Ac-like transposons in populations of wild diploid Triticeae species: comparative analysis of chromosomal distribution

High genetic diversity in Aegilops tauschii Coss. accessions from North Iran as revealed by IRAP and REMAP markers

BACKGROUND

Aegilops tauschii Coss. as a donor of wheat D genome has an important role in wheat breeding programs. Genetic and phylogeographic diversity of 79 Ae. tauschii accessions collected from north and northwest of Iran were analyzed based on retroelement insertional polymorphisms using inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) markers.

RESULTS

In total, 306 and 151 polymorphic bands were amplified in IRAP and REMAP analyses, respectively. As a result, a high level of polymorphism was observed among the studied accessions as revealed by an average of 25.5 bands per primer/primer combination and mean PIC value of 0.47 in IRAP and an average of 25.16 bands per primer combination and mean PIC value of 0.47 in REMAP. Genetic relationships of the accessions were analyzed using distance- and model-based cluster analyses.

CONCLUSION

The result showed that genetic distance did not seem to be related to geographic distribution, and the accessions could be divided into three groups, which was further supported by principal coordinate analysis. These results on genetic diversity and population structure of Ae. tauschii in Iran should provide important knowledge on genetic resources and their applications in wheat breeding programs.

Clustered and dispersed chromosomal distribution of the two classes of Revolver transposon family in rye (Secale cereale)

The chromosomal locations of a new class of Revolver transposon-like elements were analyzed by using FISH method on the metaphase chromosome in somatic cell division of the rye cultivar Petkus. First, the Revolver standard element probe λ2 was weakly hybridized throughout the rye chromosome, and comparatively large interstitial signals spotted with a dot shape were detected together with several telomeric regions. The dot shape interstitial signal was stably detected at one site on Chromosome (Chr) 1R (middle part of the interstitial region of the short arm), three sites on Chr 2R (distal part of the interstitial region and adjacent to the centromere on the short arm, middle part of the interstitial region of the long arm), and two sites on Chr 5R (middle part of the interstitial region and adjacent to the centromere on the long arm). The Revolver λ2 probe was effective for identification of 1R, 2R, and 5R chromosomes. On the other hand, Revolver nonautonomous element-specific L626-BARE-100 probe was strongly distributed throughout the rye chromosomes, and considerable numbers and diverse lengths of transcripts were detected by RT-PCR. Although the standard elements were found in localized clusters, the nonautonomous elements tended to be dispersed throughout the genome. Clustered nature of Revolver is a significantly rare case in genomics.

Field cress genome mapping: Integrating linkage and comparative maps with cytogenetic analysis for rDNA carrying chromosomes

Field cress (Lepidium campestre L.), despite its potential as a sustainable alternative oilseed plant, has been underutilized, and no prior attempts to characterize the genome at the genetic or molecular cytogenetic level have been conducted. Genetic maps are the foundation for anchoring and orienting annotated genome assemblies and positional cloning of candidate genes. Our principal goal was to construct a genetic map using integrated approaches of genetic, comparative and cytogenetic map analyses. In total, 503 F2 interspecific hybrid individuals were genotyped using 7,624 single nucleotide polymorphism markers. Comparative analysis demonstrated that ~57% of the sequenced loci in L. campestre were congruent with Arabidopsis thaliana (L.) genome and suggested a novel karyotype, which predates the ancestral crucifer karyotype. Aceto-orcein chromosome staining and fluorescence in situ hybridization (FISH) analyses confirmed that L. campestre, L. heterophyllum Benth. and their hybrids had a chromosome number of 2n = 2x = 16. Flow cytometric analysis revealed that both species possess 2C roughly 0.4 picogram DNA. Integrating linkage and comparative maps with cytogenetic map analyses assigned two linkage groups to their particular chromosomes. Future work could incorporate FISH utilizing A. thaliana mapped BAC clones to allow the chromosomes of field cress to be identified reliably.

Intraspecific and intraorganismal copy number dynamics of retrotransposons and tandem repeat in Aegilops speltoides Tausch (Poaceae, Triticeae)

Transposable elements (TE) and tandem repeats (TR) compose the largest fraction of the plant genome. The abundance and repatterning of repetitive DNA underlie intrapopulation polymorphisms and intraspecific diversification; however, the dynamics of repetitive elements in ontogenesis is not fully understood. Here, we addressed the genotype-specific and tissue-specific abundances and dynamics of the Ty1-copia, Ty3-gypsy, and LINE retrotransposons and species-specific Spelt1 tandem repeat in wild diploid goatgrass, Aegilops speltoides Tausch. Copy numbers of TEs and TR were estimated by real-time quantitative PCR in vegetative and generative tissues in original plants from contrasting allopatric populations and artificial intraspecific hybrids. The results showed that between leaves and somatic spike tissues as well as in progressive microsporogenesis of individual genotypes, the copy numbers of three TEs correlatively oscillated between 2- to 4-fold and the TR copy numbers fluctuated by 18- to 440-fold. Inter-individual and intraorganismal TEs and TR copy number dynamics demonstrate large-scale parallelism with extensive chromosomal rearrangements that were detected using fluorescent in situ hybridization in parental and hybrid genotypes. The data obtained indicate that tissue-specific differences in the abundance and pattern of repetitive sequences emerge during cell proliferation and differentiation in ontogenesis and reflect the reorganization of individual genomes in changing environments, especially in small peripheral population(s) under the influence of rapid climatic changes.

