scholarly journals Genetic structure and diversity among individuals of Copaifera langsdorffii Desf. from Mato Grosso, Brazilian Amazon, using ISSR markers

2021 ◽  
Vol 10 (16) ◽  
pp. e187101623025
Author(s):  
Daniele Paula Maltezo ◽  
Julliane Dutra Medeiros ◽  
Ana Aparecida Bandini Rossi
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Variability ◽  
Polymorphic Information Content ◽  
Issr Markers ◽  
Group Method ◽  
Mato Grosso ◽  
Copaifera Langsdorffii ◽  
Genetic Structure And Diversity ◽  
Issr Primers

The Amazon is the largest tropical forest in the world and is home to around 20% of all the biodiversity on the planet, among the species present in the Amazon is Copaifera langsdorffii, exploited mainly for the extraction of oil-resin and wood, often in ways incorrect, which can cause the loss of genetic variability. The aim of this study was to evaluate the genetic structure and diversity among individuals of C. langsdorffii located in Mato Grosso, Brazil, using ISSR markers. We sampled leaves from 27 adult individuals of C. langsdorffii, whose total genomic DNA was extracted. A total of 12 ISSR primers were used for the molecular characterization of the individuals. A grouping analysis was performed using the unweighted pair group method, Bayesian analysis and characterized by the genetic diversity. The genetic diversity among and within the groups was demonstrated by the AMOVA. As a result, 106 fragments were amplified and 98.11% were polymorphic. The polymorphic information content of each primer ranged from 0.45 to 0.81.  The dendrogram showed the formation of 4 distinct groups. The greatest genetic variability is found within the groups and not between them. The percentage of polymorphism, genetic dissimilarity values and genetic diversity indexes indicate that there is high genetic variability among Copaifera langsdorffii individuals, suggesting that ISSR primers were efficient in detecting polymorphism in this species and that the individuals have potential for compose programs aimed at the preservation of the species and the ability to integrate germplasm banks.

scholarly journals Assessment of genetic diversity in Moroccan sesame (Sesamum indicum) using ISSR molecular markers

OCL ◽  
2021 ◽  
Vol 28 ◽  
pp. 3
Author(s):  
Meriem El Harfi ◽  
Jamal Charafi ◽  
Karim Houmanat ◽  
Hafida Hanine ◽  
Abdelghani Nabloussi
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Polymorphic Information Content ◽  
Issr Markers ◽  
Sesamum Indicum ◽  
Simple Method ◽  
Low Genetic Diversity ◽  
Simple Repeats ◽  
New Germplasm ◽  
Issr Primers

There is a need for sesame (Sesamum indicum L.) breeding in Morocco to release performant and adapted varieties, which requires a large genetic variability in the germplasm to be used. In this context, genetic diversity of sesame populations from different locations in Tadla area was investigated using ISSR (Inter Sequence Simple Repeats) markers as a simple method to reveal polymorphism among them. A total of 130 individuals representing 31 populations were sampled. Twenty-four ISSR primers were used for analysis of individuals representing the 31 different sesame populations grown in different agroclimatic zones of Tadla, accounting for 90% of sesame cultivation area in Morocco. Indeed, seven primers showed legible and reproducible genomic profiles with an interesting number of bands. A total of 57 bands were obtained with ISSR primers, of which 47 were polymorphic. PIC (Polymorphic Information Content) ranged from 0.002 to 0.350, showing that ISSR markers are informative and relevant for discriminating the populations evaluated. The similarity coefficient of ISSR data ranged from 0.509 to 1, with an average of 0.870. The results obtained showed that Moroccan sesame populations are characterized by a low genetic diversity, suggesting a genetic proximity among them. Therefore, new germplasm should be either introduced from diverse geographical origins or created through mutagenesis breeding in order to broaden the existing genetic variability.

scholarly journals Characterization of genetic diversity of cactus species (Opuntia spp.) in Morocco by morphological traits and molecular markers

2017 ◽  
Vol 5 (2) ◽  
pp. 149-159 ◽  
Author(s):  
Y. El Kharrassi ◽  
M.A. Mazri ◽  
M.H. Sedra ◽  
A. Mabrouk ◽  
B . Nasser ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Morphological Traits ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Group Method ◽  
Rapd Primer ◽  
Opuntia Spp ◽  
Issr Primers

