Retrotransposon-based Molecular Markers Research Articles

TEMM: A Curated Data Resource for Transposon Element-Based Molecular Markers in Plants.

Transposon elements (TEs) are mobile genetic elements that can insert themselves into new locations and modify the plant genome. In recent years, they have been used as molecular markers in plant breeding programs. TE-based molecular markers (TE-markers) are divided into two categories depending on the transcription mechanism of the TEs. The first category is retrotransposon-based molecular markers, which include RBIP, IRAP, REMAP, and iPBS. The second group is DNA-based-TE-markers, which include MITE, TE-junction, and CACTA TE-markers. These markers are a good tool for studying genetic diversity and can provide information on plants' phylogenetic and evolutionary history. They can help improve breeding programs to increase agronomic traits and develop new varieties. Overall, TE-markers play an important role in plant genetics and plant breeding and contribute to a better understanding of plant biology. Here, we present TEMM, a curated data resource for TE-markers in plants. Relevant research articles were screened to collect primer sequences and related information. Only articles containing primer sequences are added to the present data resource. TEMM contains 784 primers with their associated PCR reaction programs and their applications in various crops. These include 203 IPBS, 191 RBIP, 140 IRAP, 78 TE-junction, 76 IRAPS, 47 RBIP-IRAP, 16 IRAP-REMAP, 12 REMAP, 12 REMA-IRAP, 6 REMA, and 3 ISBP primers. The data resource is freely available at https://bioinformatics.um6p.ma/TEMM .

Comparative retrotransposon analysis of mutant and non-mutant rice varieties grown at different salt concentrations

This study investigated the effects of retrotransposon movements on the regeneration of 15- and 30-day-old leaves and roots of four different rice varieties grown in tissue culture medium at different salt concentrations (0, 50, 100, and 200 mmol/L) by Inter Retrotransposon Amplified Polymorphism (IRAP) and Retrotransposon Microsatellite Amplified Polymorphism (REMAP) polymerase chain reaction (PCR)-based marker methods. The study used Hopi, Houba, Osr30, Tos17 primers for IRAP analysis. The (GA)9C ISSR primer was used with four IRAP primers in REMAP analyses. There were different band profiles and polymorphism results between different salts concentrations of the same variety and various rice varieties. We observed that the polymorphism ratios for Houba ranged from 0 to 98% in IRAP and REMAP analyzes in the calculation made with the Jaccard similarity index in mutant samples. We report that mutant varieties give more valuable IRAP and REMAP results than non-mutant varieties. The results reported in this study contribute to understanding the effect of salinity stress on rice in terms of retrotransposon-based molecular markers. These results suggest that all tested retrotransposons are still active, causing genomic polymorphism among rice plantlets.

An Eruption of LTR Retrotransposons in the Autopolyploid Genomes of Chrysanthemum nankingense (Asteraceae).

Whole genome duplication, associated with the induction of widespread genetic changes, has played an important role in the evolution of many plant taxa. All extant angiosperm species have undergone at least one polyploidization event, forming either an auto- or allopolyploid organism. Compared with allopolyploidization, however, few studies have examined autopolyploidization, and few studies have focused on the response of genetic changes to autopolyploidy. In the present study, newly synthesized C. nankingense autotetraploids (Asteraceae) were employed to characterize the genome shock following autopolyploidization. Available evidence suggested that the genetic changes primarily involved the loss of old fragments and the gain of novel fragments, and some novel sequences were potential long terminal repeat (LTR) retrotransposons. As Ty1-copia and Ty3-gypsy elements represent the two main superfamilies of LTR retrotransposons, the dynamics of Ty1-copia and Ty3-gypsy were evaluated using RT-PCR, transcriptome sequencing, and LTR retrotransposon-based molecular marker techniques. Additionally, fluorescence in situ hybridization(FISH)results suggest that autopolyploidization might also be accompanied by perturbations of LTR retrotransposons, and emergence retrotransposon insertions might show more rapid divergence, resulting in diploid-like behaviour, potentially accelerating the evolutionary process among progenies. Our results strongly suggest a need to expand the current evolutionary framework to include a genetic dimension when seeking to understand genomic shock following autopolyploidization in Asteraceae.

