Genetic Analysis of Isolates of Botrytis cinerea Sensitive and Resistant to Benzimidazole and Dicarboximide Fungicides

A total of 56 isolates of B. cinerea collected from ornamental crops from commercial greenhouses were examined by random amplified polymorphic DNA (RAPD) fingerprint analyses. Isolates were examined as two independent sets of 35 and 36 isolates, with 15 isolates common to both sets. The isolates had four phenotypes: 17 were sensitive to two commonly used fungicides, thiophanate-methyl (a benzimidazole) and vinclozolin (a dicarboximide) (STSV); 18 were resistant to both fungicides (RTRV); 16 were resistant to thiophanate-methyl but sensitive to vinclozolin (RTSV); and 5 were sensitive to thiophanate-methyl but resistant to vinclozolin (STRV). Relationships among the isolates were determined by cluster analyses of mean character differences using the unweighted pair group method using arithmetic average and cladograms were constructed. Isolates were clustered primarily by fungicide-sensitivity phenotype. In one set of greenhouse isolates, 6 of 10 STSV isolates clustered together with a bootstrap confidence value of 91%. In the other fingerprint set of greenhouse isolates, 9 of 11 STSV isolates clustered together and had a bootstrap confidence value of 98%. Isolates resistant to thiophanate-methyl, vinclozolin, or both fungicides usually were not clustered with other isolates or were clustered with isolates of the same phenotype. To further elucidate these relationships, variant isolates resistant to one or both fungicides were produced on fungicide-amended agar medium from 14 STSV greenhouse isolates. These 14 STSV parent isolates, 57 resistant variant isolates, and 11 resistant greenhouse isolates were analyzed as three independent RAPD fingerprint sets. Variants selected from eight STSV parent isolates were resistant to both thiophanate-methyl and vinclozolin even though parent isolates were exposed to only one of the fungicides. Isolates resistant only to vinclozolin (STRV) had fingerprint patterns similar to and clustered with those of parent isolates, while fingerprint patterns of isolates resistant to thiophanate-methyl (i.e., RTRV or RTSV), regardless of sensitivity to vinclozolin, clustered differently from both those of STSV parent isolates and those of STRV isolates derived from the same parent. RTRV and RTSV variant isolates derived from the same fungicide-sensitive parents only clustered with other variants having the same phenotype.

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RAPD analysis of cultivated and wild yellow nutsedge (Cyperus esculentusL.)

Weed Science ◽

10.1017/s0043174500089487 ◽

1998 ◽

Vol 46 (3) ◽

pp. 318-321 ◽

Cited By ~ 8

Author(s):

Paloma Abad ◽

Bernardo Pascual ◽

José V. Maroto ◽

Salvador López-Galarza ◽

María J. Vicente ◽

...

Keyword(s):

Rapd Markers ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Group Method ◽

Wild Populations ◽

Arithmetic Average ◽

Yellow Nutsedge ◽

Pair Group ◽

High Level ◽

Unweighted Pair Group Method

Cultivated and weedy clones of yellow nutsedge were analyzed using random amplified polymorphic DNA (RAPD) markers to assess the polymorphism within the species and determine if this approach was suitable for identification of cultivar and wild populations. The RAPD markers unambiguously identified all studied clones. Nei-Li similarities were computed and used in an unweighted pair group method using arithmetic average (UPGMA) cluster analyses. Cultivated and weedy clones were clustered in two groups, but two cultivated clones were more closely related to weedy clones than to cultivated clones. The results showed a high level of genetic variability among the clones tested, particularly among the cultivated ones. Identification of yellow nutsedge cultivars and analysis of genetic diversity within and among weedy populations is possible by using only a small number of primers. In this study, seven selected primers discriminated among the 10 tested clones.

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Description and analysis of genetic diversity among squash accessions

Brazilian Archives of Biology and Technology ◽

10.1590/s1516-89132009000200003 ◽

2009 ◽

Vol 52 (2) ◽

pp. 271-283 ◽

Cited By ~ 9

Author(s):

Athanasios L. Tsivelikas ◽

Olga Koutita ◽

Anastasia Anastasiadou ◽

George N. Skaracis ◽

Ekaterini Traka-Mavrona ◽

...

