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

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 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.

QTLs Controlling Physiological and Morphological Traits of Barley (Hordeum vulgare L.) Seedlings under Salinity, Drought, and Normal Conditions

“…A wide range of molecular techniques reveal polymorphisms at the DNA level. The molecular markers include simple sequence repeats (SSRs), intersimple sequence repeats (ISSRs), inter-retrotransposon amplified polymorphisms (IRAPs), CAAT box-derived polymorphisms (CAATs), start codon targeted polymorphisms (SCoTs), and inter-primer binding sites (iPBSs) [ 12 , 13 , 14 , 15 ].…”

Development of Retrotransposon-Based Molecular Markers for Characterization of Persea americana (Avocado) Cultivars and Horticultural Races

“…In that work, polymorphism detection and discrimination ability was compared between the retrotransposon-based technique Inverse Sequence Tagged Repeat (ISTR), with SSR and AFLP analysis, concluding that the number of average polymorphic bands obtained by AFLP and ISTR analysis was higher than with SSR [65]. Nevertheless, iPBS has also been used to characterize genetic variation present in several genera of agronomic interest, such as Prunus [66], Vitis [67,68], Psidium [69], Phoenix [70], Nicotiana [71], Solanum [72], Allium [73,74], Gnetum [75] or Musa [76]. The clear advantage of the iPBS strategy is that prior knowledge of nucleotide sequences from target species is not required, since a relatively small set of "universal" primers can be used for analysis of any eukaryotic organism [46,49].…”

Retrotransposons: How the continuous evolutionary front shapes plant genomes for response to heat stress

“…The genetic maps generated with several retrotransposonbased markers such as iPBS (inter-Priming Binding Site) (Kalendar et al, 2010;Doungous et al, 2020;Khapilina et al, 2021b) and REMAP (REtrotransposon-Microsatellite Amplified Polymorphism) (Kalendar et al, 1999) exhibited regions of different marker densities, indicating that the distribution of retrotransposons in lentil is non-random and widespread throughout the lentil genome. This may be useful in lentil breeding by marker-assisted selection (Rey-Banos et al, 2017).…”