Genetic diversity of Aegilops tauschii accessions and its relationship with tetraploid and hexaploid wheat using retrotransposon-based molecular markers

Aegilops is known as the ancestor species of wheat and has a major role in the evolution of wheat. Considering the importance of this species and the fact that Iran is the center of the distribution, fifteen IRAP and REMAP markers were used to evaluate the genetic diversity of Ae. tauschii accessions from different regions of Iran and its relationship with Triticum durum and Triticum aestivum. A high level of polymorphism (99%) was observed for both retrotransposon markers. Polymorphism information content, the effective number of alleles (Ne), Nei’s genetic diversity (H), and Shannon’s information index (I) for IRAP markers were more than REMAP markers. The most genetic diversity was detected in Ae. tauschii accessions. The cluster analysis separated the accessions into three distinct groups. Ae. tauschii accessions from Golestan province grouped in the same cluster with T. aestivum genotypes, indicating that these accessions are probably more like to the progenitor of the bread wheat D genome. Our results revealed that retrotransposon-based molecular markers could be used as the appropriate and reliable marker system to evaluate genetic diversity and relationship in Triticum and Aegilops accessions.

Retrotransposon-based molecular markers as a tool in delimiting species in section Ryncholotus, a recent radiation group of Macaronesian Lotus

Island species are particularly vulnerable to extinction and decline due to a range of factors, including isolation, small population sizes, climate change, or the introduction of alien species. Given their high levels of biodiversity, the preservation and protection of island endemic species are fundamental to reducing the loss of global diversity. Therefore, species delimitation, description and identification are among the most important tasks in conservation biology. However, determining species boundaries in some cases can be challenging, especially in groups that have radiated recently, where frequently used molecular markers do not have enough discrimination power. Thus, it is important to look for new approaches with higher resolution. In the present study, we test the use of retrotransposon-based molecular markers to investigate the taxonomic status of five endemic and endangered Lotus species in the Canary Islands. Our analysis revealed that the five species conform different entities, in concordance with their morphological differences, and shown that the technique named inter-Primer Binding Site (iPBS) is a reliable molecular marker system that allows to discriminate among Lotus and has a potential value for taxonomy and conservation.

Activation of transposable elements and insertional polymorphism in Opuntia offspring as assessed by inter-retrotransposon amplified polymorphism markers

Activation of retrotransposon is a pivotal factor in the genesis of genetic polymorphism. Retrotransposon-based molecular markers are excellent tools for detecting genetic diversity and genomic changes associated with their activity. The objective of this study was to use IRAP markers to detect integration events of retrotransposon in Opuntia, and to compare IRAP and ISSR polymorphisms. To achieve these aims, five IRAP and five ISSR markers were analyzed on three varieties and their progenies. All IRAP primers showed an increase in the percentage of polymorphism, number of total bands, and polymorphic bands in the seedlings compared to their mother plants; that is, the offspring showed 13, 24 and 27 more bands than the mother plants from Tobarito, Montesa and Copena varieties, respectively. Conversely, sexual reproduction did not proportionally affect the variation in the number of ISSR bands, and neither did polymorphisms between mother plants and their offspring. Cluster and multivariate analyses based on IRAP and ISSR data revealed a clear separation between varieties, and there was no overlapping between seedlings of different varieties. The activation of retrotransposons in seedlings of opuntia with variable frequencies was evidenced. The presence of insertion and active retrotransposons may help to undertake studies on genetic diversity and evolution of Opuntia.

Identification of SSR and retrotransposon-based molecular markers linked to morphological characters in oily sunflower ( $$\textit{Helianthus annuus}$$ Helianthus annuus L.) under natural and water-limited states

Sunflower is an important source of edible oil. Drought is known as an important factor limiting the growth and productivity of field crops in most parts of the world. Agricultural biotechnology mainly aims at developing crops with higher tolerance to the challenging environmental conditions, such as drought. This study examined a number of morphological characters, along with relative water content (RWC) in 100 inbred sunflower lines. A 10 × 10 simple lattice design with two replications was employed to measure the mentioned parameters under natural and water-limited states during two successive years. In molecular trial, 30 simple sequence repeat (SSR) primer pairs, as well as 14 inter-retrotransposon amplified polymorphism (IRAP) and 14 retrotransposon-microsatellite amplified polymorphism (REMAP) primer combinations were used for DNA fingerprinting of the lines. Most of the examined characters had lower average values under water-limited than natural states. Maximum and minimum reductions were observed in the cases of yield and oil percentage, respectively. The broad-sense heritabilities for all the examined characters were 0.20-0.73 and 0.10-0.34 under natural and water-limited states, respectively. In the studied samples, 8.97% of the 435 possible locus pairs of the SSRs represented significant linkage disequilibrium (LD) levels. In the association analysis using SSR markers, 22 and 21 markers were identified (P ≤ 0.05) for the studied characters under natural and water-limited states, respectively. The corresponding values were 50 and 37 using retrotransposon-based molecular markers. Some detected markers were communal between the characters under water-limited and natural states. This was in line with the phenotypic correlations detected between the characters. Communal markers facilitate the simultaneous selection of several characters and can thus improve the efficacy of selection based on markers in the plant-breeding activities.