The genetic diversity within and among 124 accessions of Opuntia spp. collected from different regions of Morocco was assessed using morphological descriptors and molecular markers. Based on 10 morphological traits, the accessions were separated into 3 main clusters; each cluster was containing accessions from different regions and species. Polymerase chain reaction (PCR) was then performed on 22 accessions from different regions and species, with 10 inter-simple sequence repeat (ISSR) primers and one random amplified polymorphic DNA (RAPD) primer. ISSR primers produced 66 bands overall, 64 (96.9 %) of which were polymorphic while 6 bands were generated by the RAPD marker, all polymorphic. The polymorphic information content (PIC) values ranged from 0.62 to 0.97, with an average of 0.82. The dendrogram of genetic differences generated using the unweighted pair-group method using arithmetic averages (UPGMA) method showed 7 different clusters at a similarity of 0.76, which was confirmed by the principal component analysis (PCA). The main conclusion of our work is the high genetic similarity between Opuntia ficus indica and Opuntia megacantha species in Morocco. Our results will be useful for plant breeding and genetic resource conservation programs.

scholarly journals ASSESSMENT OF GENETIC DIVERSITY AND RELATIONSHIPS AMONG GRAPEVINE CULTIVARS ORIGINATING IN CENTRAL AND EASTERN EUROPE AND NORTH AMERICA USING ISSR MARKERS

2019 ◽  
Vol 18 (5) ◽  
pp. 141-152
Author(s):  
Anna Lisek ◽  
Jerzy Lisek
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Polymorphic Information Content ◽  
Issr Markers ◽  
Molecular Techniques ◽  
Resolving Power ◽  
Vitis Vinifera L ◽  
Phenotypic Differences ◽  
High Degree ◽  
Issr Primers

The study shows genetic diversity of 38 Vitis vinifera L. cultivars and hybrids originating in North America and Europe, including cultivars selected in Poland, which have not been characterized with the use of DNA markers yet. The agrobiological features of the genotypes selected for testing, indicate that they may be useful for the breeding of new cultivars and grape production. The use of 12 ISSR primers allowed to obtain 94.4% of polymorphism. The polymorphic information content (PIC) value was high and varied between 0.829 and 0.953 with an average of 0.897. The resolving power (Rp) ranged between 3.678 and 8.892 with an average of 6.347. Primers UBC 809, UBC 810, UBC 812, UBC 855, UBC 891 and UBC 810 were found to be highly effective (informative). Similarity coefficient ranged between 0.167 and 1.0, which indicates high degree of diversity of tested  grape cultivars. Tested cultivars were grouped in 3 main clusters; one of them was further divided into 6 subclusters. ‘Pannonia Kincse’ and ‘Danmarpa Polonia’ were not differentiated. Phenotypic differences among those two cultivars suggest that ‘Danmarpa Polonia’ might be a clone of ‘Pannonia Kincse’ and other molecular techniques must be used to differentiate them. Morphological and agrobiological characters of cultivars support the results obtained by ISSR markers.

scholarly journals Genetic diversity and spatial genetic structure within a population of an aromatic shrub, Lippia origanoides (Verbenaceae), in the Chicamocha Canyon, northeastern Colombia

2008 ◽  
Vol 90 (6) ◽  
pp. 455-465 ◽  
Author(s):  
ADRIANA SUÁREZ G. ◽  
GENIS CASTILLO ◽  
MARIA I. CHACÓN S.
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Diversity Index ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Classical Model ◽  
Issr Markers ◽  
Breeding Systems ◽  
Group Method ◽  
Pair Group

SummaryThe geographical scale of genetic structure in a continuous population is highly dependent on its breeding system and dispersion capabilities, and this knowledge is important for the study of population dynamics as well as for conservation purposes. In the present study, spatial autocorrelation statistics and intersimple sequence repeat (ISSR) markers were used to describe the genetic structure of a natural population of a prominent aromatic plant, Lippia origanoides, native to the Chicamocha Canyon in northeastern Colombia. For this purpose, individuals were sampled from two localities within the Chicamocha Canyon, where the species is abundant and continuously distributed. Cluster (principal coordinate analysis (PCO) and unweighted pair group method using arithmetic averages (UPGMA)), analysis of molecular variance (AMOVA) and Bayesian analyses revealed a low level of genetic differentiation among the two localities, suggesting that they belong to a single population. Genetic diversity levels in this population, described as the percentage of polymorphic loci (P=86·21%) and quantified using Shannon's diversity index (I=0·453) and the average panmictic heterozygosity (HB=0·484), were shown to be comparable to or higher than that in other plant species with allogamous breeding systems and to other related Verbenaceae species. Fine-scale autocorrelation analyses showed a pattern consistent with the classical model of isolation by distance with moderate but significant levels of local spatial structure. Our results suggest that sampling individuals at distances greater than ~1·2 km may result in the collection of different genotypes, which could help preserve the levels of genetic diversity in a propagation programme. The causes of this spatial pattern are currently unknown and could be influenced by many contemporary factors such as restricted seed dispersal and/or short-distance pollen movement, among others.

