Application of Cluster Analysis for Establishment of Genetic Similarity in Gene-For-Gene Host-Parasite Relationships

Allelic diversity is common at host loci involved in parasite recognition, such as the major histocompatibility complex in vertebrates or gene-for-gene relationships in plants, and in corresponding loci encoding antigenic molecules in parasites. Diverse factors have been proposed in models to account for genetic polymorphism in host–parasite recognition. Here, a simple but general theory of host–parasite coevolution is developed. Coevolution implies the existence of indirect frequency-dependent selection (FDS), because natural selection on the host depends on the frequency of a parasite gene, and vice versa . It is shown that polymorphism can be maintained in both organisms only if there is negative, direct FDS, such that the strength of natural selection for the host resistance allele, the parasite virulence allele or both declines with increasing frequency of that allele itself. This condition may be fulfilled if the parasite has more than one generation in the same host individual, a feature which is common to most diseases. It is argued that the general theory encompasses almost all factors previously proposed to account for polymorphism at corresponding host and parasite loci, including those controlling gene-for-gene interactions.

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The impact of environmental change on host–parasite coevolutionary dynamics

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2010.2359 ◽

2010 ◽

Vol 278 (1716) ◽

pp. 2283-2292 ◽

Cited By ~ 48

Author(s):

Rafal Mostowy ◽

Jan Engelstädter

Keyword(s):

Environmental Change ◽

Environmental Changes ◽

Selective Pressure ◽

Time Windows ◽

Gene Interactions ◽

Genotype By Environment ◽

Host Parasite ◽

The Impact ◽

Antagonistic Interactions ◽

Gene For Gene

Environmental factors are known to affect the strength and the specificity of interactions between hosts and parasites. However, how this shapes patterns of coevolutionary dynamics is not clear. Here, we construct a simple mathematical model to study the effect of environmental change on host–parasite coevolutionary outcome when interactions are of the matching-alleles or the gene-for-gene type. Environmental changes may effectively alter the selective pressure and the level of specialism in the population. Our results suggest that environmental change altering the specificity of selection in antagonistic interactions can produce alternating time windows of cyclical allele-frequency dynamics and cessation thereof. This type of environmental impact can also explain the maintenance of polymorphism in gene-for-gene interactions without costs. Overall, our study points to the potential consequences of environmental variation in coevolution, and thus the importance of characterizing genotype-by-genotype-by-environment interactions in natural host–parasite systems, especially those that change the direction of selection acting between the two species.

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Detection of Genetic Polymorphism in Seven Barley Hordeum vulgare L. Varieties Using SSR

Basrah Journal of Agricultural Sciences ◽

10.37077/25200860.2020.33.2.10 ◽

2020 ◽

Vol 33 (2) ◽

pp. 115-124

Author(s):

Maha R. Khalil ◽

Hussain A. Almahasneh ◽

Salam Y. Lawand

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Polymorphism ◽

Hordeum Vulgare ◽

Simple Sequence Repeats ◽

Genetic Similarity ◽

Hordeum Vulgare L ◽

Simple Sequence

Investigation was carried out at the laboratory of Biotechnology, Faculty of Agriculture, Damascus University, during the season 2017-2018. Seven varieties were planted to determine the degree of genetic similarity using SSR-technique (Simple Sequence Repeats), and 14 double primers were used for this purpose. The analysis results revealed that all primers showed polymorphism among the evaluated varieties, except Bmag0385. primers produced a total of 42 alleles with a polymorphic percentage of 88.27%. The number of alleles for each primer varied from 1 allele for the primer (Bmac0067) to 7 alleles for the primer (Bmag0006) in average of 3 alleles per primer. Cluster analysis and Dendrogram showed the highest degree of genetic similarity between variety Arabi asuad and variety Arabi abiad (0.7619). While it was low between variety Fourat4 and variety Arabi abiad (0.3571), and varieties Fourat4 and Fourat3 (0.3571) which indicated wide genetic diversity among them.

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Analysis of intra-population variability of bald cypress (Taxodium distichum L. Rich.) in seed stand near Backa Palanka using RAPD markers

Genetika ◽

10.2298/gensr1502571p ◽

2015 ◽

Vol 47 (2) ◽

pp. 571-580

Author(s):

Vladan Popovic ◽

Aleksandar Lucic ◽

Danijela Ristic ◽

Ljubinko Rakonjac ◽

Sabahudin Hadrovic ◽

...

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Dna Markers ◽

Genetic Similarity ◽

Rapd Markers ◽

Rapd Analysis ◽

Genetic Distances ◽

Similarity Coefficients ◽

Bald Cypress ◽

Seed Stand

The analysis of Bald cypress genetic variability at the level of test trees was performed using RAPD (Random Amlified Polymorphic DNA) markers. RAPD analysis was performed on 20 test trees with 13 primers. A total of ten primers gave a clear picture while three primers amplified weakly. 60 is a total number of detected bands obtained by RAPD analysis with 10 selected primers, and the average number of bands is 6. Based on presence/absence of RAPD fragments among all 20 Bald cypress test trees were calculated similarity coefficients by Dice and they range from 0.73 to 1. Based on similarity coefficients was performed the cluster analysis and results were presented as a dendrogram. All 20 test trees were grouped into two sub-clusters. Test trees 1, 4 and 11 were grouped in the first sub-cluster while other test trees were grouped in the second sub-cluster. By analysis of relations within every sub-cluster and sub-sub-cluster the existence of genetic distances between observed test trees can be noticed. The greatest similarity is between test trees 2, 12, 15 and 18. The results of genetic similarity and distance between observed test trees indicate the overwhelming presence of genetic diversity.