Sukkula retrotransposon movements in the human genome

ABSTRACTRetrotransposons, a subclass of mobile genetic elements, have been discovered in many organisms. In this study, we identified a plant-specific retrotransposon (Sukkula) in the human genome (24 different DNA samples) by using retrotransposon-based molecular marker technique: inter-retrotransposon amplified polymorphism. There were five different groups related to the ages of the subjects. The polymorphism ratios were 8%–100% among all samples, 10%–91% among females (12 subjects) and 13%–100% among males (12 subjects). Moreover, we also observed 8%–91% polymorphism ratios when comparing males to females. To the best of our knowledge, this is one of the first reports on plant-specific retrotransposons in the human genome. The obtained findings are expected to contribute to broadening the knowledge about plant retrotransposons in the human genome and their role in human genome evolution.

Genetic linkage analysis using DNA markers in sweetpotato.

Sweetpotato is one of the most important food crop species in the world, with more than 104,000,000 tons produced each year, and the breeding of superior cultivars with agronomically important traits, such as improved disease resistance, yield, and nutrient richness, is necessary, especially in developing countries. However, as a result of the crop’s complex genomic architecture, which results from its hexaploidy (2n = 6× = 90), high heterozygosity, huge genome, and outcrossing nature, the analysis of genetic linkage in sweetpotato has been challenging. In addition, the lack of whole genome sequences or gene annotations for cultivated hexaploids has interrupted the validation of mapped QTL regions and gene cloning. In spite of these technical difficulties, linkage map construction and QTL mapping analysis have been reported. This review summarizes the results of these linkage analyses, which used SSR, AFLP, and retrotransposon-based molecular markers, and describes future directions for the genetic analysis and marker-assisted breeding of this important but genetically complex crop species.

Plant diversity and transcriptional variability assessed by retrotransposon-based molecular markers

Molecular markers have become crucial part of genetics due to their use in various branches of it, such as positional cloning, which includes identification of genes responsible for desired traits and management of backcrossing programs, as well as in modern plant breeding, and human forensics. Retrotransposons are a major component of all eukaryotic genomes, which makes them suited as molecular markers. The retrotransposons comprise most of large genomes among plants; differences in their prevalence explain most of the variation in genome size. These ubiquitous transposable elements are scattered in all of genome and their replicative transposition allows insert itself into a genome without deletion of the original elements. Retrotransposon activity can occur during development, cell differentiation and stress, and a source of chromatin instability and genomic rearrangements. Both the overall structure of retrotransposons and the domains responsible for the various phases of their replication are highly conserved in all eukaryotes. A high proportion of the retroelements have lost their autonomous transposition ability, either by point mutations and/or deletions, many of them seem to embody defective elements with deletions. Various molecular marker systems have been developed that exploit the ubiquitous nature of these genetic elements and their property of stable integration into dispersed chromosomal loci that are polymorphic within species. The utility of LTR-retrotransposon-based markers, not only for genetic analysis and map construction, in addition also for the isolation and characterization of LTR retrotransposons, such as the long terminal repeats or the internal genes they contain. This review encompasses description of the range of retrotransposon-based marker systems established for plants and evaluation of the role of retrotransposon markers in genetic diversity analysis of plant species.

Development of retrotransposon-based molecular markers and their application in genetic mapping in chokecherry (Prunus virginiana L.)

