Diversity of Long Terminal Repeat Retrotransposon Genome Distribution in Natural Populations of the Wild Diploid WheatAegilops speltoides

Abstract

The environment can have a decisive influence on the structure of the genome, changing it in a certain direction. Therefore, the genomic distribution of environmentally sensitive transposable elements may vary measurably across a species area. In the present research, we aimed to detect and evaluate the level of LTR retrotransposon intraspecific variability in Aegilops speltoides (2n = 2x = 14), a wild cross-pollinated relative of cultivated wheat. The interretrotransposon amplified polymorphism (IRAP) protocol was applied to detect and evaluate the level of retrotransposon intraspecific variability in Ae. speltoides and closely related species. IRAP analysis revealed significant diversity in TE distribution. Various genotypes from the 13 explored populations significantly differ with respect to the patterns of the four explored LTR retrotransposons (WIS2, Wilma, Daniela, and Fatima). This diversity points to a constant ongoing process of LTR retrotransposon fraction restructuring in populations of Ae. speltoides throughout the species' range and within single populations in time. Maximum changes were recorded in genotypes from small stressed populations. Principal component analysis showed that the dynamics of the Fatima element significantly differ from those of WIS2, Wilma, and Daniela. In terms of relationships between Sitopsis species, IRAP analysis revealed a grouping with Ae. sharonensis and Ae. longissima forming a separate unit, Ae. speltoides appearing as a dispersed group, and Ae. bicornis being in an intermediate position. IRAP display data revealed dynamic changes in LTR retrotransposon fractions in the genome of Ae. speltoides. The process is permanent and population specific, ultimately leading to the separation of small stressed populations from the main group. L ARGE cereal genomes are known to consist of an extraordinary number of transposable elements, in particular, LTR retrotransposons, which are highly dynamic (Bennetzen 1996;Wicker et al. 2003). Recent studies have shown that LTR retrotransposons are often found in different densities or copy numbers among individuals of the same species (Baucom et al. 2009;Belyayev et al. 2010), and "bursts" of transposable elements (TEs) in several species of angiosperms over time have been recorded (Vitte and Panaud 2003;Tsukahara et al. 2009;Belyayev et al. 2010). Although there are several known cases of temporal retroelement copy-number change, the important question of the level of current TE intraspecific variability across the area occupied by a particular species is still unclear, especially for a species whose area is declining or shifting under the influence of climate change. It is possible that populations with enhanced TE activity are more likely to survive as new forms, or even new species, during environmental fluctuations due to the production of an extended number of genomic variants for natural selection (Grant 1981;Raskina et al. 2004a;Belyayev et al. 2010). This is one of the key problems in understanding the mechanisms of sp...

Bursts of transposable elements as an evolutionary driving force

“…Recently, we published the data from our long‐term study of the dynamics of TEs in natural populations of Ae. speltoides (Belyayev et al ., ; Hosid et al ., ). The results of the study showed that the TE fraction has undergone major changes in the genomes of plants from marginal populations.…”

“…Indeed, our IRAP data on the intraspecific variability of LTR retrotransposons in Ae. speltoides show that various genotypes from the 13 populations studied differ significantly with respect to the patterns of the four explored LTR retrotransposons ( WIS2, Wilma, Daniela and Fatima ) (Hosid et al ., ).…”

Genotype- and Cell-Specific Dynamics of Tandem Repeat Patterns in <b><i>Aegilops speltoides</i></b> Tausch (Poaceae, Triticeae)

“…speltoides possesses a wide spectrum of chromosomal rearrangements and extranumerary B chromosomes [Mendelson and Zohary, 1972;Raskina et al, 2004aRaskina et al, , b, 2011 which are highly enriched with nuclear repetitive and organelle DNA [Ruban et al, 2014]. According to the chromosomal patterns of tandem repeats [Raskina et al, 2011] and inter-retrotransposon amplified polymorphism [Hosid et al, 2012], wild populations can be clustered into 3 groups, which reflect the Ae. speltoides ecogeographical gradient and highlight the impact of repetitive DNA on population divergence and evolutionarily significant events that lead to speciation at the diploid level and via allopolyploidy [Raskina et al, 2004a[Raskina et al, , b, 2008.…”

Plant diversity and transcriptional variability assessed by retrotransposon-based molecular markers

“…It has been proven that TE families evolve with different profiles, so TE marker systems based on different TEs show different levels of resolution and can be chosen to fit with the required analysis (Leigh et al, 2003;Smykal et al, 2009;Hosid et al, 2012). Retrotranspo sons insertions behave as Mendelian loci (Manninen et al, 2006;Tanhuanpaa et al, 2008).…”

“…IRAP and REMAP methods have been used in gene map ping in cereals (Manninen et al, 2000;Boyko et al, 2002;Tanhuanpaa et al, 2007), in studies of genome evolution in the Solanaceous crop species (Tek et al, 2005;Tam et al, 2009), in a variety of applications, including measurement of genetic diversity and population structure, chromatin modification and epigenetic reprogramming, similarity and cladistic relation ships, determination of essential derivation, markerassisted selection, detection of somaclonal variation (Ishizaki, Kato, 2005;Lightbourn et al, 2007;Tam et al, 2009;Belyayev et al, 2010;Smykal et al, 2011;Wenke et al, 2011;Hosid et al, 2012;Yin et al, 2013;Moisy et al, 2014;Sharma, Nandineni, 2014;Tang et al, 2014;Paz et al, 2015).…”