scholarly journals iPBS polymorphism of rare relict and endangered Allium species growing on the territory of Kazakhstan Altai

2020 ◽  
Vol 200 (9) ◽  
pp. 63-73
Author(s):  
Olesya Rayzer ◽  
Oksana Hapilina
Keyword(s):  
Genetic Diversity ◽  
Molecular Genetic ◽  
Natural Populations ◽  
Dna Amplification ◽  
Practical Significance ◽  
Primer Binding Site ◽  
Natural Habitats ◽  
Allium Species ◽  
Different Populations ◽  
High Level

Abstract. The purpose of the study. The estimation of genetic polymorphism of Kazakhstan populations of rare relict and endemic Allium species. The novelty of the research is the use of the modern molecular genetic iPBS (Inter- Primer Binding Site Polymorphism) method of DNA amplification to assess the genetic diversity of different populations of Allium sp., collected in their natural habitats in the Kazakhstan Altai. Methods. Samples of medicinal relict and endangered species A. ledebourianum, A. altaicum, A. microdiction were collected in the places of their natural growth in the territory of the Kazakhstan Altai. DNA was isolated from 3–5 day sterile seedlings using lysis STAB buffer with RNaseA. PBS primers were used to assess the genetic diversity of different populations of Allium spp. The amplification results obtained using different PBS primers were evaluated in the GenAlex 6.5 macro program for Excel. Results. The polymorphism of 16 genotypes of the rare relict and endangered Allium sp. was analyzed using 7 PBS primers. Clearly distinguishable amplicons were obtained, the number of which varied depending on the primer used. The dendrogram, based on UPGMA analysis, grouped the studied genotypes into 2 main clusters, one of which included samples from the A. altaicum population, and the second cluster included samples from the A. ledebourianum population. A. microdiction represented by one sample did not enter any cluster, and formed a basal branch in the dendrogram. The results of the study have revealed a high degree of iPBS polymorphism and genetic diversity in rare relict and endangered Allium sp. Practical significance. The use of the molecular genetic iPBS method allows to identify a high level of polymorphism, which can serve as a basis for the identification of various genotypes of the Allium sp., which will significantly supplement traditional preservation methods of natural populations of this genus.

scholarly journals Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic Species Allium ledebourianum Schult.

BioTech ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 23
Author(s):  
Oxana Khapilina ◽  
Ainur Turzhanova ◽  
Alevtina Danilova ◽  
Asem Tumenbayeva ◽  
Vladislav Shevtsov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Endemic Species ◽  
Biological Diversity ◽  
Natural Populations ◽  
Subsequent Development ◽  
Dna Profiling ◽  
Primer Binding Site ◽  
Anthropogenic Factors ◽  
Habitat Specificity ◽  
Interspersed Repeats

Endemic species are especially vulnerable to biodiversity loss caused by isolation or habitat specificity, small population size, and anthropogenic factors. Endemic species biodiversity analysis has a critically important global value for the development of conservation strategies. The rare onion Allium ledebourianum is a narrow-lined endemic species, with natural populations located in the extreme climatic conditions of the Kazakh Altai. A. ledebourianum populations are decreasing everywhere due to anthropogenic impact, and therefore, this species requires preservation and protection. Conservation of this rare species is associated with monitoring studies to investigate the genetic diversity of natural populations. Fundamental components of eukaryote genome include multiple classes of interspersed repeats. Various PCR-based DNA fingerprinting methods are used to detect chromosomal changes related to recombination processes of these interspersed elements. These methods are based on interspersed repeat sequences and are an effective approach for assessing the biological diversity of plants and their variability. We applied DNA profiling approaches based on conservative sequences of interspersed repeats to assess the genetic diversity of natural A. ledebourianum populations located in the territory of Kazakhstan Altai. The analysis of natural A. ledebourianum populations, carried out using the DNA profiling approach, allowed the effective differentiation of the populations and assessment of their genetic diversity. We used conservative sequences of tRNA primer binding sites (PBS) of the long-terminal repeat (LTR) retrotransposons as PCR primers. Amplification using the three most effective PBS primers generated 628 PCR amplicons, with an average of 209 amplicons. The average polymorphism level varied from 34% to 40% for all studied samples. Resolution analysis of the PBS primers showed all of them to have high or medium polymorphism levels, which varied from 0.763 to 0.965. Results of the molecular analysis of variance showed that the general biodiversity of A. ledebourianum populations is due to interpopulation (67%) and intrapopulation (33%) differences. The revealed genetic diversity was higher in the most distant population of A. ledebourianum LD64, located on the Sarymsakty ridge of Southern Altai. This is the first genetic diversity study of the endemic species A. ledebourianum using DNA profiling approaches. This work allowed us to collect new genetic data on the structure of A. ledebourianum populations in the Altai for subsequent development of preservation strategies to enhance the reproduction of this relict species. The results will be useful for the conservation and exploitation of this species, serving as the basis for further studies of its evolution and ecology.

