Population structure of Moniliophthora perniciosa in the main cacao producing departments of Colombia

Plant Disease ◽  
2021 ◽  
Author(s):  
Yeirme Jaimes ◽  
Carolina Gonzalez ◽  
Jairo Rojas ◽  
Jessica Johana Rivera ◽  
Christian Cilas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Geographic Origin ◽  
Genetic Change ◽  
Linkage Disequilibrium Analysis ◽  
Host Genotype ◽  
Dispersal Patterns ◽  
Moniliophthora Perniciosa ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance

The witches’ broom (Moniliophthora perniciosa) is considered as one of the main threats for cacao production and, consequently, for chocolate production worldwide.. In this work, the genetic diversity and population structure of M. perniciosa were analyzed for 59 isolates collected in five departments of Colombia and using 10 microsatellite markers. Analyses revealed 35 multilocus genotypes (MLGs) and clonal populations structure according to linkage disequilibrium analysis. One of the objectives of this study was to determine whether populations were differentiated by geographic origin or T. cacao host genotype. Analysis of molecular variance, Discriminant Analysis of Principal Components (DAPC) and Bruvo genetic distance suggested that the genetic structure was driven by geographic origin and not by T. cacao genotype. The results of this study were consistent with previous findings obtained in other cocoa producing countries. Important insights were discussed regarding the dispersal patterns of the pathogen in Colombia and the genetic change of its populations due to different environmental conditions.

Genetic variation of populations of Pinus oocarpa revealed by resistance gene analog polymorphism (RGAP)

Genome ◽  
2003 ◽  
Vol 46 (3) ◽  
pp. 404-410 ◽  
Author(s):  
V Díaz ◽  
E Ferrer
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Molecular Markers ◽  
Resistance Gene ◽  
Population Diversity ◽  
Resistance Gene Analog ◽  
Resistance Gene Analogs ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Pinus Oocarpa

Primers based on conserved motifs of plant resistance genes were used to generate multilocus molecular markers — referred to as resistance gene analog polymorphisms (RGAPs) — in Pinus oocarpa subsp. oocarpa. Ten populations from three regions of Nicaragua were analyzed with 53 RGAPs. The aim of this study was to determine the levels of within- and between-population diversity with this kind of marker, and to compare estimates with previously obtained results based on RAPD and AFLP. All populations showed high levels of diversity. GST values and the analysis of molecular variance (AMOVA) revealed most variation to be within populations, although significant differences between populations and regions were also detected. This pattern of genetic diversity was similar to that obtained for RAPD and AFLP, which suggests that variation at RGAP loci as detected in this work is mostly influence by non-selective forces.Key words: resistance gene analogs, molecular markers, genetic diversity, population structure, Pinus oocarpa.

scholarly journals Genetic diversity of the Northern Morocco goat population assessed with microsatellite markers

2017 ◽  
Vol 15 (3) ◽  
pp. e0404 ◽  
Author(s):  
Najat El Moutchou ◽  
Ana M. González-Martínez ◽  
Mouad Chentouf ◽  
Khalid Lairini ◽  
Evangelina Rodero
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Equilibrium Analysis ◽  
Factorial Correspondence Analysis ◽  
High Genetic Diversity ◽  
Analysis Of Molecular Variance ◽  
Closed Population ◽  
Molecular Variance ◽  
Goat Population ◽  
Hardy Weinberg Equilibrium

The main goal of this work was to study the genetic diversity of the Northern Morocco goat population through the analysis of 19 microsatellites in 144 animals from 61 herds. To detect a possible population structure, three distinct geographic subpopulations were characterized as a function of climate and environmental influences. Most of the markers were highly polymorphic, and the results revealed considerable genetic variation across the studied loci. A total of 204 alleles were detected, with an average number of 10.7 per locus. The PIC average was 0.728, and four microsatellites showed a significant deviation (p< 0.05) from Hardy-Weinberg Equilibrium. Analysis of molecular variance (AMOVA) indicated that only 0.5% of the variation corresponded to differences among subpopulations, and 99.5% corresponded to differences among individuals. Factorial correspondence analysis showed intense admixtures across the putative subpopulations, and the subdivision related to geographical or environmental adaptation was undetectable. The Northern Morocco goat population presented high genetic diversity and a lack of population structure. The main reason for these findings is the absence of the breed concept (reproductively closed population), resulting in uncontrolled crossbreeding with exotic breeds and other local goats.

scholarly journals Determining Whether Geographic Origin and Potato Genotypes Shape the Population Structure of Phytophthora infestans in the Central Region of Colombia

