Genetic differentiation of charcoal rot pathogen, Macrophomina phaseolina, into specific groups using URP-PCR

2005 ◽  
Vol 51 (2) ◽  
pp. 159-164 ◽  
Author(s):  
T K Jana ◽  
N K Singh ◽  
K R Koundal ◽  
T R Sharma
Keyword(s):  
Pathogenic Fungus ◽  
Rice Genome ◽  
Pcr Primers ◽  
Macrophomina Phaseolina ◽  
Group Method ◽  
Broad Host Range ◽  
Pair Group ◽  
Dna Repeat ◽  
Dna Repeat Sequences ◽  
First Time

Forty isolates of Macrophomina phaseolina, a pathogen causing charcoal dry root rot of soybean, cotton, and chickpea, were genetically characterized with universal rice primers (URP; primers derived from DNA repeat sequences in the rice genome) using polymerase chain reaction (URP-PCR). Out of 12 URPs used in this study, 5 primers were effective in producing polymorphic fingerprint patterns from the DNA of M. phaseolina isolates. Three primers (URP-2F, URP-6R, and URP-30F) were quite informative and produced high levels of polymorphism among the isolates of M. phaseolina. Analysis of the entire fingerprint profiles using unweighted pair-group method with arithmetic averages (UPGMA) clearly differentiated M. phaseolina isolates obtained from soybean, cotton, and chickpea hosts into specific groups. In this study, we found for the first time transferability and use of PCR primers derived from plant genomes to generate host-specific fingerprint profiles of M. phaseolina, a broad host range plant pathogenic fungus. These results demonstrate that URPs are sensitive and technically simple to use for assaying genetic variability in M. phaseolina populations.Key words: Macrophomina phaseolina, molecular variability, soybean, cotton, chickpea.

scholarly journals Molecular Characterization of Macrophomina phaseolina, the Incitant of Coleus forskohlii Revealed by RAPD Markers

2012 ◽  
Vol 5 (1) ◽  
pp. 44-50 ◽  
Author(s):  
Chathuri Mudalige ◽  
ST Girisha ◽  
VB Raghavendra ◽  
MH Niranjan ◽  
K Ravikumar ◽  
...  
Keyword(s):  
Root Rot ◽  
Rapd Analysis ◽  
Macrophomina Phaseolina ◽  
Climatic Conditions ◽  
Similarity Coefficient ◽  
Group Method ◽  
Coleus Forskohlii ◽  
Severe Problem ◽  
Pair Group ◽  
Pathogenicity Tests

Coleus forskohlii belong to family lamiaceae is one of the commercial plants grown extensively in the country, the chemical found in the Coleus which has both medicinal application and gives great economy to the industrial organizations. Unfortunately, these plants are being highly succumbed to serious diseases like wilt and root rot caused by a fungus, hence the growers and industrialists are facing severe problem in safeguarding this crop in the field irrespective of the agro climatic conditions. Root rot disease, is one of the major diseases of Coleus forskohlii which, is caused by Macrophomina phaseolina, Pathogen variability was studied at both morphological and molecular level using cultural characteristics and Rapid Amplification of Polymorphic DNA (RAPD) analysis respectively. Totally thirty two isolates were isolated from roots of Coleus forskohlii. In RAPD 165 bands were obtained out of them 121 bands (73.3%) were polymorphic with a similarity coefficient of 0.48-0.66. Clusters analysis of RAPD data when Unweighted Pair Group Method with Arithmetic Mean (UPGMA) Tree constructed using NTSYS, it showed 6 groups. Among them two were major clusters and 4 were minor clusters with similarity coefficient 0.48-0.66. The pathogenicity of the isolates was tested on Coleus forskohlii plants. Analysis of the pathogenicity tests results revealed that the isolates grouped under two major clusters which were different from the one obtained using RAPD data. The results indicate that the data from RAPD analysis and Pathogenicity tests do not correlate with each other.DOI: http://dx.doi.org/10.3126/ijls.v5i1.5598 International Journal of Life Sciences Vol.5(1) 2011 44-50

scholarly journals Karyomorphological variations in some populations of Allium subgenus Melanocrommyum section Acanthoprason in Iran

2018 ◽  
Vol 19 (2) ◽  
pp. 670-675
Author(s):  
HASSAN MASTALI ◽  
MAHBOOBEH ZARE-MEHRJERDI ◽  
MARYAM NOROUZI ◽  
JALAL REZAEI
Keyword(s):  
Cluster Analysis ◽  
Chromosome Number ◽  
Natural Variation ◽  
Karyotype Analysis ◽  
Group Method ◽  
Allium Species ◽  
Arithmetic Average ◽  
Pair Group ◽  
Upgma Cluster Analysis ◽  
First Time

