Prediction of retrotransposons and assessment of genetic variability based on developed retrotransposon-based insertion polymorphism (RBIP) markers in Pyrus L

Abstract

Interspecific hybridization has been considered the major mode of evolution in Pyrus (pear), and thus, the genetic relationships within this genus have not been well documented. Retrotransposons are ubiquitous components of plant genomes and 42.4 % of the pear genome was reported to be long terminal repeat (LTR) retrotransposons, implying that retrotransposons might be significant in the evolution of Pyrus. In this study, 1,836 putative full-length LTR retrotransposons were isolated and 196 retrotransposon-based insertion polymorphism (RBIP) primers were developed, of which 24 pairs to the Ppcr1 subfamily of copia retrotransposons were used to analyze genetic diversity among 110 Pyrus accessions from Eurasia. Our results showed that Ppcr1 replicated many times in the development of cultivated Asian pears. The genetic structure analysis and the unweighted pair group method with arithmetic mean (UPGMA) dendrogram indicated that all accessions could be divided into Oriental and Occidental groups. In Oriental pears, wild pea pears clustered separately into independent groups in accordance with their morphological classifications. Cultivars of P. ussuriensis Maxim, P. pyrifolia Nakai, and P. pyrifolia Chinese white pear were mingled together, which inferred that hybridization events occurred during the development of the cultivated Asian pears. In Occidental pears, two clades were obtained in the UPGMA dendrogram in accordance with their geographical distribution; one contained the European species and the other included species from North Africa and West Asia. New findings in this study will be important to further understand the phylogeny of Pyrus and origins of cultivated pears.

Isolation and characterization of putative functional long terminal repeat retrotransposons in the Pyrus genome

“…In this study, we identified predicted LTR-retrotransposons in the ‘Suli’ genome, and focused on LTR-retrotransposons that had the highest likelihood of being functional based on the presence of annotated inner protein domains. Previously, we identified 1836 retrotransposons by running LTR-harvest based on two nearly sister LTR flanking sequences and some conserved sequence motifs [ 27 ]. However, the current study showed that only 440 retrotransposons had at least two inner protein domains.…”

“…In a previous study, 1836 full-length LTR-retrotransposons were mined from the whole-genome data of Pyrus (AJSU00000000) [ 27 ]. The details of each retrotransposon were obtained from the output of LTRharvest.…”

“…For example, retrotransposons accounted for 37.6 and 18.6 % of the genomes of Malus and Prunus species, respectively [ 25 , 26 ]. Jiang et al (2015) reported that the retrotransposon Ppcr1 was inserted in many loci in the genomes of cultivated Pyrus species, but only in a few loci in the genomes of wild Pyrus species [ 27 ]. This suggested that retrotransposons might play a major role in species evolution.…”

“…In this study, we predicted the LTR-retrotransposons present in the ‘Suli’ genome, and annotated all LTR-retrotransposons with three inner functional domains (RT, INT and GAG) to identify putative functional LTR-retrotransposons. LTR-retrotransposons in the ‘Suli’ genome [ 24 ] were extremely divergent [ 27 , 28 ], which made it difficult to analyze every predicted LTR-retrotransposon. Therefore, we focused on conserved LTR-retrotransposon families with a high copy number in ‘Suli’ genome, and investigated the distribution of these families in different Pyrus species and other closely related species to evaluate the roles of LTR-retrotransposon replication and mutation in the evolution of the Pyrus genome.…”

Use of retrotransposon-derived genetic markers to analyse genomic variability in plants

“…A marker from any of the anonymous multilocus RTE-based applications can be modified into an equivalent retrotransposon-based insertion polymorphism marker (Fig. 2) and vice versa (Jing et al 2010, Jiang et al 2015. Markers from the former methods are straightforward to harvest and can be rapidly analysed for their informativeness before investing in the advancement of a matching retrotransposon-based insertion polymorphism marker.…”