Microsatellite analysis of genetic diversity in four populations of Populus tremuloides in Quebec

2003 ◽  
Vol 81 (4) ◽  
pp. 360-367 ◽  
Author(s):  
Janet Wyman ◽  
Anne Bruneau ◽  
M -Francine Tremblay
Keyword(s):  
Genetic Diversity ◽  
Populus Tremuloides ◽  
Gene Diversity ◽  
Morphological Characteristics ◽  
Dna Fingerprint ◽  
Morphological Identification ◽  
Infinite Allele Model ◽  
Clone Size ◽  
Stepwise Mutation ◽  
Individual Potential

To determine overall genetic variability in aspen (Populus tremuloides Michx.) along the clay belt of northwestern Quebec, four populations were sampled at the transition zone between mixed-wood and conifer-dominated forests using a hierarchical strategy. Our objectives were (i) to estimate gene diversity among and within populations using microsatellite markers and (ii) to examine whether clonal structuring in aspen could be detected. For each population, three stands at least 1 km apart were sampled. Within each stand, five putative clones were sampled with a distance of 50 m between each clone. To examine potential genetic diversity within clones, for three of the putative clones sampled per stand, the three trees closest to this individual (potential ramets) were also sampled. All samples were analysed at four microsatellite loci. Measures of genetic variation all indicated that most of the variation occurred within rather than among the populations. Rst, based on a stepwise mutation model, was 0.0409, slightly higher than Fst, which was based on infinite allele model (0.0323). Within each stand, DNA fingerprint of five putative clones allowed the differentiation of genetically distinct individuals within these putative clones, and from 1.62 to 2.2 times more genetically distinct individuals were identified than by morphological identification. In the present study there was no correlation between the mean distance of the potential ramet to the central trunk (potential ramets were often within 2–3 m of the central trunk) and the possibility of the central trunk and ramet sharing the same genotype. The number of unique genotypes for the three putative clones sampled per stand varied from 11 genotypes per 15 samples to 14 per 15 samples. Consequently, it was not possible to identify clones by either distance from a given central trunk or morphological characteristics. Thus, after stand disturbance, suckers from different genotypes are likely to be closely mixed.Key words: genetic diversity, Populus tremuloides, microsatellites, clone size.

scholarly journals Genetic diversity of long-established populations of Elaeis guineensis jacquin (Arecaceae)

2019 ◽  
Vol 41 (4) ◽  
Author(s):  
Kyvia Pontes Teixeira das Chagas ◽  
Ageu da Silva Monteiro Freire ◽  
Luciana Gomes Pinheiro ◽  
Cristiane Gouvêa Fajardo ◽  
Fábio de Almeida Vieira
Keyword(s):  
Genetic Diversity ◽  
Elaeis Guineensis ◽  
Sustainable Use ◽  
Diversity Indices ◽  
Ex Situ ◽  
Effective Population ◽  
Infinite Allele Model ◽  
Population Decrease ◽  
Stepwise Mutation ◽  
Conservation Projects

Abstract This study aimed to estimate the genetic diversity of three Elaeis guineensis populations in Rio Grande do Norte state, as well as to verify the decreases in effective population size. The population with the highest polymorphism was MAT (Mata) with+ 57 loci (72%), followed by RIA (Riacho) with 54 loci (68%) and HOR (Horta) with 34 loci (43.03%). The RIA population was shown to be the most genetically diverse, with Nei (h = 0.28) and Shannon (I = 0.41) diversity indices. There was high genetic differentiation among populations (AMOVA, analysis of molecular variance = 42%), which was separated into three distinct genetic groups according to a Bayesian analysis. There was a significant population decrease (P < 0.05) for the HOR population in the IAM (infinite allele model) and SMM (stepwise mutation model), and for the RIA population in the IAM. The data obtained in this study may support ex-situ conservation projects for Elaeis guineensis, contributing to the selection of genotypes and their sustainable use.

scholarly journals Genetic Diversity Within and Among Populations of Roseroot (Rhodiola rosea L.) Based on Molecular Markers

2012 ◽  
Vol 40 (2) ◽  
pp. 266 ◽  
Author(s):  
Zsuzsanna GYORGY ◽  
Maria SZABO ◽  
Dmitry BACHAROV ◽  
Andrzej PEDRYC
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Geographic Origin ◽  
Morphological Characteristics ◽  
Population Level ◽  
Shannon Index ◽  
Rhodiola Rosea ◽  
Pharmacologically Active ◽  
Cool Climate