Keyword(s):

Genetic Diversity ◽

Rapd Markers ◽

Clustering Algorithm ◽

Random Amplified Polymorphic Dna ◽

Principal Component ◽

Molecular Data ◽

Optimal Number ◽

Group Method ◽

Arithmetic Average ◽

Pair Group

In this work, the part of the squash core collection, maintained in the Greek Gene Bank, was assessed using the morphological and molecular data. Sixteen incompletely classified accessions of the squash were characterized along with an evaluation of their resistance against two isolates of Fusarium oxysporum. A molecular analysis using Random Amplified Polymorphic DNA (RAPD) markers was also performed, revealing high level of polymorphism. To study the genetic diversity among the squash accessions, a clustering procedure using Unweighed Pair Group Method and Arithmetic Average (UPGMA) algorithm was also adopted. Two independent dendrograms, one for the morphophysiological and one for molecular data were obtained, classifying the accessions into two and three main clusters, respectively. Despite the different number of the clusters there were many similarities between these two dendrograms, and a third dendrogram resulting from their combination was also produced, based on Gower's distance and UPGMA clustering algorithm. In order to determine the optimal number of clusters, the upper tail approach was applied. The more reliable clustering of the accessions was accomplished using RAPD markers as well as the combination of the two different data sets, classifying the accessions into three significantly different groups. These groups corresponded to the three different cultivated species of C. maxima Duch., C. moschata Duch., and C. pepo L. The same results were also obtained using Principal Component Analysis.

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Diversidade genética entre três linhagens de codorna selecionadas para produção de ovos

Arquivo Brasileiro de Medicina Veterinária e Zootecnia ◽

10.1590/s0102-09352010000300030 ◽

2010 ◽

Vol 62 (3) ◽

pp. 725-731 ◽

Cited By ~ 2

Author(s):

R.A. Prioli ◽

E. Gasparino ◽

M.A.M. Soares ◽

D.S. Marques ◽

D.V. Blanck ◽

...

Keyword(s):

Random Amplified Polymorphic Dna ◽

Coturnix Japonica ◽

Group Method ◽

Arithmetic Average ◽

Pair Group ◽

Unweighted Pair Group Method

A diversidade genética entre três linhagens de codorna (Coturnix japônica) foi avaliada utilizando-se a técnica de random amplified polymorphic DNA (RAPD). As linhagens selecionadas para produção de ovos foram identificadas como amarela, azul e vermelha por meio de anilhas no pé esquerdo. Seis primers de RAPD amplificaram 55 loci, os quais geraram padrão de bandas intensa e reproduzível em gel de agarose. Os resultados indicaram polimorfismos dentro e entre as linhagens. A similaridade de Jaccard média e o índice de diversidade Shannon revelaram alta diversidade dentro das linhagens de codornas. O teste de Mantel por meio do algoritmo unweighted pair-group method using arithmetic average (UPGMA) e a dispersão de coordenadas principais indicaram diferenciação genética significativa, embora em baixo nível. Os resultados sugerem que a diversidade genética dentro e entre as linhagens de codornas da Universidade Estadual de Maringá são promissoras para uso em programas de melhoramento.

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Genetic diversity of Pleurotus ostreatus (Jacq.) P. Kumm. strains in Java based on random amplified polymorphic DNA markers

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d220658 ◽

2021 ◽

Vol 22 (6) ◽

Author(s):

NURAENI EKOWATI ◽

ARIS MUMPUNI ◽

JUNI SAFITRI MULJOWATI ◽

NUNIEK INA RATNANINGTYAS ◽

ARDHINI RIN MAHARNING

Keyword(s):

