Genetic analysis of the grapevine genotypes of the Russian Vitis ampelographic collection using iPBS markers

Abstract

Cultivated grapevine (Vitis vinifera L. ssp. sativa D.C.) is one of the oldest agricultural crops, each variety comprising an array of clones obtained by vegetative propagation from a selected vine grown from a single seedling. Most clones within a variety are identical, but some show a different form of accession, giving rise to new divergent phenotypes. Understanding the associations among the genotypes within a variety is crucial to efficient management and effective grapevine improvement. Inter-primer binding-site (iPBS) markers may aid in determining the new clones inside closely related genotypes. Following this idea, iPBS markers were used to assess the genetic variation of 33 grapevine genotypes collected from Russia. We used molecular markers to identify the differences among and within five grapevine clonal populations and analysed the variation, using clustering and statistical approaches. Four of a total of 30 PBS primers were selected, based on amplification efficiency. Polymerase chain reaction (PCR) with PBS primers resulted in a total of 1412 bands ranging from 300 to 6000 bp, with a polymorphism ratio of 44%, ranging from 58 to 75 bands per group. In total, were identified seven private bands in 33 genotypes. Results of molecular variance analysis showed that 40% of the total variation was observed within groups and only 60% between groups. Cluster analysis clearly showed that grapevine genotypes are highly divergent and possess abundant genetic diversities. The iPBS PCR-based genome fingerprinting technology used in this study effectively differentiated genotypes into five grapevine groups and indicated that iPBS markers are useful tools for clonal selection. The number of differences between clones was sufficient to identify them as separate clones of studied varieties containing unique mutations. Our previous phenotypic and phenological studies have confirmed that these genotypes differ from those of maternal plants. This work emphasized the need for a better understanding of the genotypic differences among closely related varieties of grapevine and has implications for the management of its selection processes.

Genetic diversity of Alternaria species associated with black point in wheat grains

“…The main diversity in the iPBS profile arose from Alternaria alternata isolates (160 polymorphic bands out of 198), which was the most abundant species among the isolates (15 out of 25). Notably, the level of detectable polymorphism detected in our study is lower than that reported in similar studies using the iPBS method on both plants (Doungous et al, 2015;Doungous et al, 2020) and other fungi species (Milovanov et al, 2019;Monden, Yamaguchi & Tahara, 2014;Teo et al, 2005;Vukich et al, 2009). The amplified PCR products ranged from 200 to 3000 bp and had on average 10-30 bands per isolate.…”

“…In this regard, the iPBS method developed by Kalendar et al (2010) has advantages for applications in the evaluation of genetic diversity, because it allows direct detection of polymorphism regardless of the eukaryotic species. It is particularly beneficial when detecting genetic diversity among fungi isolates; since it can detect polymorphisms in many anonymous loci across the genome simultaneously, it is a highly effective method for studying clonal variability (Doungous et al, 2020;Kalendar et al, 2010;Milovanov et al, 2019). Moreover, since most of the retrotransposons are often mixed with each other, the PCR process amplifies many products because the primers are designed to target conserved regions of retrovirus and LTR retrotransposon primer binding sites.…”

“…The fact that most retrotransposons are nested, inverted, and truncated allows them to be easily amplified from nearly every organism using inverted PBS primers. Moreover, this method can be used as a universal and high-efficiency tool for direct detection of DNA polymorphism (Doungous et al, 2020;Milovanov et al, 2019). Primers that were developed for amplification of the conserved PBS regions showed their effectiveness in the cloning of LTR retrotransposons (Kalendar et al, 2010), including non-autonomous elements that did not contain protein-coding regions such as TRIM (Terminal Repeat Retrotransposons In Miniature) (Kalendar et al, 2008) and LARD (Large Retrotransposon Derivatives) (Kalendar et al, 2004).…”

DNA profiling and assessment of genetic diversity of relict speciesAllium altaicumPall. on the territory of Altai

“…Primers complementary to interspersed repeats allow amplification of the region between these repeats if the distance between the repeats does not exceed the processivity of the used DNA polymerases (Kalendar et al, 2019). Therefore, this approach, based on PCR between interspersed repeats and mobile genetic elements, can be easily adapted for any eukaryotic species for the rapid detection of molecular genetic polymorphisms even in an agarose gel (Doungous et al, 2019;Hosid et al, 2012;Kalendar, Amenov & Daniyarov, 2018;Kalendar & Schulman, 2013;Milovanov et al, 2019;Turzhanova et al, 2020). Thus, application of PCR methods based on the use of conserved sequences of interspersed repeats and mobile genetic elements allows universal and efficient detection of polymorphisms for almost every eukaryotic species (Kalendar, Amenov & Daniyarov, 2018;Smykal et al, 2009).…”

High-throughput retrotransposon-based genetic diversity of maize germplasm assessment and analysis

“…The stability of retrotransposon integration sites and recombination events allows them to be used as molecular genetic markers in genetic map construction [28][29][30][31][32]. Retrotransposon markers have also been widely used to assess genetic diversity in many species [33][34][35][36][37][38][39]. Given that plant retrotransposons are stressactivated [15,40], their role in generating ecogeographical patterns of genomic diversity is of particular interest.…”