Rhodiola rosea L. is a perennial adaptogenic medicinal plant found in cool climate of the northern hemisphere. The species is very diverse both in terms of morphological characteristics and in the content of the pharmacologically active substances. The genetic diversity of four geographically distant roseroot populations was studied with ISSR and SSR markers. Using 7 ISSR primers 64 DNA fragments were generated and 85,94% of those were found to be polymorphic, indicating high genetic variability at the species level (gene diversity = 0.33, Shannon index = 0.48). Lower level of diversity was detected at the population level (Shannon-index ranged from 0.2173 to 0.2696). Only four out of the eight SSR markers used were informative during this study. The primer pairs for these four SSR markers produced 25 fragments with an average of 6.25 putative alleles per locus. Observed heterozygosity ranged from 0.4 to 1.0, whereas expected heterozygosity ranged from 0.47 to 0.84. Cluster analysis based on both markers revealed the same groups, individuals clustered according to their geographic origin. The Southern-Uralian population was the most genetically isolated. ITS analysis was used for the determination whether these Southern-Uralian individuals belong to the same species.

scholarly journals The Use of DNA Microsatellite Markers for Genetic Diversity Identifi cation of Soybean (Glycine max (L) Meriil.) as a Supplementary Method in Reference Collections Management

2016 ◽  
Vol 19 (2) ◽  
pp. 136 ◽  
Author(s):  
Nina Agusti Widaningsih ◽  
Edi Purwanto ◽  
N. Nandariyah ◽  
R. Reflinur
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Morphological Characteristics ◽  
Morphological Characters ◽  
Practical Applications ◽  
Plant Collection ◽  
New Varieties ◽  
Variety Protection ◽  
Dna Microsatellite ◽  
Biology Laboratory

Large number of new soybean varieties are mostly derived from crosses of elite genotypes resulted ina narrowing of both the genetic diversity and the phylogenetic relationship between soybean varieties. Thus,discrimination among soybean varieties is becoming more diffi cult, especially when morphological traits wereapplied. In Plant Variety Protection (PVP) system, new varieties of soybeans including granted PVP right, localand breeding varieties registered in PVP offi ce were frequently increased, implicate on increasingly the numberof soybean varieties collections. To assist the management of varieties collections, a standard fi ngerprinting datais further needed. In comparison to the management of plant collection in the fi eld, molecular marker systemswhich are rapid, reliable, informative and relatively simple are continually sought for practical applications ingermplasm conservation, management and enhancement. This study aimed to identify the genetic diversity andphylogenetic relationship of soybean varieties that have earned PVP Right as well as local varieties and breedingvarieties registered in the PVP offi ce using microsatellite or simple sequence repeats (SSR) markers.This study was conducted in Molecular Biology laboratory, Indonesian Center for Agricultural Biotechnologyand Genetic Resources Research and Development (ICABIOGRAD) Bogor, from February to May 2013. The datawere analyzed using the genetic analysis package NTSYSpc 2.02i and PowerMarker V3.25. The result showed arelatively narrow genetic diversity among 45 varieties of soybean analyzed in present study which were indicatedby the small number of genotypes and total number of alleles (NA), and the low value of gene diversity and PICvalues (<0.75). Cluster analysis showed that the grouping varieties are not related to morphological characters butrelated to phylogeny relationship between varieties. Despite the group of varieties were not clustered in accordancewith morphological characteristics, SSR marker can be a powerful tool for discriminating varieties, so that it couldbe useful for initial varieties identity in conjunction with genetic diversity analysis.

scholarly journals Assessing the Genetic Diversity of Chrysanthemum Cultivars with Microsatellites

2013 ◽  
Vol 138 (6) ◽  
pp. 479-486 ◽  
Author(s):  
Yuan Zhang ◽  
Chen Wang ◽  
HongZheng Ma ◽  
SiLan Dai
Keyword(s):  
Genetic Diversity ◽  
Magnetic Beads ◽  
Genomic Library ◽  
Gene Diversity ◽  
Sustainable Use ◽  
Morphological Characteristics ◽  
Breeding Programs ◽  
Genetic Studies ◽  
Mean Values ◽  
Cultivar Classification