Genetic Diversity ◽

Dna Sequences ◽

Dna Markers ◽

Pleurotus Ostreatus ◽

Genetic Similarity ◽

Random Amplified Polymorphic Dna ◽

Dna Amplification ◽

Group Method ◽

Arithmetic Average ◽

Pair Group

Abstract. Ekowati N, Mumpuni A, Muljowati JS, Ratnaningtyas NI, Maharning AR. 2021. Genetic diversity of Pleurotus ostreatus (Jacq.) P. Kumm. strains in Java based on Random Amplified Polymorphic DNA markers. Biodiversitas 22: 3488-3493. Genetic variation in a fungal population can occur due to mutation and recombination, resulting in changes in the nucleotides that encode specific DNA sequences. Strains with a high genetic distance and good production capabilities can be used to develop genetic breeding. This study aimed to investigate genetic relationship among Pleurotus ostreatus strains cultivated in Java (Bogor, Cianjur, Tasikmalaya, Purwokerto, Yogyakarta, Tawangmangu, Malang, and Madiun) based on random amplified polymorphic DNA (RAPD) markers. The research method consisted of DNA isolation and DNA amplification using six primers, i.e. OPA2, OPA3, OPA4, OPA7, OPA9, and OPA10. DNA band data were analyzed using NTSYSpc21 software to determine the level of genetic similarity, based on the Unweighted Pair Group Method with Arithmetic Average Algorithm (UPGMA). In all, 101 amplified DNA bands were obtained, with sizes ranging from 136 to 2320 bp and 96.0% of the bands were polymorphic. Based on cluster analysis, it shows that three clusters were formed. There were genetic variations and relationships among eight P. ostreatus strains in Java with a genetic similarity varying from 37-98%.

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Genetic Diversity and Relationships in Malus sp. Germplasm Collections as Determined by Randomly Amplified Polymorphic DNA

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.126.3.318 ◽

2001 ◽

Vol 126 (3) ◽

pp. 318-328 ◽

Cited By ~ 15

Author(s):

Nnadozie C. Oraguzie ◽

Sue E. Gardiner ◽

Heather C.M. Basset ◽

Mirko Stefanati ◽

Rod D. Ball ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Relationships ◽

Random Amplified Polymorphic Dna ◽

Group Method ◽

Scatter Plot ◽

Arithmetic Average ◽

Germplasm Collections ◽

Food Research ◽

Pair Group ◽

Upgma Cluster Analysis

Four subsets of apple (Malus Mill.) germplasm representing modern and old cultivars from the repository and apple genetics population of the Horticulture and Food Research Institute of New Zealand Limited were used in this study. A total of 155 genotypes randomly chosen from the four subsets were analyzed for random amplified polymorphic DNA (RAPD) variation. Nine decamer primers generated a total of 43 fragments, 42 of which were polymorphic across the 155 genotypes. Pairwise distances were calculated between germplasm subsets using the distance metric algorithm in S-PLUS, and used to examine intra-and inter-subset variance components by analysis of molecular variation (AMOVAR). A phenogram based on unweighted pair group method with arithmetic average (UPGMA) cluster analysis was constructed from the pairwise distances and a scatter plot was generated from principal coordinate analysis. The AMOVAR showed that most of the variation in the germplasm (94.6%) was found within subsets, suggesting that there is significant variation among the germplasm. The grouping of genotypes based on the phenogram and scatter plot generally did not reflect the pedigree or provenance of the genotypes. It is possible that more RAPD markers are needed for determining genetic relationships in apple germplasm. Nevertheless, the variation observed in the study suggests that the current practice of sublining populations in the first generation to control inbreeding may not be necessary in subsequent generations. If these results are confirmed by fully informative molecular markers, germplasm managers should reassess the structure of their genetics populations. There may be a need to combine sublines in order to capture the maximum genetic diversity available and to streamline breeding efforts.

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Genetic Diversity Among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

Sustainability ◽

10.3390/su13126830 ◽

2021 ◽

Vol 13 (12) ◽

pp. 6830

Author(s):

Murat Guney ◽

Salih Kafkas ◽

Hakan Keles ◽

Mozhgan Zarifikhosroshahi ◽

Muhammet Ali Gundesli ◽

...

Keyword(s):

Genetic Diversity ◽

Plant Genetic Resources ◽

Juglans Regia ◽

Genetic Distances ◽

Mean Value ◽

Central Anatolia ◽

Group Method ◽

Arithmetic Average ◽

Pair Group ◽

Principal Coordinates

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

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Optimal use of SSR markers for varietal identification of upland cotton

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2015000700007 ◽

2015 ◽

Vol 50 (7) ◽

pp. 571-581 ◽

Cited By ~ 1

Author(s):

Guilherme da Silva Pereira ◽

Ana Luíza Ramos Cazé ◽

Michelle Garcia da Silva ◽

Vanessa Cavalcante Almeida ◽

Fernanda Oliveira da Cunha Magalhães ◽

...

