Molecular-Genetic Methods in Plant Ecology

Дорогина, О. В.; Zhmud, E. V.

doi:10.1134/s1995425520040058

Cited by 5 publications

(3 citation statements)

References 69 publications

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“…Due to the large copy number of LTR retrotransposons and their abundance in eukaryotic genomes, the use of conserved sequences of elements as PCR-based DNA fingerprinting is convenient as an effective method. When compared with other markers, DNA fingerprinting methods based on LTR retrotransposons can be used to assess genetic polymorphism and evolutionary and phylogenetic studies [ 23 , 33 ]. Variations of these markers have been used in humans and in various species of fungi, plants, and animals [ 2 , 10 , 31 , 34 , 35 ].…”

Section: Introductionmentioning

confidence: 99%

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

Хапилина

Turzhanova

Danilova³

et al. 2021

BioTech

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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.

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Section: Introductionmentioning

confidence: 99%

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

Хапилина

Turzhanova

Danilova³

et al. 2021

BioTech

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“…To research polymorphism in populations, DNA marker systems are the most convenient, characterized by significant polymorphism and non-dependent on environment conditions where the plant grows. The most practical and easily reproducible tools include techniques for amplifying genomic DNA with a high intraspecific variability [9]. The method of the intermicrosatellite sequences (ISSR) analysis is used to study the genetic relationship of objects, analysis of taxa genetic diversity and phylogeny, and is most effective to investigate variability within a single species [10].…”

Section: Introductionmentioning

confidence: 99%

Analysis of intraspecific polymorphism ofNitraria sibiricaPall. using the ISSR technique

Khozyaykina

Банаев

2021

BIO Web Conf.

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The analysis of DNA polymorphism of Nitraria sibirica Pall. was carried out at 13 natural populations of the Republic of Altai and Altai Territory using the ISSR technique. Seven effective ISSR primers have been identified to analyze DNA polymorphism in N. sibirica. 99 DNA fragments were yielded at DNA amplification with these primers, 66 of them were polymorphic. The genetic distance Nei (D) between the studied populations of N. sibirica averaged 0.32, at mean 0.09 - within populations. An identification ISSR marker has been revealed, which can be used to study the genetic variability of the genus Nitraria L. (Nitrariaceae) species.

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“…The polymorphism of nucleotide sequences between individual DNA samples is detected by the presence or absence of specific DNA fragments in the spectrum during electrophoresis. The absence of a DNA fragment can be the result of point mutations, insertions, deletions, or inversions in the DNA template sequence (Dorogina and Zhmud, 2020).…”

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confidence: 99%

Genetic State of Pulsatilla Patens (L.) Mill. Coenopopulations Based on DNA Labeling

Beishov¹,

Sultangazina²,

Бейшова³

et al. 2021

OnLine Journal of Biological Sciences

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In the article, the results of studying the gene pools of the Kazakhstan coenopopulations of a rare plant species Pulsatilla patens (L.) Mill. are shown. The biomaterial taken from five coenopopulations located in Northern Kazakhstan has been used as samples. To identify the multilocus DNA polymorphism, the authors have used ISSR (Inter Simple Sequence Repeats, or intermicrosatellite analysis) labeling. The most effective primers have been selected, which provide reproducible results with a length of 17-19 nucleotides. As a result, multiple genomic labeling of five Pulsatilla patens coenopopulations has been performed. The main indicators of genetic diversity (P95 -0.965, HE -0.162, I -0.373 for the total sample), the structure and differentiation of the populations (HT -0.232, HS -0.162, GST -0.3 for the total sample) and the type and state of the gene pools of the studied coenopopulations have been determined. The specificity of the gene pools has been characterized by the number of rare alleles and the Coefficient of Genetic Originality (CGO). The maximum value of CGO has been noted at Pp5 (2.964) and the minimum one -at Pp4 (2.666). The gene pools of the Pp1 and Pp4 coenopopulations have been characterized as typical and gene pools of the Pp2, Pp3 and Pp5 -as specific. Based on the obtained data, tree diagrams have been made that reflect the degree of similarity of the studied coenopopulations as to the ISSR spectra. Identification of the state of the gene pools of rare plant species will allow recommending scientifically based measures for preserving them.

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Molecular-Genetic Methods in Plant Ecology

Cited by 5 publications

References 69 publications

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

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

Analysis of intraspecific polymorphism ofNitraria sibiricaPall. using the ISSR technique

Genetic State of Pulsatilla Patens (L.) Mill. Coenopopulations Based on DNA Labeling

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