scholarly journals Genetic Diversity of Groundnut (Arachis hypogaea L.) Accessions using Inter Simple Sequence Repeats (ISSRs) Marker

2020 ◽  
Author(s):  
Mohammed Abdela ◽  
Mulugeta Kebede ◽  
Tiliye Feyissa
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Arachis Hypogaea ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Issr Markers ◽  
Similarity Coefficients ◽  
Average Value ◽  
Band Size ◽  
Arachis Hypogaea L

Abstract Background: Groundnut (Arachis hypogaea L.) belongs to the family Leguminoseae. It is the world’s most important source of edible oil and vegetable protein. To our knowledge, little is known about the genetic variability of cultivated Ethiopian A. hypogaea at a molecular level. It is important to understand the genetic diversity of the crop to collect, conserve and use the germplasm for variety development. In the present study, ISSR markers were used to determine the genetic variability and diversity of 43 accessions of A. hypogaea collected from different regions of Ethiopia.Results: Four ISSR primers were used to generate 56 reproducible bands of which 29 (51.8%) were polymorphic. The band size ranges from 120 bp to 1100 bp. The number of amplified bands varied from 12 in primer UBC841 to 18 in primer UBC 881. The polymorphic bands percentage ranges from 27.8 % of Primer UBC 881 to 84.6 % of primer UBC 857. The polymorphic information content (PIC) value ranges from 0.29 to 0.76 with the average value 0.49. The mean Nei’s gene diversity and Shannon’s information index were 0.25 and 0.33, respectively. Genetic relationship between A. hypogaea accessions based on Jaccard’s pair wise similarity coefficients varies from 44% to 83% with an average value of 63.5%. The UPGMA dendrogram based on cluster analysis grouped A. hypogaea accessions into five distinct clusters at 63.5% similarity coefficient, and the principal coordinate analysis revealed similar grouping. Conclusions: Even though in both UPGMA and PCoA most of the accessions were grouped in separate clusters irrespective of their geographic origins, the ISSR marker-based analysis shows the presence of genetic variability among the accessions. Moreover, the current study demonstrated the potential informativeness of ISSR markers in estimating the extent of genetic variation in A. hypogaea accessions.

scholarly journals Genetic diversity of Matrinxã breeding stocks: implications for management and conservation

2021 ◽  
Vol 42 (2) ◽  
pp. 757-768
Author(s):  
Angela Maria Urrea Rojas ◽  
◽  
Felipe Pinheiro de Souza ◽  
Ed Christian Suzuki de Lima ◽  
Claudete de Fátima Ruas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Genetic Differentiation ◽  
Genetic Drift ◽  
Polymorphic Information Content ◽  
Common Origin ◽  
Null Alleles ◽  
Mato Grosso ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium

The formation of fish breeding stocks for fish farming or conservation programs is commonly carried out from the capture of fish in natural environments. Information on the geographic and genetic origin of these stocks is important to guide actions that allow correct management in captivity and, when lost, harm production and genetic conservation. In this sense, the objective of this study was to evaluate the genetic diversity and origin of two breeding stocks of matrinxã, Brycon amazonicus (INPA, Amazonas - INPA and Nova Motum, Mato Grosso - NM). A total of 68 caudal fin samples were collected, including 33 INPA samples and 35 NM samples. Twenty pairs of microsatellite primers were tested, but only seven primers showed satisfactory amplification, amplifying 41 alleles ranging from 187-318 bp. The polymorphic information content ranged from 0.135 (Borg25) to 0.782 (Bh6). Exclusive alleles were observed for both populations (INPA: 04 and NM: 18). Allelic richness results revealed that there was increased loss of genetic variation in NM, indicating a lower evolutionary potential of this stock. The average values of the observed heterozygosity corroborated this statement; however, there were high values for INPA (0.545) and NM (0.475), signifying an adequate genetic variability. An imbalance was found in the Hardy-Weinberg equilibrium at the Borg59 locus in INPA (P < 0.05), possibly due to the effect of null alleles, but was attributed to a founder effect. For NM, an imbalance in the Hardy-Weinberg equilibrium was observed at loci BoM13 and Bh6, which together with the results of the mean inbreeding coefficient values demonstrated the presence of genetic drift. The analysis of molecular variance showed greater variation within populations than between them, and was confirmed by the genetic differentiation value (0.086 - moderate genetic differentiation) and by the distance and genetic identity values (0.273 and 0.761, respectively). Bayesian analysis designated a value of K = 2, with the presence of structuring for NM and INPA; however, with correlated allelic frequencies, confirming a common origin. This origin was corroborated by the presence of gene flow through the number of migrants (5.691). Based on these results, there was a moderate genetic variability for INPA and NM and their common origin was confirmed. Recommendations are also included to minimize the probability of inbreeding processes or genetic drift in the studied stocks.

