diversity, population relatedness and molecular breeding in pepper. Moreover, this study demonstrates that the genetic structure of the pepper varieties is significantly influenced by breeding programs focused on fruit shape.

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Admixture Analysis Using Genotyping-by-Sequencing Reveals Genetic Relatedness and Parental Lineage Distribution in Highbush Blueberry Genotypes and Cross Derivatives

International Journal of Molecular Sciences ◽

10.3390/ijms22010163 ◽

2020 ◽

Vol 22 (1) ◽

pp. 163

Author(s):

Krishnanand P. Kulkarni ◽

Nicholi Vorsa ◽

Purushothaman Natarajan ◽

Sathya Elavarthi ◽

Massimo Iorizzo ◽

...

Keyword(s):

Genetic Relatedness ◽

Principal Component ◽

Genotyping By Sequencing ◽

Fixation Index ◽

Nucleotide Polymorphisms ◽

Admixture Analysis ◽

Single Nucleotide ◽

Cross Derivatives ◽

Southern Highbush ◽

Genomic Introgression

Blueberries (Vaccinium section Cyanococcus) are perennial shrubs widely cultivated for their edible fruits. In this study, we performed admixture and genetic relatedness analysis of northern highbush (NHB, primarily V. corymbosum) and southern highbush (SHB, V. corymbosum introgressed with V. darrowii, V. virgatum, or V. tenellum) blueberry genotypes, and progenies of the BNJ16-5 cross (V. corymbosum × V. darrowii). Using genotyping-by-sequencing (GBS), we generated more than 334 million reads (75 bp). The GBS reads were aligned to the V. corymbosum cv. Draper v1.0 reference genome sequence, and ~2.8 million reads were successfully mapped. From the alignments, we identified 2,244,039 single-nucleotide polymorphisms, which were used for principal component, haplotype, and admixture analysis. Principal component analysis revealed three main groups: (1) NHB cultivars, (2) SHB cultivars, and (3) BNJ16-5 progenies. The overall fixation index (FST) and nucleotide diversity for NHB and SHB cultivars indicated wide genetic differentiation, and haplotype analysis revealed that SHB cultivars are more genetically diverse than NHB cultivars. The admixture analysis identified a mixture of various lineages of parental genomic introgression. This study demonstrated the effectiveness of GBS-derived single-nucleotide polymorphism markers in genetic and admixture analyses to reveal genetic relatedness and to examine parental lineages in blueberry, which may be useful for future breeding plans.

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