2019 ◽  
Vol 109 (1) ◽  
pp. 145-154
Author(s):  
Sandra Catalina Chaves ◽  
María Camila Rodríguez ◽  
María Fernanda Mideros ◽  
Florencia Lucca ◽  
Carlos E. Ñústez ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Phytophthora Infestans ◽  
Central Region ◽  
Geographic Origin ◽  
Geographic Area ◽  
Potato Cultivars ◽  
Clonal Lineage ◽  
Host Genotype ◽  
Genetic Population

Pathogen variation plays an important role in the dynamics of infectious diseases. In this study, the genetic variation of 279 Phytophthora infestans isolates was assessed using a combination of 12 microsatellite simple-sequence repeat markers. Isolates were collected from 11 different potato cultivars in 11 different geographic localities of the central region of Colombia. The objective of this study was to determine whether populations were differentiated by host genotype or geographic origin. Within a single clonal lineage, EC-1, 76 genotypes were detected. An analysis of molecular variance attributed most of the variation to differences within host genotypes rather than among the host genotypes, suggesting that host cultivars do not structure the populations of the pathogen. Furthermore, the lack of a genetic population structure according to the host cultivar was confirmed by all of the analyses, including the Bayesian clustering analysis and the minimum spanning network that used the Bruvo genetic distance, which suggested that there are no significant barriers to gene flow for P. infestans among potato cultivars. According to the geographic origin, the populations of P. infestans were also not structured, and most of the variation among the isolates was attributed to differences within localities. Only some but not all localities in the north and west of the central region of Colombia showed some genetic differentiation from the other regions. The absence of sexual reproduction of this pathogen in Colombia was also demonstrated. Important insights are discussed regarding the genetic population dynamics of the P. infestans populations of the central region of Colombia that were provided by the results. In Colombia, there is a high genetic variation within the EC-1 clonal lineage with closely related genotypes, none dominant, that coexist in a wide geographic area and on several potato cultivars.

Analysis of molecular variance and population structure in southern Indian finger millet genotypes using three different molecular markers

2016 ◽  
Vol 19 (4) ◽  
pp. 275-283 ◽  
Author(s):  
Host Antony David Rajendran ◽  
Ramakrishnan Muthusamy ◽  
Antony Caesar Stanislaus ◽  
Thirugnanasambantham Krishnaraj ◽  
Sivasankaran Kuppusamy ◽  
...  
Keyword(s):  
Population Structure ◽  
Molecular Markers ◽  
Finger Millet ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance

scholarly journals Genetic diversity in natural populations of Buriti (Mauritia flexuosa L. f.)

2011 ◽  
Vol 11 (3) ◽  
pp. 216-223 ◽  
Author(s):  
Liene Rocha Picanço Gomes ◽  
Maria Teresa Gomes Lopes ◽  
Jania Lilia da Silva Bentes ◽  
Willian Silva Barros ◽  
Pedro de Queiroz Costa Neto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Length Polymorphism ◽  
Fragment Length Polymorphism ◽  
Natural Populations ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Polymorphic Loci ◽  
Mauritia Flexuosa ◽  
Geographical Distances ◽  
Traditional Communities

This study aimed to characterize the genetic diversity of buriti populations by AFLP (Amplified Fragment Length Polymorphism) markers. The analysis was performed in four populations used by traditional communities in the state of Amazonia (Bom Jesus do Anamã, Lauro Sodré, Santa Luzia do Buiçuzinho, and Esperança II). From each population 30 plants were randomly selected. To obtain the markers four primer combinations were used. The percentage of polymorphic loci was estimated, the molecular variance among and within populations analyzed and a dendrogram constructed. The primers detected 339 polymorphic loci ranging from 81.1 % to 91.1 % among populations. Analysis of molecular variance attributed 77.18 % to variation within and 22.8 % to variation between populations. The dendrogram indicated the formation of two groups, showing that the populations of Bom Jesus do Anamã and Lauro Sodré are genetically most similar and thet the genetic and geographical distances are not correlated.

scholarly journals GENETIC DIVERSITY AMONG NATURAL POPULATIONS OF Keteleeria evelyniana Mast. IN CENTRAL HIGLANDS OF VIETNAM USING SSR MARKERS

2018 ◽  
Vol 56 (3) ◽  
pp. 275
Author(s):  
Tran Thi Lieu ◽  
Dinh Thi Phong ◽  
Vu Thi Thu Hien
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Similarity ◽  
Natural Populations ◽  
Similarity Coefficient ◽  
Similarity Matrix ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Private Alleles ◽  
Softwood Species