Retrotransposons are the largest group of transposable elements (TEs) that are ubiquitous and well dispersed in plant genomes. Transposition/insertion of TEs on chromosomes often generates unique repeat junctions (RJs) between TEs and their flanking sequences. Long terminal repeats (LTR) are well conserved and abundant in plant genomes, making LTR retrotransposons valuable for development of TE junction-based markers. In this study, LTR retrotransposons and their RJs were detected from chokecherry genome sequences generated by Roche 454 sequencing. A total of 1246 LTR retrotransposons were identified, and 338 polymerase chain reaction primer pairs were designed. Of those, 336 were used to amplify DNA from chokecherry and other rosaceous species. An average of 283 of 336 (84.2 %) LTR primer pairs effectively amplified DNA from chokecherries. One hundred and seventeen chokecherry LTR primers also produced amplification in other Prunus (99) or rosaceous species (19). A total of 59 of 78 polymorphic LTR markers were qualified for linkage map construction according to the segregation distortion Chi-square (χ 2) test. Forty-eight LTR markers were successfully located on a previously constructed chokecherry map. The majority of the LTR markers were mapped on LG XI of the chokecherry map. Our results suggest that LTR marker development using random genome sequences is rapid and cost-efficient. Confirmed applicability of LTR markers in map construction and genetic mapping will facilitate genetic research in chokecherry and other rosaceous species.

Retrotransposon molecular markers resolve cocoyam (Xanthosoma sagittifolium) and taro (Colocasia esculenta) by type and variety

Retrotransposon-based molecular markers were applied for the first time within the genera Xanthosoma and Colocasia to assess intraspecific variability among 27 accessions of cocoyam (Xanthosoma sagittifolium) and taro (Colocasia esulenta). Retrotransposons were isolated and sequenced; long terminal repeat (LTR) primers were designed to obtain inter-retrotransposon amplified polymorphism (IRAP) fingerprints. A set of six chosen LTR primers yielded 433 reproducible bands across 20 X. sagittifolium samples. Out of the 433 bands, 400 fragments (92 %) were polymorphic. In seven C. esculenta accessions, the six primers amplified a total of 354 reproducible, informative data points, of which 285 (80.5 %) were polymorphic. Cluster analysis placed all the accessions in two groups according to their species. The accessions of X. sagittifolium were further divided into two subgroups corresponding to their ploidy level. Moreover, the genetic variability accessed by IRAP markers allowed separation of X. sagittifolium and C. esculenta accessions according to their type and botanical variety respectively. The results suggest that retrotransposon activity continued after Xanthosoma speciation. The data and approach provides a basis for better germplasm management, future systematic studies and genetic improvement, as well as for exploration of the role of retrotransposons in cocoyam and taro polyploid formation and genome dynamics.

Chemotypic and genetic diversity in Epimedium sagittatum from different geographical regions of China

Different geographical plant populations within a single species can exhibit variation, in the production of secondary metabolites. Genetic and environmental variations both contribute to differences between populations; however, the relative importance of these factors is unclear. Here, the extent of variation in the production of four flavonoid glycosides (epimedin A, B, C and icariin) were investigated in eleven wild populations of Epimedium sagittatum used in traditional Chinese medicine. Secondary metabolite profiles were classified into five chemotypes. A common garden experiment indicated this chemotype variation has a significant genetic basis. Extensive genetic variation among intraspecific populations was shown using a retrotransposon-based molecular marker system. These results will assist in development of strategies for conservation, utilization and domestication of E. sagittatum.

Evaluation of new IRAP markers of pear and their potential application in differentiating bud sports and other Rosaceae species

Inter-retrotransposon amplified polymorphisms (IRAP) are one of the main components of the retrotransposon-based molecular marker system, but currently have no applications in pear. In this context, new IRAP markers were developed and used to study the genetic polymorphism of pear cultivars and bud mutants. In total, eight polymorphic IRAP markers were selected in ten genotypes of pear with a wide variation in genetic backgrounds and for further genotypic identification of cultivars and bud sports. A total of 76 alleles with an average of 9.5 per locus were amplified and 96.05 % showed polymorphism. Through genetic structure analysis, 62 pear cultivars were divided into two groups, i.e., Oriental and Occidental pears, with a few samples showing a distinct admixed genetic background. When polymorphic IRAP markers were tested on a total of 33 bud sports and their corresponding parent cultivars, the genetic similarity coefficient ranged from 0.54 to 0.96. Each bud mutation was separated from its original variety, and 92.3 % of bud sports clustered perfectly with their original varieties. Furthermore, the transferability of pear IRAP to apples and other Rosaceae species was very high, ranging from 87.5 to 100 %. Our results demonstrate that IRAP markers are an excellent tool for the study of genetic relationships and comparative genomics analysis in pear and Rosaceae species.