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Analisis Keragaman Genetik Acremonium yang Berasosiasi dengan Tanaman Gaharu Menggunakan Teknik Random Amplified Polymorphic DNA (RAPD)

Jurnal AgroBiogen ◽

10.21082/jbio.v5n2.2009.p65-70 ◽

2016 ◽

Vol 5 (2) ◽

pp. 65

Author(s):

Dewi Rahmawati ◽

Nurita Toruan-Mathius

Keyword(s):

Cluster Analysis ◽

Genetic Variation ◽

Genetic Similarity ◽

Random Amplified Polymorphic Dna ◽

Economic Value ◽

Similarity Index ◽

Similarity Coefficients ◽

West Sumatra ◽

High Degree ◽

Geographical Locations

Agarwood or gaharu is a plant that has a high economic value in Asia, due to its use for production of incense and traditional medicines. The agarwood formation occurs in the trunk and roots of trees that have been infected by a fungus, such as Acremonium spp. Various fungi were associated with the agarwood formation. Acremonium is generally considered as highly polyphyletic, contains distantly related fungi. A study was done to identify genetic diversities in 10 isolates of Acremonium spp. from four different areas in Indonesia that are associated with Aquilaria and Gyrinops verstigii using the Random Amplified Polymorphic DNA (RAPD) technique. Eight RAPD primers, i.e., OPA 02, OPB 04, OPB 07, OPB 17, OPC 11, OPD 03, OPD 05, and OPE 07 were used in the analyses. The results indicated that similarity index values of the genetic variation ranged from 0.21 to 0.97. Based on the Nei and Li’s similarity coefficients, these values indicating the presence of high degree of genetic variability. The lowest degree of genetic similarity were found between isolates F (Acremonium spp., which is associated with G. verstigii from Mataram, Nusa Tenggara Barat), and LM2 from south coastal area of West Sumatra. The highest genetic similarity value (0.97) was found between isolates Sr2 and Sr4 from Sorong, Papua. Results from the cluster analysis indicated that the isolates could be grouped into two major clusters that were associated with their geographical locations.

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Two Properties of a Gene-for-Gene Coevolution System under Human Perturbations

Phytopathology ◽

10.1094/phyto.1999.89.9.811 ◽

1999 ◽

Vol 89 (9) ◽

pp. 811-816 ◽

Cited By ~ 9

Author(s):

P. Sun ◽

X. B. Yang

Keyword(s):

Real World ◽

Host Population ◽

Resistant Genotype ◽

Human Perturbation ◽

Boom And Bust ◽

Human Perturbations ◽

Pathogen Populations ◽

Host Parasite ◽

Over Time ◽

Gene For Gene

Recently, the gene-for-gene host-parasite coevolution model of Leonard was extended by incorporating two kinds of perturbations. The first kind was the natural perturbations that include those caused by pathogen migration between the two subpopulations of the host, forward and backward mutations in the host or pathogen populations, and some others. The second kind was human perturbations, such as constantly increasing the percentage of the resistant genotype within the host population each season. In this study, we quantitatively compared the two kinds of perturbations and extended the constantly changing human perturbation to include non-constant perturbations that are more likely to occur in the real world. Two properties of the modified Leonard model were revealed from this study. First, when both human perturbations and natural perturbations are involved, the effects of natural perturbations are very small compared with those of human perturbations. This finding ensures that, in the study of human perturbations, we can simplify the study by ignoring the effects of natural perturbations. Second, through the simulation of nonconstant perturbations, which assumes that the proportion of the resistant genotype of the host population increases over time, we found that the model reproduces the “boom and bust” epidemic cycles that are often found in agroecosystems.

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Gene-for-gene relationships in the Avena: Puccinia graminis host–parasite system in Canada

Canadian Journal of Botany ◽

10.1139/b70-135 ◽

1970 ◽

Vol 48 (5) ◽

pp. 969-975 ◽

Cited By ~ 19

Author(s):

J. W. Martens ◽

R. I. H. McKenzie ◽

G. J. Green

Keyword(s):

North America ◽

Resistance Genes ◽

Stem Rust ◽

Host Population ◽

Puccinia Graminis ◽

Physiologic Race ◽

Host Genotype ◽

Physiologic Races ◽

Host Parasite ◽

Gene For Gene

The results of 48 years of oat stem rust physiologic race surveys are interpreted in terms of the prevailing host genotype. Changes in the frequencies of genes that govern virulence in the pathogen can be explained only in part by changes in the resistance genes carried by the host population. Genes for virulence on newly released types of resistance have spread very quickly through the rust population, after initial 'breakdown' of the resistance. The most successful physiologic races carry genes for virulence in excess of those required for successful parasitism in North America. Many races carry genes for virulence on types of resistance that have never been used on this continent.

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