Transposable elements in a marginal plant population: temporal fluctuations provide new insights into genome evolution of wild diploid wheat

Abstract

Background: How new forms arise in nature has engaged evolutionary biologists since Darwin's seminal treatise on the origin of species. Transposable elements (TEs) may be among the most important internal sources for intraspecific variability. Thus, we aimed to explore the temporal dynamics of several TEs in individual genotypes from a small, marginal population of Aegilops speltoides. A diploid cross-pollinated grass species, it is a wild relative of the various wheat species known for their large genome sizes contributed by an extraordinary number of TEs, particularly long terminal repeat (LTR) retrotransposons. The population is characterized by high heteromorphy and possesses a wide spectrum of chromosomal abnormalities including supernumerary chromosomes, heterozygosity for translocations, and variability in the chromosomal position or number of 45S and 5S ribosomal DNA (rDNA) sites. We propose that variability on the morphological and chromosomal levels may be linked to variability at the molecular level and particularly in TE proliferation.

Results: Significant temporal fluctuation in the copy number of TEs was detected when processes that take place in small, marginal populations were simulated. It is known that under critical external conditions, outcrossing plants very often transit to self-pollination. Thus, three morphologically different genotypes with chromosomal aberrations were taken from a wild population of Ae. speltoides, and the dynamics of the TE complex traced through three rounds of selfing. It was discovered that: (i) various families of TEs vary tremendously in copy number between individuals from the same population and the selfed progenies; (ii) the fluctuations in copy number are TE-family specific; (iii) there is a great difference in TE copy number expansion or contraction between gametophytes and sporophytes; and (iv) a small percentage of TEs that increase in copy number can actually insert at novel locations and could serve as a bona fide mutagen.

Conclusions: We hypothesize that TE dynamics could promote or intensify morphological and karyotypical changes, some of which may be potentially important for the process of microevolution, and allow species with plastic genomes to survive as new forms or even species in times of rapid climatic change.

Figure 1

Copy numbers and morphology. (a) Dynamics of transposable element (TE) copy numbers in three self-pollinated generations of three genotypes from the Kishon population of Aegilops speltoides (shown by lines). TE copy numbers of the TS-84 population were used as controls. TE copy numbers for available sibs in selfing generations are shown by separate dots. (b) Changes in spike morphology in three self-pollinated generations of three genotypes from the Kishon population of Ae. speltoides. Spike morphology of plants from the TS-84 population was used as the control.

Figure 2

Inter-retrotransposon amplified polymorphism (IRAP) analyses for several transposable elements (TEs) in the progeny of three genotypes. Unique bands that appear in S2 and are inherited in S3 are shown by red arrows. An example of heterozygosity displayed in the IRAP pattern is shown in the blue square. An example of band loss in S2 and S3 is shown in the green square. An example of band appearance in S2 and S3 is shown in the yellow square.

Figure 3

Analysis of unique inter-retrotransposon amplified polymorphism (IRAP) bands. In this example, IRAP was conducted with primer 2109, matching the Daniela retrotransposon long terminal repeat (LTR) (Table S2 in Additional file 2). The band was cut and sequenced. Two new primers were designed to match the sequence and the uniqueness of the band was checked on the set of DNA samples. This new insertion is in repetitive DNA (Table S2 in Additional file 2).

Figure 4

Principle component analysis (PCA). (a) PCA analysis: spikes versus leaves for transposable element (TE) copy number changes over the generations, normalized by the TS-84 control. (b) PCA analysis: two groups of TE, spike active and leaf active. (c) Second principal component (PC2)-based order of TE activation. (d) Normalized and centralized patterns of the three genotypes for Spelt 52 and TEs across tissues and generations. (e) Deviations of real copy numbers in leaves and spikes from the stochastic model.