scholarly journals Genetic Diversity as Revealed by Intersimple Sequence Repeat Polymorphism in Narcissus Accessions to Identify the Tolerant Genotypes for Deficit Irrigation

2019 ◽  
Vol 144 (2) ◽  
pp. 92-106 ◽  
Author(s):  
Mozhgan Zangeneh ◽  
Hassan Salehi
Keyword(s):  
Genetic Diversity ◽  
Deficit Irrigation ◽  
Polymorphic Information Content ◽  
Issr Markers ◽  
Resolving Power ◽  
Group Method ◽  
Sequence Repeat ◽  
Issr Primer ◽  
Average Percentage ◽  
Drought Tolerant

There are many species of Narcissus in diverse areas of the world in natural or cultured form and there is no complete information about their genetic status, especially the relatedness within a species. Thus, the current study applied intersimple sequence repeat (ISSR) markers to estimate the genetic diversity of 31 accessions, including 30 accessions of Narcissus tazetta, collected from 16 regions of Iran and one known exotic narcissus species that is being cultivated in Iran, and identification of tolerant genotypes for deficit irrigation by evaluation of their morpho-physiological characteristics. Seventeen anchored ISSR primers from a total of 19 tested ISSR primer pairs were used and produced 206 bands of different sizes. The average percentage of polymorphic bands was 96.02%. The maximum resolving power (8.32), polymorphic information content average (0.44), and marker index values (5.61) were observed for the primers of 811, 828, and 811, respectively. The unweighted pair group method with arithmetic mean based on Jaccard’s coefficients was used to assign the genotypes to one of two major clusters. Both clusters were divided into two subclusters, with single and double flowers separating into subgroups. The results showed that ISSR markers can be used as a diagnostic tool to evaluate genetic variation in Narcissus genotypes and reveal their relationships. The results of screening study identified drought-tolerant accessions. They were clustered into two major groups: drought-tolerant accessions with single flowers and drought-sensitive accessions having double and semidouble flowers. The findings presented can be used in breeding programs for different Narcissus genotypes.

scholarly journals Genetic variability of lemon basil (Ocimum × africanum Lour.) from Indonesian archipelago based on morphological and inter-simple sequence repeats markers

2020 ◽  
Vol 21 (12) ◽  
Author(s):  
Kurnia Makmur ◽  
TATIK CHIKMAWATI ◽  
SOBIR SOBIR
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Similarity Index ◽  
Morphological Characters ◽  
Molecular Data ◽  
Issr Markers ◽  
Morphological Observation ◽  
Indonesian Archipelago ◽  
Morphological And Molecular Data ◽  
Issr Primers

Abstract. Makmur K, Chikmawati T, Sobir. 2020. Genetic variability of lemon basil (Ocimum × africanum Lour.) from Indonesia based on morphological characters and ISSR markers. Biodiversitas 21: 5948-5953. Lemon basil (Ocimum × africanum Lour.) or kemangi is a highly beneficial plant, yet still underutilized. Therefore, providing necessary information on genetic diversity of this species is essential for further utilization. The aim of this study was to elucidate genetic diversity of 33 accessions of O. × africanum collected from four Islands of Indonesia along with three accessions of Ocimum basilicum L. Morphological observation was conducted on 37 morphological characters following the International Union for the Protection of New Varieties of Plants descriptor guidelines; subsequently, 13 ISSR primers were employed in molecular analysis. Both morphological and molecular data were analyzed based on simple matching similarity index using UPGMA method. Morphologically, O. × africanum and O. basilicum were clearly separated at the similarity index of 0.52, and among two species were divided into two groups according to two either character. ISSR analysis using 13 ISSR primers produced 111 DNA bands, and 108 of them (97.29%) were polymorphic. Cluster analysis based on ISSR data could not explicitly separate O. × africanum and O. basilicum accessions. Besides, Ocimum accessions collected from the same area did not always cluster into one group.

