Retrotransposon-based molecular markers for grapevine species and cultivars identification

Abstract

Insertional polymorphisms of two copia-like (Vine-1, Tvv1) and one gypsy-like (Gret1) retrotransposon found in the grapevine genome were studied in 29 Vitis genotypes (Vitis arizonica, Vitis cinerea, Vitis labrusca, Vitis rupestis, Vitis rotundifolia, Vitis vinifera subsp. sylvestris and 23 V. vinifera subsp. sativa) using interretrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP) and sequence-specific amplified polymorphism (SSAP) techniques. IRAP, REMAP and SSAP polymorphisms were compared with amplified fragment length polymorphism (AFLP), Inter-single sequence repeats (ISSR) and SSR polymorphisms by evaluating the information content, the number of loci simultaneously analysed per experiment, the effectiveness of the analyses in assessing the relationship between accessions and the number of loci needed to obtain a coefficient of variation of 10%. The UPGMA dendrograms of each molecular marker system were compared and the Mantel matrix correspondence test was applied. Furthermore, the corresponding insertion ages of the transposable elements were estimated for each retrotransposon subfamily analysed. The presence of Gret1, Tvv1 and Vine-1 retrotransposons in all analysed genotypes suggests that copia-like and gypsylike retrotransposons are widespread in Vitis genus. The results indicate that these retrotransposons were active before Vitis speciation and contributed to Vitis genus evolution. IRAP, REMAP and SSAP markers allow the discrimination of Vitis species and V. vinifera subsp. sativa cultivars with certainty as has been shown with AFLP, ISSR and SSR analyses, but phylogenetic trees obtained by retrotransposonbased molecular markers polymorphisms show some significant differences in the allocation of the analysed accessions compare to those obtained by ISSR, AFLP and SSR molecular markers. The phylogenetic tree resulting from REMAP polymorphism appeared the most representative of the effective relationship between all analysed accessions

A new strategy for complete identification of sea buckthorn cultivars by using random amplified polymorphic DNA markers

“…In recent years, various DNA-based markers have been developed and used in genetic diversity, fingerprinting, and cultivar origin studies (Fang et al, 2006;Cheng and Huang, 2009;D'Onofrio et al, 2009;Elidemir and Uzun, 2009;Melgarejo et al, 2009;Papp et al, 2010). Among the DNA-based markers, the random amplified polymorphic DNA (RAPD) (William et al, 1990) marker technique is useful for cultivar analysis and has advantages such as its simplicity, efficiency, and non-requirement of any previous sequence information.…”

Development and Characterisation of Irap Markers From Expressed Retrotransposon-like sequences in Pinus sylvestris L.

“…RE-based markers can also be more sensitive than other marker systems. For example, they can differentiate breeding lines and clones, which are indistinguishable by SSR analysis (Tam et al, 2005;D'Onofrio et al, 2010;Baranek et al, 2012;Carvalho et al, 2012;Castro et al, 2012;Subudhi et al, 2013). Another characteristic feature of RE markers is that a relatively small amount of sequence information is required to obtain large amounts of genotypic data.…”

A novel and efficient strategy for practical identification of tomato (Solanum lycopersicon) varieties using modified RAPD fingerprints

“…Many DNA-based markers, such as RFLP (Williams et al, 1991), RAPD (Williams et al, 1990), SSR (Powell et al, 1996), I-SSRs (Zietkiewicz et al, 1994), AFLP (Vos et al, 1995), SNPs, SAMPL (Morgante and Vogel, 1994), M-AFLP (Albertini et al, 2003), SRAP (Li and Quiros, 2001), CAPS (Williams et al, 1991), andSCoT (Collard andMackill, 2009), have been developed and used in studies on genetic diversity, fingerprinting and origins of cultivars in many crops (Fang et al, 2005;D'Onofrio et al, 2009;Melgarejo et al, 2009;Papp et al, 2010). Among these markers, the dominant RAPD marker (Williams et al, 1990) is generally accepted for basic genotype characterization, genome analysis and gene mapping in various species due to its simplicity, speed and efficiency, ability to detect relatively small amounts of genetic variation and non-requirement of prior information on the genome.…”