Keteleeria evelyniana Mast. is a big softwood species with high economic values. Therefore, the number of these trees are rapidly decreasing due to rampant exploitation as well as its habitat loss and recently, the species is considered vulnerablein Vietnam. In this study, we assessed the genetic variation among seventy K. evelyniana samples of three natural populations in Lam Dong, Dak Lak and Kon Tum using 16 microsatellite markers. The results showed that thirteen markers were polymorphic. A total 39 DNA fragments were amplified, among them, thirty – five were polymorphic (accounting for 89.74%). Among studied populations, the level of genetic diversity at Lam Dong (Na = 2.063; Ne = 1.730; Ap = 0.375; I = 0.558; Ho = 0.459 and He = 0.367) was the highest. Analysis of molecular variance (AMOVA) showed that the total level of molecular changes between populations was 34.65% and between individuals in the same population was 65.35%. Private alleles (Ap) and inbreeding values (Fis) of K. evelyniana species were founded of all three populations in Lam Dong, Dak Lak and Kon Tum (0.375 and -0.234; 0.188 and -0.065; 0.063 and -0.047, respectively). The gene flow (Nm) also occurred among the K. evelyniana populations with the average of Nm = 5.423. A dendrogram (UPGMA) constructed based on the similarity matrix of 70 K. evelyniana samples divided into two main groups with their genetic similarity coefficient ranged from 76.5% (Ke26 and Ke44) to 99% (Ke23 and Ke25). The obtained results indicated the importance of conserving the genetic resources of K. evelyniana species in Tay Nguyen.

scholarly journals Genetic Diversity and Population Structure in a Regional Collection of Kersting’s Groundnut (Macrotyloma geocarpum (Harms) Maréchal & Baudet)

2020 ◽  
Author(s):  
Konoutan M. Kafoutchoni ◽  
Eric E. Agoyi ◽  
Symphorien Agbahoungba ◽  
Achille E. Assogbadjo ◽  
Clément Agbangla
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Scientific Community ◽  
Gene Diversity ◽  
Breeding Strategies ◽  
Analysis Of Molecular Variance ◽  
Macrotyloma Geocarpum ◽  
Very High ◽  
Kersting’S Groundnut ◽  
Private Alleles

Kersting&rsquo;s groundnut is an important source of protein and essential nutrients that contribute to food security in West Africa. However, the crop is still underexploited by the populations and under-researched by the scientific community. This study aimed to investigate the genetic diversity and population structure of 217 Kersting&rsquo;s groundnut accessions from five origins using 886 DArTseq markers. Gene diversity was low and ranged from 0.049 to 0.064. The number of private alleles greatly varied among populations (42&ndash;192) and morphotypes (40&ndash;339). Moderate to very high levels of selfing and inbreeding were observed among populations (s=56&ndash;85%, FIS=0.389&ndash;0.736) and morphotypes (s=57&ndash;82%, FIS=0.400&ndash;0.691). Moreover, little to very high genetic differentiations were observed among populations (0.006&le;FIS&le;0.371) and morphotypes (0.029&le;FIS&le;0.307). Analysis of molecular variance partitioned 38.5% of the genetic variation among and 48.7% within populations (P&lt;0.001). Significant isolations by distance were detected between populations (R2=0.612, P=0.011) and accessions (R2=0.499, P&lt;0.001). Discriminant analysis of principal components and neighbour joining consistently distinguished eight distinct clusters. These data provide a global picture of the existing genetic diversity for Kersting&rsquo;s groundnut and will guide the choice of breeding strategies to increase production.

scholarly journals Genomic Analysis of Spanish Wheat Landraces Reveals Their Huge Potential for Breeding

2019 ◽  
Author(s):  
Laura Pascual ◽  
Magdalena Ruiz ◽  
Matilde López-Fernández ◽  
Helena Pérez-Peña ◽  
Elena Benavente ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Durum Wheat ◽  
Bread Wheat ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Geographic Origin ◽  
Local Conditions ◽  
Reference Set ◽  
Wheat Landraces

Abstract Background One of the main goals for the XXI century breeding is the development of crop cultivars that can maintain current yields under unfavorable environments. Landraces that have been grown under varied local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research (CRF-INIA) holds a wide collection of wheat landraces. These accessions, locally adapted to a really wide diversity of eco-climatic conditions, represent a highly valuable material for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping. Results DArTseq GBS approach generated 10K SNPs and 40K DArT high-quality markers that were mapped against the currently available bread wheat reference genome. The markers with known location were distributed in all the chromosomes, having a relatively well-balanced genome-wide coverage. The genetic analysis showed that Spanish wheat landraces are clustered in different groups, thus representing genetic pools capable to provide different allelic variation. The subspecies had a major impact on the population structure of durum wheat landraces, identifying three different clusters that corresponded to subsps. durum, turgidum and dicoccon. The population structure of bread wheat landraces was more biased by geographic origin. Conclusions The results showed a wider genetic diversity in landraces when compared to a reference set that included commercial varieties, and a higher divergence between landraces and the reference set in durum wheat than in bread wheat. Some genomic regions with patterns of variation that differ between landraces and reference varieties could be detected, pointing out loci under selection during crop improvement that could help to target breeding efforts. The results obtained from this work will be highly valuable for future GWAS analysis.

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