scholarly journals Genetic diversity in Brazilian tall coconut populations by microsatellite markers

2013 ◽  
Vol 13 (4) ◽  
pp. 356-362 ◽  
Author(s):  
Francisco Elias Ribeiro ◽  
Luc Baudouin ◽  
Patricia Lebrun ◽  
Lázaro José Chaves ◽  
Claudio Brondani ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Cape Verde ◽  
Coconut Palm ◽  
Different Populations ◽  
The Mean ◽  
High Level ◽  
Brazilian Populations

The tall coconut palm was introduced in Brazil in 1553, originating from the island of Cape Verde. The aim of the present study was to evaluate the genetic diversity of ten populations of Brazilian tall coconut by 13 microsatellite markers. Samples were collected from 195 individuals of 10 different populations. A total of 68 alleles were detected, with an average of 5.23 alleles per locus. The mean expected and observed heterozygosity value was 0.459 and 0.443, respectively. The number of alleles per population ranged from 36 to 48, with a mean of 40.9 alleles. We observed the formation of two groups, the first formed by the populations of Baía Formosa, Georgino Avelino and São José do Mipibu, and the second by the populations of Japoatã, Pacatuba and Praia do Forte. These results reveal a high level of genetic diversity in the Brazilian populations.

scholarly journals Chloroplast microsatellites reveal genetic diversity and population structure in natural populations of Himalayan Cedar (Cedrus deodara (Roxb.) G. Don) in India

2020 ◽  
Vol 69 (1) ◽  
pp. 86-93
Author(s):  
H. S. Ginwal ◽  
Rajesh Sharma ◽  
Priti Chauhan ◽  
Kirti Chamling Rai ◽  
Santan Barthwal
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Natural Populations ◽  
Conservation Strategies ◽  
Restricted Gene Flow ◽  
Chloroplast Microsatellites ◽  
Timber Species ◽  
Western Himalayas ◽  
Cedrus Deodara ◽  
High Level

AbstractHimalayan cedar (Cedrus deodara) is one of the most important temperate timber species of Western Himalayas and is considered to be among the endangered conifer species in the region. Knowledge of genetic diversity and population structure will help guide gene conservation strategies for this species. Ten polymorphic chloroplast microsatellites (cpSSR) were used to study genetic diversity and population structure in twenty one natural populations of C. deodara throughout its entire distribution range in Western Himalayas. When alleles at each of the 10 loci were jointly analysed, 254 different haplotypes were identified among 1050 individuals. The cpSSRs indicate that C. deodara forests maintain a moderately high level of genetic diversity (mean h = 0.79 ). AMOVA analysis showed that most of the diversity in C. deodara occurs within populations. Bayesian analysis for population structure (BAPS) revealed spatial structuration of the variation (22 % of the total variation) and substructuring captured nineteen genetic clusters in the entire divisions of the populations. Most of the populations were clustered independently with minor admixtures. The distribution of genetic diversity and sub-structuring of C. deodara may be due to restricted gene flow due to geographic isolation, genetic drift, and natural selection. These findings indicated existence of genetically distinct and different high diversity and low diversity clusters, which are potential groups of populations that require attention for their conservation and management. The results are interpreted in context of future conservation plans for C. deodara.

scholarly journals Genetic Diversity and Population Structure Revealed by SSR Markers on Endemic Species Osmanthus serrulatus Rehder from Southwestern Sichuan Basin, China

Forests ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1365
Author(s):  
Lin Chen ◽  
Tingting Pan ◽  
Huirong Qian ◽  
Min Zhang ◽  
Guodong Yang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Sichuan Basin ◽  
Polymorphic Information Content ◽  
Population Decline ◽  
Natural Populations ◽  
Genetic Population ◽  
Endangered Status ◽  
High Level

