Transferability of retrotransposon primers derived from Persimmon (Diospyros kaki Thunb.) across other plant species

Abstract

ABSTRACT.Retrotransposon-based molecular markers are powerful molecular tools. However, these markers are not readily available due to the difficulty in obtaining species-specific retrotransposon primers. Although recent techniques enabling the rapid isolation of retrotransposon sequences have facilitated primer development, this process nonetheless remains time-consuming and costly. Therefore, research into the transferability of retrotransposon primers developed from one plant species onto others would be of great value. The present study investigated the transferability of retrotransposon primers derived from 'Luotian-tianshi' persimmon (Diospyros kaki Thunb.) across other fruit crops, as well as within the genus using inter-retrotransposon amplified polymorphism molecular marker. Fourteen of the 26 retrotransposon primers tested (53.85%) produced robust and reproducible amplification products across all fruit crops tested, indicating their applicability across plant species. Four of the 13 fruit crops showed the best transferability performances: persimmon, grape, citrus, and peach. Furthermore, similarity coefficients and UPGMA clustering indicated that these primers could further offer a potential tool for germplasm differentiation, parentage identification, genetic diversity assessment, classification, and phylogenetic studies across a variety of plant species. Transferability was further confirmed by examining published primers derived from Rosaceae, Gramineae, and Solanaceae. This study is one of the few currently available studies concerning the transferability of retrotransposon primers across plant species in general, and is the first successful study of the transferability of retrotransposon primers derived from persimmon. The primers presented here will help reduce costs for future retrotransposon primer development and therefore contribute to the popularization of retrotransposon molecular markers.

Transferability of barley retrotransposon primers to analyze geneticstructure in Iranian Hypericum perforatum L. populations

“…Amplification based on primer combinations indicated the integration of retrotransposons in tail-to-tail, headto-head, and head-to-tail orientations in H. perforatum. Retrotransposon markers from other sources have been applied in various plant species (Kalendar et al, 1999;Manninen et al, 2000;Baumel et al, 2002;Boyko et al, 2002;Branco et al, 2007;Du et al, 2013).…”

“…They are present in high copy numbers and are highly heterogeneous in plant genomes, and can be transmitted both vertically and horizontally across generations and between different plant spe cies, respectively (Du et al, 2013). Retrotransposon-based molecular markers have a number of advantages over other molecular markers, such as their abundance and dispersion throughout almost the entire length of all host chromosomes.…”

“…Investigations about the transferability of retrotransposon primers developed from one plant species onto others would be of great value to enable the low-cost and highly efficient development of retrotransposon-based molecular markers in plant species with very little or no information on retrotransposon sequences. For those plant species with abundantly available public data of retrotransposon sequences or retrotransposon-based marker systems, transferable primers from other plant species would be useful to further increase the number of markers Du et al, 2013).…”

High genetic and epigenetic variation of transposable elements: Potential drivers to rapid adaptive evolution for the noxious invasive weed Mikania micrantha

“…Based on genome sequence of Helianthus annuus (Badouin et al., 2017 ; Gill et al., 2014 ; Giordani et al., 2014 ; Staton et al., 2012 ) and horizontal transferability of transposons (Du et al., 2013 ; Flavell et al., 1992 ; Yaakov et al., 2013 ), we screened active transposons and obtained relative primers (Table 1 ). Additionally, in order to fully investigate genetic and epigenetic variation, different TE classes were selected to cover as many transposons as possible (Table 1 ).…”

Assessment of Genetic Diversity in Yeast and Barley by Retrotransposon-Based Molecular Markers

“…They replicate through an mRNA intermediate (Boeke and Sandmever, 1991;Havecker et al, 2004). One of the powerful molecular tools; Retrotransposonbased molecular markers, although these markers are not readily available due to the difficulty in obtaining species-specific retrotransposon primers (Du et al, 2013). Three retrotransposon-based techniques; Inter retrotransposon amplified polymorphism (IRAP), Retrotransposon Microsatellite Amplified Polymorphism (REMAP) and RAPD-retrotransposon amplified polymorphism (RRAP) were used to study the genetic diversity in different organisms; in rice (Branco et al, 2007), in fungus (Santana et al, 2012) and in tomato (Mansour et al, 2010).…”