Figure 5

Fluorescence in situ hybridization (FISH) and differential staining with 4',6-diamidino-2-phenylindole (DAPI) on somatic and meiotic chromosomes of Aegilops speltoides (part 1). (a) FISH with 5S rDNA, 45S rDNA and staining with DAPI on somatic chromosomes of the original G9 plant (left). Chromosomes 1, 6 (arrows), and B chromosomes carry additional 5S rDNA sites (right). (b) FISH with Spelt 52, Spelt 1 (arrows on B chromosomes), 5S rDNA and 45S rDNA on the somatic chromosomes of the G9 S1 plant (left); FISH with 5S rDNA (right). Chromosomes 1 and 6 carry additional 5S rDNA sites (arrowed). (c) From left to right: FISH with 5S rDNA and 45S rDNA, and DAPI on the meiotic chromosomes of the G9 S2 plant; 5S rDNA probe alone, chromosomes 1, 6 (arrows), and B chromosomes carry additional 5S rDNA sites; FISH with Spelt 52 and Spelt 1 on the same chromosomes; FISH with CCS-1 and 45S rDNA (a pericentric inversion is arrowed); the scheme of the main chromosomal rearrangements (see legend). (d) DAPI (left) and FISH (middle) with 5S rDNA and 45S rDNA on the meiotic chromosomes of the G13 S2 plant. A scheme of the main chromosomal rearrangements (right). (e) FISH with Spelt 52 and Spelt 1 on the meiotic chromosomes of the G13 S3 plant (left). Small Spelt 52 cluster (arrow) marks paracentric inversion in the long arm of the chromosome 5. FISH with 5S rDNA and 45S rDNA with DAPI staining (middle). Both termini of chromosome 5 are involved in heterologous synapses (white arrows); heterozygous deletion on the chromosome 6 is shown by yellow arrow. Chromosomes 1 and 6 carry additional 5S rDNA clusters (arrows in right). The DNA probes and staining: (a-e) 5S rDNA, Spelt 52 and cereal centromere-specific sequence 1 (CCS-1) in red; 45S rDNA and Spelt 1 in green; differential staining with DAPI in blue; (b) 5S rDNA (yellow) and 45S rDNA (blue) in pseudocolors.

Figure 6

Fluorescence in situ hybridization (FISH) and differential staining with 4',6-diamidino-2-phenylindole (DAPI) on somatic and meiotic chromosomes of Aegilops speltoides (part 2). (a) From left to right: DAPI and FISH with the CCS-1 and 45S rDNA on the meiotic chromosomes of the original G14 plant; FISH with Spelt 52 and Spelt 1. The clusters of Spelt 1 that mark a homozygous paracentric inversion on chromosome 4, and a Spelt 1 cluster on the B chromosome are arrowed. FISH with 5S rDNA and 45S rDNA on the same chromosomes. A scheme of the main chromosomal rearrangements. (b) FISH with Spelt 52 and Spelt 1 on the meiotic chromosomes of the G14 S2 plant (left). The clusters of Spelt 1 that mark a homozygous paracentric inversion on chromosome 4 and cluster of Spelt 52 that marks a heterozygous inversion on the chromosome 5 are arrowed. FISH with 5S rDNA and 45S rDNA (middle). B chromosomes carry 5S rDNA clusters in both arms. The scheme of the main chromosomal rearrangements (right). (c) FISH with Spelt 52 and Spelt 1 on the meiotic chromosomes of the G14 S3 plant (left). Homozygous paracentric inversion on chromosome 4 is arrowed. FISH with 5S rDNA and 45S rDNA on the same chromosomes (right). (d) Somatic chromosomes of TS 84, staining with DAPI (left). FISH with Spelt 52 and Spelt 1 on the same chromosomes (right). The DNA probes and staining: (a-d) 5S rDNA, Spelt 52 and cereal centromere-specific sequence 1 (CCS-1) in red; 45S rDNA and Spelt 1 in green; differential staining with DAPI in blue; (a) 5S rDNA (yellow) and 45S rDNA (blue) in pseudocolors.