Osmanthus serrulatus Rehder (Oleaceae) is an endemic spring-flowering species in China. It is narrowly distributed in the southwestern Sichuan Basin, and is facing the unprecedented threat of extinction due to problems associated with natural regeneration, habitat fragmentation and persistent and serious human interference. Here, the genetic diversity and population structure of 262 individuals from ten natural populations were analyzed using 18 microsatellites (SSR) markers. In total, 465 alleles were detected across 262 individuals, with a high polymorphic information content (PIC = 0.893). A high level of genetic diversity was inferred from the genetic diversity parameters (He = 0.694, I = 1.492 and PPL = 98.33%). AMOVA showed that a 21.55% genetic variation existed among populations and the mean pairwise Fst (0.215) indicated moderate genetic population differentiation. The ten populations were basically divided into three groups, including two obviously independent groups. Our results indicate that multiple factors were responsible for the complicated genetic relationship and endangered status of O. serrulatus. The concentrated distribution seems to be the key factor causing endangerment, and poor regeneration, human-induced habitat loss and fragmentation seem to be the primary factors in the population decline and further genetic diversity loss. These findings will assist in future conservation management and the scientific breeding of O. serrulatus.

Using RAPD-markers in studying molecular genetic polymorphism in the genus Miscanthus species

2019 ◽  
pp. 6-12
Author(s):  
A. Bab'jazh ◽  
O. Cherednychok ◽  
N. Hryhorenko
Keyword(s):  
Genetic Polymorphism ◽  
Molecular Genetic ◽  
Bioenergy Crops ◽  
Genetic Method ◽  
Plant Groups ◽  
Rapd Pcr ◽  
Model Sample ◽  
Different Populations ◽  
The Difference ◽  
High Level

Aim. The study aims to investigate molecular genetic polymorphism in the representatives of different populations and bioenergy crops plant groups of the genus Miscanthus of the collection of the Institute of Bioenergy Crops and Sugar Beet of the NAAS of Ukraine as well as to search and select the molecular markers to differentiate them using RAPD PCR methods. Methods. The studies used the molecular genetic method for detecting polymorphism by analyzing the lengths of amplification fragments and the method of electrophoretic distribution of amplification products in agarose gel. Results. In the course of amplification with 7 RAPD primers, 28 loci were obtained, of which 23 were polymorphic. The polymorphism degree averaged 65 %. The index of polymorphism locus ranged from 0.17 to 0. 56. There were identified six alleles by marker P822 -with sizes ranging from 230 to 613 bp. P820 primer amplified two loci of 311 and 482 bp, three alleles sized from 219 to 530 bp were identified by P816 and P817 markers. The spectra of the amplicons obtained using the above-mentioned primers make it possible to differentiate representatives of the Miscanthus genus of different species, since the difference in the number of loci for each species representative is established. A unique allele with the frequency of 0.35 and the size of 605 bp was obtained using the RAPD2 primer. Conclusions. According to the results it was found that the use of primers P816 and RAPD2 allowed to separate genotypes of M. sacchariflorus, M. gigantheus, M. sinensis. A large proportion of polymorphic loci confirm the population composition of the model sample which resulted in high level of polymorphism. Key words: genus Miscanthus, RAPD primers, PCR, polymorphism, allele frequencies.

scholarly journals Morphological and Isozyme Variation in Natural Populations of the Genus Medicago L. Prospected in Northern Algeria

2015 ◽  
Vol 43 (1) ◽  
pp. 86-95 ◽  
Author(s):  
Imane MEDOUKALI ◽  
Ines BELLIL ◽  
Douadi KHELIFI
Keyword(s):  
Genetic Diversity ◽  
Natural Populations ◽  
Morphological Characteristics ◽  
Genetic Distances ◽  
Glutamate Oxaloacetate Transaminase ◽  
High Genetic Diversity ◽  
Isozyme Markers ◽  
Northern Algeria ◽  
Isozyme Variability ◽  
High Level