scholarly journals Genetic divergence in basil cultivars and hybrids

2019 ◽  
Vol 37 (2) ◽  
pp. 180-187
Author(s):  
Rodrigo P Alves ◽  
Ana Veruska C Silva ◽  
Camila S Almeida-Pereira ◽  
Tatiana S Costa ◽  
Sheila V Alvares-Carvalho ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Variability ◽  
Polymorphic Information Content ◽  
Dna Amplification ◽  
Issr Markers ◽  
Economic Importance ◽  
Dissimilarity Index ◽  
The World ◽  
Issr Molecular Markers

ABSTRACT Basil is an aromatic herb that stands out for its economic importance. It is consumed in natura and used to obtain essential oil. The cultivation of this species in several regions of the world has allowed variations by natural crosses and euploidy, leading to the wide genetic variability found nowadays. Considering the importance of this species, we aimed to analyze the genetic diversity of 27 basil genotypes using ISSR molecular markers. Fourteen primers were employed for DNA amplification, resulting in 86% polymorphism. Based on the Jaccard’s dissimilarity index, the highest index (0.80) was observed between the individuals BAS001 and BAS012, while the lowest index (0.18) was detected between the genotypes BAS014 and BAS015. The genetic similarity among individuals was calculated, forming four distinct clusters. Most individuals (40.7%) were allocated in cluster I. The polymorphic information content (PIC) (0.89) indicated considerable levels of genetic diversity among genotypes. In this sense, the ISSR markers were efficient in the detection of polymorphisms between the accessions, suggesting the genetic variability of the collection. This result demonstrates the importance of the use of molecular markers and the advantages that this information provides to the breeding of the species.

scholarly journals A Polyphasic Approach to Compare the Genomic Profiles of Aflatoxigenic and Non-Aflatoxigenic Isolates of Aspergillus Section Flavi

Toxins ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 56
Author(s):  
Asmaa Abbas ◽  
Taha Hussien ◽  
Tapani Yli-Mattila
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Issr Markers ◽  
The Philippines ◽  
Polyphasic Approach ◽  
Group Method ◽  
Aspergillus Section Flavi ◽  
Aspergillus Section ◽  
Issr Primers

Aflatoxins (AF) are highly toxic compounds produced by Aspergillus section Flavi. They spoil food crops and present a serious global health hazard to humans and livestock. The aim of this study was to examine the phylogenetic relationships among aflatoxigenic and non-aflatoxigenic Aspergillus isolates. A polyphasic approach combining phylogenetic, sequence, and toxin analyses was applied to 40 Aspergillus section Flavi isolates collected from eight countries around the world (USA, Philippines, Egypt, India, Australia, Indonesia, China, and Uganda). This allows one to pinpoint the key genomic features that distinguish AF producing and non-producing isolates. Based on molecular identification, 32 (80%) were identified as A. flavus, three (7.5%) as A. parasiticus, three (7.5%) as A. nomius and one (2.5%) as A. tamarii. Toxin analysis showed that 22 (55%) Aspergillus isolates were aflatoxigenic. The majority of the toxic isolates (62.5%) originated from Egypt. The highest aflatoxin production potential was observed in an A. nomius isolate which is originally isolated from the Philippines. DNA-based molecular markers such as random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) were used to evaluate the genetic diversity and phylogenetic relationships among these 40 Aspergillus isolates, which were originally selected from 80 isolates. The percentage of polymorphic bands in three RAPD and three ISSR primers was 81.9% and 79.37%, respectively. Analysis of molecular variance showed significant diversity within the populations, 92% for RAPD and 85% for ISSR primers. The average of Polymorphism Information Content (PIC), Marker Index (MI), Nei’s gene diversity (H) and Shannon’s diversity index (I) in ISSR markers are higher than those in RAPD markers. Based on banding patterns and gene diversities values, we observed that the ISSR-PCR provides clearer data and is more successful in genetic diversity analyses than RAPD-PCR. Dendrograms generated from UPGMA (Unweighted Pair Group Method with Arithmetic Mean) cluster analyses for RAPD and ISSR markers were related to the geographic origin.

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