Keyword(s):

Genetic Distance ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Group Method ◽

Discrimination Power ◽

Arithmetic Average ◽

Pair Group ◽

Varietal Identification ◽

The World ◽

The Mean

Abstract: The objective of this work was to identify polymorphic simple sequence repeat (SSR) markers for varietal identification of cotton and evaluation of the genetic distance among the varieties. Initially, 92 SSR markers were genotyped in 20 Brazilian cotton cultivars. Of this total, 38 loci were polymorphic, two of which were amplified by one primer pair; the mean number of alleles per locus was 2.2. The values of polymorphic information content (PIC) and discrimination power (DP) were, on average, 0.374 and 0.433, respectively. The mean genetic distance was 0.397 (minimum of 0.092 and maximum of 0.641). A panel of 96 varieties originating from different regions of the world was assessed by 21 polymorphic loci derived from 17 selected primer pairs. Among these varieties, the mean genetic distance was 0.387 (minimum of 0 and maximum of 0.786). The dendrograms generated by the unweighted pair group method with arithmetic average (UPGMA) did not reflect the regions of Brazil (20 genotypes) or around the world (96 genotypes), where the varieties or lines were selected. Bootstrap resampling shows that genotype identification is viable with 19 loci. The polymorphic markers evaluated are useful to perform varietal identification in a large panel of cotton varieties and may be applied in studies of the species diversity.

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AFLP-based assessment of genetic diversity among nine alfalfa germplasms using bulk DNA templates

Genome ◽

10.1139/g02-100 ◽

2003 ◽

Vol 46 (1) ◽

pp. 51-58 ◽

Cited By ~ 46

Author(s):

A Segovia-Lerma ◽

R G Cantrell ◽

J M Conway ◽

I M Ray

Keyword(s):

Genetic Diversity ◽

Medicago Sativa ◽

High Throughput ◽

Genetic Distances ◽

Group Method ◽

Aflp Analysis ◽

Dna Templates ◽

Arithmetic Average ◽

Pair Group ◽

Large Numbers

Improving commercial utilization of perennial Medicago collections requires developing approaches that can rapidly and accurately characterize genetic diversity among large numbers of populations. This study evaluated the potential of using amplified fragment length polymorphism (AFLP) DNA markers, in combination with DNA bulking over multiple genotypes, as a strategy for high-throughput characterization of genetic distances (D) among alfalfa (Medicago sativa L.) accessions. Bulked DNA templates from 30 genotypes within each of nine well-recognized germplasms (African, Chilean, Flemish, Indian, Ladak, Medicago sativa subsp. falcata, Medicago sativa subsp. varia, Peruvian, and Turkistan) were evaluated using 34 primer combinations. A total of 3754 fragments were identified, of which 1541 were polymorphic. The number of polymorphic fragments detected per primer combination ranged from 20 to 85. Pairwise D estimates among the nine germplasms ranged from 0.52 to 1.46 with M. sativa subsp. falcata being the most genetically dissimilar. Unweighted pair-group method arithmetic average (UPGMA) analysis of the marker data produced two main clusters, (i) M. sativa subsp. sativa and M. sativa subsp. varia, and (ii) M. sativa subsp. falcata. Cluster-analysis results and D estimates among the Chilean, Peruvian, Flemish, and M. sativa subsp. varia germplasms supported the hypothesis that Peruvian was more similar to original Spanish introductions into Central and South America than Chilean. Hierarchical arrangement of the nine germplasms was supported by their respective geographic, subspecific, and intersubspecific hybrid origins. Subsets of as few as seven highly informative primer pairs were identified that produced comparable D estimates and similar heirarchical arrangements compared with the complete dataset. The results indicate that use of primer-pair subsets for AFLP analysis of bulk DNA templates could serve as a high-throughput system for accurately characterizing genetic diversity among large numbers of alfalfa populations.Key words: Medicago sativa, DNA bulking, genetic distance.