Mastali H, Zare-Mehrjerdi M, Norouzi M, Rezaei J. 2018. Karyomorphological variations in some populations of Allium subgenus Melanocrommyum section Acanthoprason in Iran. Biodiversitas 19: 670-675. Allium is the largest genus of Amaryllidaceae comprising more than 900 species belonging to 15 subgenera. Iran is reported to be a center of diversity for subgenus Melanocrommyum. Acanthoprason is a section in this subgenus. In this paper, karyomorphological variations of nine populations of four species including Allium derderianum, A. kurdistanicum, A. minutiflorum and A. subakaka of the section Acanthoprason growing in Iran were undertaken using squash technique and 2% (w/v) aceto-orcein stain. All of the populations have the same chromosome numbers 2n = 2x = 16 with the exception in Kochka population of A. derderianum 2n = 18. In the present study, the chromosome number of A. minutiflorum and new chromosome number of A. derderianum were revealed for the first time. Chromosomal characteristics were determined using photographs complemented by cluster analysis. According to dendrogram generated by the unweighted pair-group method with arithmetic average (UPGMA) cluster analysis, nine populations studied were separated into five groups at a cut off value of 5. Karyotype analysis indicated that Allium species studied here generally have metacentric and submetacentric chromosomes and symmetric karyotypes. Results of the present study revealed the natural variation in nine populations of four species of Acantoprason section which can further serve conservation and breeding planning.

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

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.

scholarly journals Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for the Melilotus Genus

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 890
Author(s):  
Zifeng Ouyang ◽  
Yimeng Wang ◽  
Tiantian Ma ◽  
Gisele Kanzana ◽  
Fan Wu ◽  
...  
Keyword(s):  
Group Method ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Important Data ◽  
Breeding Programs ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Medicinal Value ◽  
Genome Wide ◽  
Melilotus Albus

Melilotus is an important genus of legumes with industrial and medicinal value, partly due to the production of coumarin. To explore the genetic diversity and population structure of Melilotus, 40 accessions were analyzed using long terminal repeat (LTR) retrotransposon-based markers. A total of 585,894,349 bp of LTR retrotransposon sequences, accounting for 55.28% of the Melilotus genome, were identified using bioinformatics tools. A total of 181,040 LTR retrotransposons were identified and classified as Gypsy, Copia, or another type. A total of 350 pairs of primers were designed for assessing polymorphisms in 15 Melilotus albus accessions. Overall, 47 polymorphic primer pairs were screened for their availability and transferability in 18 Melilotus species. All the primer pairs were transferable, and 292 alleles were detected at 47 LTR retrotransposon loci. The average polymorphism information content (PIC) value was 0.66, which indicated that these markers were highly informative. Based on unweighted pair group method with arithmetic mean (UPGMA) dendrogram cluster analysis, the 18 Melilotus species were classified into three clusters. This study provides important data for future breeding programs and for implementing genetic improvements in the Melilotus genus.

scholarly journals Genetic diversity in table grapes based on RAPD and microsatellite markers

2011 ◽  
Vol 46 (9) ◽  
pp. 1035-1044 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Sérgio Yoshimitsu Motoike
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Similarity Index ◽  
Genetic Distances ◽  
Table Grape ◽  
Group Method ◽  
Molecular Characteristics ◽  
Table Grapes ◽  
Pair Group

The objective of this work was to analyze the genetic diversity of 47 table grape accessions, from the grapevine germplasm bank of Embrapa Semiárido, using 20 RAPD and seven microsatellite markers. Genetic distances between pairs of accessions were obtained based on Jaccard's similarity index for RAPD data and on the arithmetic complement of the weighted index for microsatellite data. The groups were formed according to the Tocher's cluster analysis and to the unweighted pair‑group method with arithmetic mean (UPGMA). The microsatellite markers were more efficient than the RAPD ones in the identification of genetic relationships. Information on the genetic distance, based on molecular characteristics and coupled with the cultivar agronomic performance, allowed for the recommendation of parents for crossings, in order to obtain superior hybrids in segregating populations for the table grape breeding program of Embrapa Semiárido.

scholarly journals Molecular Diversity and Genetic Relatedness of Candida albicans Isolates from Birds in Hungary

2021 ◽  
Vol 186 (2) ◽  
pp. 237-244
Author(s):  
M. Domán ◽  
L. Makrai ◽  
Gy. Lengyel ◽  
R. Kovács ◽  
L. Majoros ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Molecular Diversity ◽  
Genetic Relatedness ◽  
Group Method ◽  
Pair Group ◽  
Degree Of Separation ◽  
Avian Origin ◽  
Species Specific ◽  
Sequence Types ◽  
Unweighted Pair Group Method

AbstractThe molecular epidemiology of Candida albicans infections in animals has been rarely studied. In this study, multilocus sequence typing was used to characterise the genetic diversity and population structure of 24 avian origin C. albicans isolates collected from different birds with candidiasis and compared to human isolates. Fourteen diploid sequence types (DSTs) including six new DSTs were determined. Cluster analysis revealed that isolates grouped into 8 clades. Bird isolates mainly belonged to minor clades and Clade 15 with DST 172 was the most common (11 isolates; 45.8%). The remaining isolates were clustered into Clade 7 (5 isolates; 20.8%), Clade 10 (4 isolates; 16.6%), Clade 8 (2 isolates; 8.3%), Clade 4 (1 isolate; 4.2%) and Clade 16 (1 isolate; 4.2%). Unweighted pair group method with arithmetic averages (UPGMA) and eBURST analyses showed that the genetic construction of avian origin C. albicans population is fairly diverse. Although species-specific lineages were not found, some degree of separation in the evolution of bird and human strains could be observed.