The morphological characteristics of chrysanthemum (Chrysanthemum ×morifolium) are rich in variation. However, as a result of the aneuploid polyploidy of the chrysanthemum genome and the lack of proper tools, the genomic information of this crop is limited. Development of microsatellite markers has been an increasing trend in crop genetic studies because of the applicability of these markers in breeding programs. In this study, we reported the development of a simple sequence repeat in chrysanthemums using a magnetic beads enrichment method. An enriched genomic library with AC and GT microsatellite motifs was constructed, and 53 positive clones were detected by a colony polymerase chain reaction (PCR) technique. Of these clones, 35 showed high-quality sequences, and 35 primer pairs were designed accordingly. Twenty-six (74.29%) of the 35 primer pairs revealed polymorphisms on a set of 40 chrysanthemum cultivars. There were 172 alleles amplified over 26 loci with an average of 6.615 alleles per locus. The mean values of gene diversity corrected for the sample size and the inbreeding coefficient were 0.609 and 0.119 over 26 loci, respectively, which indicated that the majority of the microsatellite loci is highly informative. Cluster analysis based on 26 polymorphic loci demonstrated that the selected cultivars were clustered according to geographical origin. This study shows the isolation efficiency of the magnetic beads technique; the abundance of microsatellites in chrysanthemum; and the potential application for the cultivar classification, the studies on genetic diversity, and molecular breeding of chrysanthemums, which is beneficial to promoting the conservation and sustainable use of this crop.

scholarly journals Morphological characterization and Genetic diversity analysis of a Tunisian durum wheat (Triticum turgidum var. durum) collection

2020 ◽  
Author(s):  
Maroua Ouaja ◽  
Bochra Amina Bahri ◽  
Lamia Aouini ◽  
Sahbi Ferjaoui ◽  
Maher Medini ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Durum Wheat ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Morphological Characterization ◽  
Genetic Variations ◽  
Ex Situ ◽  
Morphological Identification ◽  
The South ◽  
Population Structure Analysis

Abstract Background: Tunisia is a center of genetic diversity of durum wheat and has a large number of abandoned old local landraces. An accurate investigation and characterization of the morphological and genetic features of these landraces would allow their rehabilitation and use for practical and beneficial purposes. In this context, a collection of 304 local accessions of durum wheat, collected from five regions and three climatic zones of central and southern Tunisia, was studied. Results: Morphological characterization was carried out using 12 spike-related traits and rendered a mean Shannon-Weaver Index (H') of 0.80 indicating the presence of a high level of polymorphism among accessions. Based on these traits 11 local landraces, namely Mahmoudi, Azizi, Jneh Khotifa, Mekki, Biskri, Taganrog, Biada, Badri, Richi, Roussia and Souri were identified. Spike length (H’=0.98) and shape (H’=0.86) with grains size (H’=0.94), form (H’=0.87) and color (H’=0.86) were the most polymorphic morphological traits. The genetic diversity was assessed using 10 SSR markers, with a polymorphic information content (PIC) of 0.69. Levels of genetic diversity were generally high, with a Shannon's Information Index (I) of 0.62 and a gene diversity (He) of 0.35. In addition, population structure analysis distinguished 11 genetic subpopulations significantly correlated with the morphological identification. Analysis of molecular variance (AMOVA) showed high genetic variations within regions (81%) and within wheat subpopulations (41%) reflecting a considerable amount of admixture between landraces. The moderate (19%) and high (59%) genetic variations among regions and among wheat subpopulations observed highlighted farmers selection practices . Furthermore, Mahmoudi landrace showed spike densities significantly different between the center to the south of Tunisia; notably loose spikes with open glumes in the south and compact ones in the center, which may represent an adaptation form for tolerance to high temperature. Conclusion: Overall, this study underlined the genetic richness of local resources for better in situ or ex situ conservation and for their subsequent use in plant breeding programs.

scholarly journals A systematic revision of Capparaceae and Cleomaceae in Egypt: an evaluation of the generic delimitations of Capparis and Cleome using ecological and genetic diversity

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Mohamed Abd. S. El zayat ◽  
Mahmoud El Sayd Ali ◽  
Mohamed Hamdy Amar
Keyword(s):  
Genetic Diversity ◽  
Morphological Characteristics ◽  
Systematic Position ◽  
Diversity Analysis ◽  
Polymorphic Markers ◽  
Ecological Distribution ◽  
Specific Group ◽  
Systematic Revision ◽  
Dna Evidence ◽  
The Family