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Partial diallel and genetic divergence analyses in maize inbred lines

Acta Scientiarum Agronomy ◽

10.4025/actasciagron.v43i1.53540 ◽

2020 ◽

Vol 43 ◽

pp. e53540

Author(s):

Maria Fernanda de Souza Dias Maioli ◽

Ronald José Barth Pinto ◽

Tereza Aparecida da Silva ◽

Diego Ary Rizzardi ◽

Robson Akira Matsuzaki ◽

...

Keyword(s):

Grain Yield ◽

Genetic Divergence ◽

Block Design ◽

Inbred Lines ◽

Group Method ◽

Arithmetic Average ◽

Pair Group ◽

Maize Inbred Lines ◽

Randomized Block Design ◽

Partial Diallel

In this study, we aimed to estimate general and specific combining abilities (GCA and SCA, respectively) and to verify genetic divergence (Rogers distance, Unweighted Pair-Group Method Using Arithmetic Average - UPGMA) using microsatellite markers in maize inbred lines. Using a partial diallel scheme, a total of 19 inbred lines were crossed as (9 x 10), which were derived from the single hybrids SG6015 and P30F53, respectively. The 90 hybrids were evaluated in an incomplete randomized block design with common checks and three replications during the 2017-2018 growing season. Flowering time, average plant height, ear height insertion, average ear diameter, ear length, number of lodged and broken plants, mass of 100 grains and grain yield were measured. According to the analysis of variance, GCA, and SCA were significant (p < 0.05) in all the measured traits; inbred line B as well as 1 and 8, derived from the single hybrids SG6015 and P30F53, respectively, were selected due to their higher GCA values in grain yield to be used in crosses as testers, while the single cross hybrid (B x 1) was selected due to their higher SCA value in grain yield to be used in future breeding programs. The molecular marker analysis divided the inbred lines into two groups, where the highest dissimilarity (0.74) was observed between lines A and 9; however, these did not result in a high SCA value, therefore the hybrids obtained by such crossings were not selected for grain yield.

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Analysis of Genetic Variability Amongst Polyploid Genotypes of Pteris vittata L. From Various Geographic Locales of India

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.613847 ◽

2021 ◽

Vol 9 ◽

Author(s):

Jyoti Mathur ◽

P. B. Khare ◽

Apurva Panwar ◽

S. A. Ranade

Keyword(s):

Random Amplified Polymorphic Dna ◽

Genomic Structure ◽

Inter Simple Sequence Repeat ◽

Pteris Vittata ◽

Group Method ◽

Bootstrap Analysis ◽

Pair Group ◽

Fern Species ◽

Outgroup Taxon ◽

Effective Multiplex Ratio

Pteris vittata L. is very common and a widely distributed species belongs to the family Pteridaceae. Various cytotypes from diploid to octaploid is available in this fern species. The present work has been carried out for genetic diversity in this fern both within and between the cytotypes. The molecular analysis at inter- as well as intra-species has been carried out with 57 accessions of P. vittata as well as of other species of Pteris with Microsorium punctatum considered as an out group taxon. For the present study 48 P. vittata (36 tetraploid and 12 pentaploid) and five of other species (four P. cretica, one P. pellucida, one P. tremula, one P. quadriaurita, and two P. ensiformis) accessions were used. The UPGMA (unweighted pair group method with arithmetic mean) dendrograms were generated for each method separately, as well as for all methods cumulatively, after a 1000 replicate bootstrap analysis. In order to determine the utility of each of the method, a comparative statistical assessment was done and marker index (MI), expected average heterozygosity, fraction of polymorphic loci and effective multiplex ratio (EMR) were calculated in case of each of the methods used in the present study. At the level of individual methods highest MI was obtained for directed amplification of minisatellites DNA (DAMD) method. Our findings of the present study concluded that out of the three methods Random Amplified Polymorphic DNA (RAPD), Inter-Simple Sequence Repeat (ISSR), and Directed Amplification of Minisatellite DNA (DAMD), DAMD was the best in term of polymorphism and heterozygosity as scores exhibited highest MI. The different accessions of P. vittata collected from different phytogeographical regions falls into six groups. Out of six clusters, one cluster is of pentaploid cytotype, four clusters are of tetraploid cytotype and one for outgroup taxon (M. punctatum). The result thus showed that within tetraploid, heterozygosity with variable genomic structure exists.

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