An integrated cytogenetic and physical map reveals unevenly distributed recombination spots along the papaya sex chromosomes

Papaya is a model system for the study of sex chromosome evolution in plants. However, the cytological structures of the papaya chromosomes remain largely unknown and chromosomal features have not been linked with any genetic or genomic data. We constructed a cytogenetic map of the papaya sex chromosome (chromosome 1) by hybridizing 16 microsatellite markers and 2 cytological feature-associated markers on pachytene chromosomes using fluorescence in situ hybridization (FISH). Except for three markers, the order of the markers was concordant to that of marker loci along the linkage map. This discrepancy was likely caused by skewed segregation in the highly heterochromatic or centromeric regions. The papaya sex chromosome is largely euchromatic, its heterochromatin spans about 15 % of the Y chromosome and is mostly restricted to the centromeric and pericentromeric regions. Analysis of the recombination frequency along the papaya sex chromosome revealed a complete suppression of recombination in the centromere and pericentromere region and 60 % higher recombination rate in the long arm than in the short arm. The uneven distribution of recombination events might be caused by differences in sequence composition. Sequence analysis of 18 scaffolds in total length of 15 Mb revealed higher gene density towards the telomeres and lower gene density towards the centromere, and a relatively higher gene density in the long arm than in the short arm. In an opposite trend, the centromeric and pericentromeric region contained the highest repetitive sequences and the long arm showed the lowest repetitive sequences. This cytogenetic map provides essential information for evolutionary study of sex chromosomes in Caricaceae and will facilitate the analysis of papaya sex chromosomes.

Survey of sugar beet (Beta vulgaris L.) hAT transposons and MITE-like hATpin derivatives

Genome-wide analyses of repetitive DNA suggest a significant impact particularly of transposable elements on genome size and evolution of virtually all eukaryotic organisms. In this study, we analyzed the abundance and diversity of the hAT transposon superfamily of the sugar beet (B. vulgaris) genome, using molecular, bioinformatic and cytogenetic approaches. We identified 81 transposase-coding sequences, three of which are part of structurally intact but nonfunctional hAT transposons (BvhAT), in a B. vulgaris BAC library as well as in whole genome sequencing-derived data sets. Additionally, 116 complete and 497 truncated non-autonomous BvhAT derivatives lacking the transposase gene were in silico-detected. The 116 complete derivatives were subdivided into four BvhATpin groups each characterized by a distinct terminal inverted repeat motif. Both BvhAT and BvhATpin transposons are specific for species of the genus Beta and closely related species, showing a localization on B. vulgaris chromosomes predominantely in euchromatic regions. The lack of any BvhAT transposase function together with the high degree of degeneration observed for the BvhAT and the BvhATpin genomic fraction contrasts with the abundance and activity of autonomous and non-autonomous hAT transposons revealed in other plant species. This indicates a possible genus-specific structural and functional repression of the hAT transposon superfamily during Beta diversification and evolution.

Genomic diversity of Ac-like transposable elements in sphaerococcum mutant forms of common wheat (Triticum aestivum L.) and triticale (X Triticosecale Witt.)

DNA sequences homologous to the maize Activator (Ac) element are widespread in plant genomes. Nowadays, several reports are available concerning the distribution and characterisation of Ac-homologous sequences in natural populations of different cereal species. but these mobile genetic elements still remain to be comprehensively characterised. In this respect, there is a particular lack of information about the dynamics of Ac-homologous sequences within mutant germplasm collections. Here, we present data on the genomic diversity and methylation patterns of Ac-homologous sequences in ethyl methanesulphonate (EMS)-induced sphaerococcum mutant forms of common wheat (Triticum aestivum L.) and triticale (X Triticosecale Witt.). The results show that the initial EMS treatment has influenced the wheat genome stability by enhancing the dynamics of Ac transposon-homologous sequences.

Retroelement insertional polymorphisms, diversity and phylogeography within diploid, D-genome Aegilops tauschii (Triticeae, Poaceae) sub-taxa in Iran

BACKGROUND AND AIMS

The diploid goat grass Aegilops tauschii (2n = 2x = 14) is native to the Middle East and is the D-genome donor to hexaploid bread wheat. The aim of this study was to measure the diversity of different subspecies and varieties of wild Ae. tauschii collected across the major areas where it grows in Iran and to examine patterns of diversity related to the taxa and geography.

METHODS

Inter-retroelement amplified polymorphism (IRAP) markers were used to analyse the biodiversity of DNA from 57 accessions of Ae. tauschii from northern and central Iran, and two hexaploid wheats. Key Results Eight IRAP primer combinations amplified a total of 171 distinct DNA fragments between 180 and 3200 bp long from the accessions, of which 169 were polymorphic. On average, about eight fragments were amplified with each primer combination, with more bands being amplified from accessions from the north-west of the country than from other accessions.

CONCLUSIONS

The IRAP markers showed high levels of genetic diversity. Analysis of all accessions together did not allow the allocation of individuals to taxa based on morphology, but showed a tendency to put accessions from the north-west apart from others regions. It is speculated that this could be due to different activity of retroelements in the different regions. Within the two taxa with most accessions, there was a range of IRAP genotypes that could be correlated closely with geographical origin. This supports suggestions that the centre of origin of the species is towards the south-east of the Caspian Sea. IRAP is an appropriate marker system to evaluate genetic diversity and evolutionary relationships within the taxa, but it is too variable to define the taxa themselves, where more slowly evolving morphological, DNA sequence or chromosomal makers may be more appropriate.