As part of the evaluation and enhancement of genetic resources, morphological and isozyme variability within and among 169 accessions, representing 14 species of the genus Medicago L. collected in northern Algeria, was assessed using twelve quantitative traits and two enzymatic systems. Phenotype frequencies were scored in six enzyme zones to determine isozyme variability within and among populations. The data analysis resolved a high level of genetic diversity. Ten morphometric characteristics contributed to the discrimination of the species. The relationship between the collection site environment and phenotypic characteristics was also studied. Esterase (EST) enzyme system was more polymorphic than glutamate oxaloacetate transaminase (GOT) system. Were scored 2 zones with 10 bands and 21 phenotypes for GOT (glutamate oxaloacetate transaminase) and 4 zones with 22 bands and 71 phenotypes for EST (esterase) Polymorphism index and Jaccard’s genetic distances revealed the existence of a high genetic diversity within and among the studied populations. The annual species M. polymorpha presented an intraspecific polymorphism index of 0.57, which was higher than all other species indices. Clustering of the species based on isozyme markers was in agreement with taxonomic criteria and showed no significant correlation with morphological characteristics. Conservation programs should take into account the level of genetic diversity within and between populations revealed by isozyme markers.

Simple Sequence Repeat (SSR) Polymorphisms and Population Genetics in Sichuan Wild Rhesus Macaques

2011 ◽  
Vol 343-344 ◽  
pp. 690-697
Author(s):  
Di Yan Li ◽  
Yong Fang Yao ◽  
Xiao Feng Huang ◽  
An Chun Cheng ◽  
Huai Liang Xu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Polymorphic Information Content ◽  
Rhesus Macaques ◽  
Genetic Management ◽  
Future Studies ◽  
Ssr Loci ◽  
Different Populations ◽  
Polymerase Chain ◽  
High Level ◽  
Simple Sequence

Cross-species amplification of twenty-five SSR loci from the DNA of five rhesus macaques of diverse regional origins was conducted using human primers for the polymerase chain reaction (PCR). Seven of these primer pairs, which consistently and unambiguously amplified polymorphic fragments from these five samples, were also used to amplify SSR loci for 111 Sichuan wild rhesus macaques of five different populations. The analysed microsatellite markers produced 109 alleles, varied from 4 to 16 alleles each locus. The number of alleles per population ranged from 6.79 to 11.38. Polymorphic information content showed that all seven loci were highly informative (mean = 0.9017±0.0166, >0.5). The average observed heterozygosity was less than the expected (mean = 0.6795 and mean = 0.8559, respectively). Genetic differentiation among the populations was considerably low with the overall and pairwise FST values (mean = 0.0375), and showed fairly low level of inbreeding (indicated by a mean FIS value of 0. 0.1991). Maintaining genetic diversity is a major issue in conservation biology. In comparison to other captive Macaca mulatta studies, these wild rhesus macaque populations showed a relatively high level of genetic diversity, and there was low gene flow among these populations. Careful genetic management is important for maintaining genetic variability levels. None of the seven informative loci are linked which screened in this study can be applied in future studies on population and conservation genetics of natural primate populations.

Genetic diversity of arctic bramble (Rubus arcticus L. subsp. arcticus) as measured by amplified fragment length polymorphism

2003 ◽  
Vol 81 (8) ◽  
pp. 805-813 ◽  
Author(s):  
Hannele Lindqvist-Kreuze ◽  
Hilkka Koponen ◽  
Jari P.T Valkonen
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Fragment Length ◽  
Natural Habitat ◽  
Genotypic Variation ◽  
Natural Populations ◽  
Shannon Index ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
High Level

The levels of genotypic and genetic variation were estimated in six natural populations of arctic bramble (Rubus arcticus L. subsp. arcticus) in Finland. Using three primer combinations, a total of 117 amplified fragment length polymorphisms (AFLP) were found. The results were highly reproducible and allowed identification of 78 genets among the 122 plants of arctic bramble studied. Genotypic variation measured as Simpson index (D) was high in all populations, ranging from 0.72 to 0.94. Also, the level of genetic variation measured as Shannon index was relatively high in all populations, ranging from 0.19 to 0.32 (average 0.26). The high levels of genetic diversity indicate that sexual reproduction has played a significant role in these populations. The hierarchical analysis of molecular variance (AMOVA) partitioned 48% of the genetic variation among populations, suggesting a high level of population differentiation and a low level of interpopulation gene flow. Genetic diversity among ten currently grown cultivars of arctic bramble and hybrid arctic bramble (R. arcticus subsp. arcticus × R. arcticus subsp. stellatus) was large, and the subspecies were clearly distinguished from each other based on the AFLP marker data.Key words: AFLP, AMOVA, population, natural habitat, Rubus arcticus subsp. arcticus, Rubus arcticus subsp. stellatus.