Occurrence and spread of Ceroplastes cirripediformis Comstock (Hemiptera: Coccomorpha: Coccidae) in India

Zootaxa ◽  
2021 ◽  
Vol 5039 (4) ◽  
pp. 561-570
Author(s):  
SUNIL JOSHI ◽  
HASEENA BHASKAR ◽  
V.S. AASHIQ POON ◽  
B.R. JAYANTHI MALA ◽  
P.D. KAMALA JAYANTHI ◽  
...  
Keyword(s):  
Host Range ◽  
Natural Enemies ◽  
Scale Insect ◽  
Indian Species ◽  
Broad Host Range ◽  
Management Options ◽  
Soft Scale ◽  
Plant Pest ◽  
Plant Families ◽  
First Time

The notoriously destructive and invasive soft scale, Ceroplastes cirripediformis Comstock (Hemiptera: Coccomorpha: Coccidae), is recorded for the first time from India. The scale is redescribed to facilitate its identification and information on its host range, natural enemies and distribution is provided. An identification key to the Indian species in this genus is given. Management options in the event of an outbreak are discussed briefly. The establishment of this scale insect warrants special attention in India as it is a potentially damaging plant pest and has a broad host range across many plant families.  

scholarly journals Null expectation of spatial correlograms under a stochastic process of genetic divergence with small sample sizes

2000 ◽  
Vol 23 (4) ◽  
pp. 739-743 ◽  
Author(s):  
Mariana Pires de Campos Telles ◽  
José Alexandre Felizola Diniz-Filho
Keyword(s):  
Stochastic Process ◽  
Genetic Divergence ◽  
Isolation By Distance ◽  
Genetic Distances ◽  
Small Sample ◽  
Group Method ◽  
Gene Frequencies ◽  
Exponential Relationship ◽  
Local Populations ◽  
Pair Group

An Ornstein-Uhlenbeck process was used to simulate the exponential relationship between genetic divergence and geographic distances, as predicted by stochastic processes of population differentiation, such as isolation-by-distance, stepping-stone or coalescence models. These simulations were based only on the spatial coordinates of the local populations that defined a spatial unweighted pair-group method using arithmetic averages (UPGMA) link among them. The simulated gene frequency surfaces were then analyzed using spatial autocorrelation procedures and Nei's genetic distances, constructed with different numbers of variables (gene frequencies). Stochastic divergence in space produced strong spatial patterns at univariate and mutivariate levels. Using a relatively small number of local populations, the correlogram profiles varied considerably, with Manhattan distances greater than those defined by other simulation studies. This method allows one to establish a range of correlogram profiles under the same stochastic process of spatial divergence, thereby avoiding the use of unnecessary explanations of genetic divergence based on other microevolutionary processes.

Genetic analysis of a heritage variety collection

2018 ◽  
Vol 17 (03) ◽  
pp. 232-244 ◽  
Author(s):  
J. M. Preston ◽  
B. V. Ford-Lloyd ◽  
L. M. J. Smith ◽  
R. Sherman ◽  
N. Munro ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Group Method ◽  
Niche Markets ◽  
Principal Coordinates Analysis ◽  
Pair Group ◽  
Landrace Diversity ◽  
Principal Coordinates ◽  
Length Polymorphisms ◽  
Seed Saving ◽  
History Of

AbstractLandraces (including heritage varieties) are an important agrobiodiversity resource offering considerable value as a buffer against crop failures, as a crop for niche markets, and as a source of diversity for crop genetic improvement activities underpinning future food security. Home gardens are reservoirs of landrace diversity, but some of the accessions held in them are vulnerable or threatened with extinction. Those associated with seed saving networks have added security, for example, ca. 800 varieties are stored in the Heritage Seed Library (HSL) of Garden Organic, UK. In this study, Amplified Fragment Length Polymorphisms-based genetic analysis of accessions held in the HSL was used to (a) demonstrate the range of diversity in the collection, (b) characterize accessions to aid collection management and (c) promote broader use of the collection. In total, 171 accessions were included from six crops: Vicia faba L., Pisum sativum L., Daucus carota L., Cucumis sativus L., Lactuca sativa L. and Brassica oleracea L. var. acephala (DC.) Metzq. Average expected heterozygosity ranged from 0.18 to 0.28 in D. carota; 0.02–0.18 in P. sativum; 0.05–0.18 in L. sativa; 0.15–0.26 in B. oleracea var. acephala; 0.15–0.37 in C. sativus and 0.07–0.36 in V. faba. Genetic diversity and Fst values generally reflected the breeding system and cultivation history of the different crops. Comparisons of the diversity found in heritage varieties with that found in commercial varieties did not show a consistent pattern. Principal coordinates analysis and Unweighted Pair Group Method with Arithmetic Mean cluster analysis were used to identify four potential duplicate accession pairs.

Sign in / Sign up

Export Citation Format

Share Document