Abstract Background The Capparaceae family is commonly recognized as a caper, while Cleomaceae represents one of small flowering family within the order Brassicales. Earlier, Cleomaceae was included in the family Capparaceae; then, it was moved to a distinct family after DNA evidence. Variation in habits and a bewildering array of floral and fruit forms contributed to making Capparaceae a “trash-basket” family in which many unrelated plants were placed. Indeed, family Capparaceae and Cleomaceae are in clear need of more detailed systematic revision. Results Here, in the present study, the morphological characteristics and the ecological distribution as well as the genetic diversity analysis among the twelve species of both Capparaceae and Cleomaceae have been determined. The genetic analysis has been checked using 15 ISSR, 30 SRAP, and 18 ISTR to assess the systematic knots between the two families. In order to detect the molecular phylogeny, a comparative analysis of the three markers was performed based on the exposure of discriminating capacity, efficiency, and phylogenetic heatmap. Our results indicated that there is a morphological and ecological variation between the two families. Moreover, the molecular analysis confirmed that ISTR followed by SRAP markers has superior discriminating capacity for describing the genetic diversity and is able to simultaneously distinguish many polymorphic markers per reaction. Indeed, both the PCA and HCA data have drawn a successful annotation relationship in Capparaceae and Cleome species to evaluate whether the specific group sort individual or overlap groups. Conclusion The outcomes of the morphological and ecological characterization along with the genetic diversity indicated an insight solution thorny interspecies in Cleome and Gynandropsis genera as a distinct family (Cleomaceae) and the other genera (Capparis, Cadaba, Boscia, and Maerua) as Capparaceae. Finally, we recommended further studies to elucidate the systematic position of Dipterygium glaucum.

scholarly journals Molecular diversity analysis in hexaploid wheat (Triticum aestivum L.) and two Aegilops species (Aegilops crassa and Aegilops cylindrica) using CBDP and SCoT markers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Ghazal Ghobadi ◽  
Alireza Etminan ◽  
Ali Mehras Mehrabi ◽  
Lia Shooshtari
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Crop Improvement ◽  
Wild Relatives ◽  
Resolving Power ◽  
Start Codon ◽  
Aegilops Cylindrica ◽  
Aegilops Crassa

Abstract Background Evaluation of genetic diversity and relationships among crop wild relatives is an important task in crop improvement. The main objective of the current study was to estimate molecular variability within the set of 91 samples from Triticum aestivum, Aegilops cylindrica, and Aegilops crassa species using 30 CAAT box–derived polymorphism (CBDP) and start codon targeted (SCoT) markers. Results Fifteen SCoT and Fifteen CBDP primers produced 262 and 298 fragments which all of them were polymorphic, respectively. The number of polymorphic bands (NPB), polymorphic information content (PIC), resolving power (Rp), and marker index (MI) for SCoT primers ranged from 14 to 23, 0.31 to 0.39, 2.55 to 7.49, and 7.56 to 14.46 with an average of 17.47, 0.34, 10.44, and 5.69, respectively, whereas these values for CBDP primers were 15 to 26, 0.28 to 0.36, 3.82 to 6.94, and 4.74 to 7.96 with a mean of 19.87, 0.31, 5.35, and 6.24, respectively. Based on both marker systems, analysis of molecular variance (AMOVA) indicated that the portion of genetic diversity within species was more than among them. In both analyses, the highest values of the number of observed (Na) and effective alleles (Ne), Nei’s gene diversity (He), and Shannon’s information index (I) were estimated for Ae. cylindrica species. Conclusion The results of cluster analysis and population structure showed that SCoT and CBDP markers grouped all samples based on their genomic constitutions. In conclusion, the used markers are very effective techniques for the evaluation of the genetic diversity in wild relatives of wheat.

scholarly journals Gene diversity explains variation in biological features of insect killing fungus, Beauveria bassiana

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Laila Gasmi ◽  
Sehyeon Baek ◽  
Jong Cheol Kim ◽  
Sihyeon Kim ◽  
Mi Rong Lee ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Beauveria Bassiana ◽  
Gene Diversity ◽  
Dna Photolyase ◽  
Cyclophilin B ◽  
Biological Features ◽  
Number Variation ◽  
Potential Impact ◽  
Chitinase Genes ◽  
Fungus Beauveria Bassiana

