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

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Khapilina, O.; Turzhanova, A.; Danilova, A.; Tumenbayeva, A.; Shevtsov, V.; Kotukhov, Y.; Kalendar, R. Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic Species Allium ledebourianum Schult.. BioTech 2021, 10, 23.

Title: Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic Species Allium ledebourianum Schult.
Author: Khapilina, Oxana; Turzhanova, Ainur; Danilova, Alevtina; Tumenbayeva, Asem; Shevtsov, Vladislav; Kotukhov, Yuri; Kalendar, Ruslan
Publisher: Multidisciplinary Digital Publishing Institute
Date: 2021-10-13
URI: http://hdl.handle.net/10138/335593
Abstract: 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 <i>Allium ledebourianum</i> is a narrow-lined endemic species, with natural populations located in the extreme climatic conditions of the Kazakh Altai. <i>A. ledebourianum</i> 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 <i>A. ledebourianum</i> populations located in the territory of Kazakhstan Altai. The analysis of natural <i>A. ledebourianum</i> 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 <i>A. ledebourianum</i> populations is due to interpopulation (67%) and intrapopulation (33%) differences. The revealed genetic diversity was higher in the most distant population of <i>A. ledebourianum</i> LD64, located on the Sarymsakty ridge of Southern Altai. This is the first genetic diversity study of the endemic species <i>A. ledebourianum</i> using DNA profiling approaches. This work allowed us to collect new genetic data on the structure of <i>A. ledebourianum</i> 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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