scholarly journals Optimization of RAPD-PCR conditions for the study of genetic diversity in Nepal’s Swertia chirayita (Roxb. Ex Fleming) H. Karst

2011 ◽  
Vol 6 (8) ◽  
pp. 35-40
Author(s):  
Sangita Shrestha ◽  
Jaishree Sijapati ◽  
Neesha Rana ◽  
Diwa Malla ◽  
Prabha Regmi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Polymerase Chain Reaction ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Molecular Diagnostic ◽  
Chain Reaction ◽  
Natural Habitats ◽  
Molecular Genetic Diversity ◽  
Rapd Pcr ◽  
Polymerase Chain

Of the 30 species (including five varieties) of the genus Swertia in Nepal, nine have been reported to possess medicinal properties. Among these, S. chirayita is the most valuable species, with high demand in domestic and international markets. Nepal’s S. chirayita and related species are being recklessly exploited for commercial purposes. Two problems that have emerged with this lucrative market are (a) adulteration and fraudulent labeling of S. chirayita, and (b) depletion of S. chirayita and allied species from their natural habitats. To address the problem of adulteration and conservation, we studied molecular genetic diversity in S. chirayita populations and developed a molecular diagnostic tool for the purposes of authentication. We studied intra-specific genetic diversity in S. chirayita using Polymerase Chain Reaction (PCR)-based Random Amplified Polymorphic DNA (RAPD) technique. As a preliminary step, we identified optimal RAPD-PCR reaction and cycling conditions by varying PCR reaction parameters such as concentration of template DNA, MgCl2, dNTPs, primer, Taq DNA polymerase and RAPD-PCR programs. The optimized PCR reaction and cycling conditions were then used in subsequent RAPD profiling experiments for the study of genetic diversity within S. chirayita populations from various geographical locations. Genetic diversity characterization of S. chirayita populations at the molecular level would furnish information with significant applications in the conservation and sustainable utilization of S. chirayita and its allied species in Nepal. Key words: Polymerase Chain Reaction, Random Amplified Polymorphic DNA, DNA fingerprinting, genetic diversity DOI: http://dx.doi.org/10.3126/hjs.v6i8.2699 Himalayan Journal of Sciences Vol.6 Issue 8 2010 pp.35-40

scholarly journals High Levels of Outcrossing in a Family Trial of Western Australian Sandalwood (Santalum spicatum)

2007 ◽  
Vol 56 (1-6) ◽  
pp. 222-230 ◽  
Author(s):  
K. Muir ◽  
M. Byrne ◽  
E. Barbour ◽  
M. C. Cox ◽  
J. E. D. Fox
Keyword(s):  
Genetic Diversity ◽  
Mating System ◽  
Natural Populations ◽  
Seed Orchard ◽  
Seed Crop ◽  
The Mean ◽  
Santalum Spicatum ◽  
High Level ◽  
Western Australian ◽  
Seed Collections

Abstract The mating system of Western Australian sandalwood (Santalum spicatum) was investigated in seed collections from a family trial. The mean outcrossing rate was high (95.2%) although there was variation among families and one family showed particularly low outcrossing, high bi-parental inbreeding and high correlated paternity. Variation in flowering time between this family and others in the trial was the most likely cause of the high inbreeding and low number of fathers contributing to the seed crop in trees from this family. The high level of outcrossing in the rest of the families indicated that S. spicatum has a preferentially outcrossed mating system, but that it is capable of selfing when conditions are unsuitable for outcrossing. The seedling progeny showed no influence of inbreeding on seedling height at 4 months. Analysis of genetic diversity revealed high levels of genetic diversity have been captured in the seed crop from the trial, and this diversity is comparable to that identified in a previous study of natural populations from throughout the range of the species. These results indicated that production of seed through seed orchards will be a successful means of deployment of breeding gains in the species, however it is essential to ensure overlap in flowering times among different families planted in a seed orchard.

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