AbstractBeauveria bassiana is a species complex whose isolates show considerable natural genetic variability. However, little is known about how this genetic diversity affects the fungus performance. Herein, we characterized the diversity of genes involved in various mechanisms of the infective cycle of 42 isolates that have different growth rates, thermotolerance and virulence. The analysed genes showed general genetic diversity measured as non-synonymous changes (NSC) and copy number variation (CNV), with most of them being subjected to positive episodic diversifying selection. Correlation analyses between NSC or CNV and the isolate virulence, thermotolerance and growth rate revealed that various genes shaped the biological features of the fungus. Lectin-like, mucin signalling, Biotrophy associated and chitinase genes NSCs correlated with the three biological features of B. bassiana. In addition, other genes (i.e. DNA photolyase and cyclophilin B) that had relatively conserved sequences, had variable CNs across the isolates which were correlated with the variability of either virulence or thermotolerance of B. bassiana isolates. The data obtained is important for a better understanding of population structure, ecological and potential impact when isolates are used as mycoinsecticides and can justify industrialization of new isolates.

Utilisation of wild Cicer in chickpea improvement — progress, constraints, and prospects

2003 ◽  
Vol 54 (5) ◽  
pp. 429 ◽  
Author(s):  
J. S. Croser ◽  
F. Ahmad ◽  
H. J. Clarke ◽  
K. H. M. Siddique
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Morphological Characteristics ◽  
Biotic Stresses ◽  
Yield And Quality ◽  
Cicer Species ◽  
Cultivated Species ◽  
Wild Cicer Species ◽  
Improvement Programs ◽  
Primary Focus

Efforts to improve the yield and quality of cultivated chickpea (Cicer arietinum L.) are constrained by a low level of intraspecific genetic diversity. Increased genetic diversity can be achieved via the hybridisation of the cultivated species with the unimproved 'wild' relatives from within the 43 species of the Cicer genus. To date, the 8 species sharing an annual growth habit and chromosome number with C. arietinum have been the primary focus of screening and introgression efforts. Screening of these species has uncovered morphological characteristics and resistance to a number of abiotic and biotic stresses that are of potential value to chickpea improvement programs. Detailed analysis of protein and DNA, karyotyping, and crossability studies have begun to elucidate the relationships between the annual Cicer species. In comparison, perennial species have received little attention due to difficulties in collection, propagation, and evaluation. This review discusses the progress towards an understanding of genetic relationships between the Cicer species, and the introgression of genes from the wild Cicer species into the cultivated species.

scholarly journals Genetic Diversity of Common Bean Genotypes as Revealed By Seed Storage Proteins and Some Agronomic Traits

2014 ◽  
Vol 67 (1) ◽  
pp. 125-137 ◽  
Author(s):  
Akbar Marzooghian ◽  
Mohammad Moghaddam ◽  
Mostafa Valizadeh ◽  
Mohammad Hasan Kooshki
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Yield Components ◽  
Storage Proteins ◽  
Agronomic Traits ◽  
Morphological Characteristics ◽  
Seed Proteins ◽  
Seed Storage ◽  
Seed Storage Proteins ◽  
Seed Morphology

AbstractEvaluation of the genetic diversity present within species is essential for conservation, management and utilization of the genetic resources. The objective of this study was to evaluate genetic variability of 70 common bean genotypes for seed storage proteins, grain morphological characteristics and agronomic traits. Two methods of extracting soluble seed proteins in salt were used.Positive correlations were observed among both seed morphological characters and developmental characters while yield components showed negative correlations with each other. Factor analysis for agronomic and grain morphological traits resulted in three factors were named yield components, seed morphology and phenology, respectively. Most genotypes had lower or medium scores for yield components and phenology factors. Considerable diversity was observed for seed morphology factor among the common bean genotypes.Nei’s diversity coefficient (He= 0.4), effective number of alleles (Ae= 1.69) and number of polymorphic loci (N = 17) indicated larger variation in the extraction method of soluble proteins in low salt (0.2 M NaCl) than high salt (1 M NaCl) condition. Considering that the centers of diversity for common bean are different in seed size, the result of Gst statistics showed that bands with relative mobility of 30, 32, 38 and 40 differentiated two weight groups more than other bands. Furthermore, significant differences were observed between these bands for number of pods per plant and number of seeds per plant.

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