DKRE1—The first full-length Ty1-copia-like retrotransposon in persimmon: Isolation, characteristic and potential involvement in occurrence of bud mutations

The focus of this study revolved around persimmon (Diospyros kaki Thunb.) retrotransposable element 1 (DKRE1), a complete long terminal repeat (LTR) retrotransposon (RTN) that was isolated from persimmons. Its structure, phylogenetic classification, copy number, active characteristics and potential roles involved in the occurrence of bud mutations in persimmons were investigated. Having a length of 6, 235bp, DKRE1 possessed all of the sequence features associated with Ty1-copia-like retrotransposons. Phylogenetic analysis showed significant, but not strong, identity in amino acid sequences with BARE1 (barley retrotransposable element-1), RIRE1 (rice retrotransposable element-1) and Ppcrt (Pyrus pyrifolia copia retrotransposon) groups. The estimated copy number of 45 copies per haploid genome suggested that DKRE1 possesses a low constitution in the persimmon genome. Furthermore, the transcription of DKRE1 could be detected in leaf tissue treated with salicylic acid (SA), methyl jasmonate (MJA), and abscisic acid (ABA), indicating its active characteristics when subjected to exogenous phytohormones. Polymorphisms were revealed between several pairs of bud mutations by way of either inter-retrotransposon amplified polymorphism (IRAP) or sequence-specific amplified polymorphism (SSAP) retrotransposon-based molecular markers, showing a potential involvement in their occurrence. To our knowledge, this is the first report of the isolation of a complete LTR retrotransposon with transcriptional activity in persimmons. This study is valuable for future research on the mechanisms of bud mutation and development of retrotransposon-based molecular markers for genetic analysis.

C-2009: Assessment of genetic stability of cryopreserved fraser photinia via retrotransposon-based molecular markers

Fraser photinia ( Photinia × fraseri Dress.) with its impressive leaf colour is an evergreen woody ornamental plant that has commercial importance. Due to the rooting problems faced in the traditional vegetative propagation of the species, biotechnological methods such as plant tissue culture is used as a complementary strategy to propagation. Moreover, medium and long-term (cryopreservation) preservation of the species also gained importance recently as photinia has economic importance. However, occurence of risk of possible genetic variation between the donor plant and cryopreserved individuals after cryopreservation, reveals the necessity of assessment of genetic stability of the long-term preserved species. Therefore, genetic stability of the plantlets proliferated from cryopreserved fraser photinia shoot tips was assessed by two retrotransposon-based molecular markers (IRAP and REMAP) in addition to the optimization of cold hardening stage of the cryopreservation. 52.1% of mean polymorphism (mean PIC value is 0.307) was found between donor plant and clones by IRAP analysis while 47.2% of mean polymorphism (mean PIC value is 0.353) was detected via REMAP. According to the results of observed with these two marker systems, applied cryopreservation protocol caused an reasonable polymorphism (PIC value).

Application of iPBS in high-throughput sequencing for the development of retrotransposon-based molecular markers

Retrotransposons are major components of higher plant genomes, and long terminal repeat (LTR) retrotransposons are especially predominant. Thus, numerous LTR retrotransposon families with high copy numbers exist in most plant genomes. As the integrated copies of these retrotransposons are genetically inherited, their insertion polymorphisms among crop cultivars have been used as functional molecular markers such as inter-retrotransposon amplification polymorphism (IRAP), retrotransposon microsatellite amplification polymorphism (REMAP), retrotransposon-based insertion polymorphism (RBIP) and sequence-specific amplification polymorphism (S-SAP). However, the effective use of these methods requires suitable LTR sequences showing high insertion polymorphism among crop cultivars. Recently, we conducted an efficient screening of LTR retrotransposon families that showed high insertion polymorphism among closely related strawberry cultivars using a next-generation sequencing platform. This method focuses on the primer binding site (PBS), which is adjacent to the 5′ LTR sequence and is conserved among different LTR retrotransposon families. Construction of a sequencing library using the PBS motif allowed us to identify a large number of LTR sequences and their insertion sites throughout the genome. The LTR sequences identified by our method showed high insertion polymorphism among closely related strawberry cultivars, and these families should thus be useful in the development of molecular markers for phylogenetic and genetic diversity studies. This article briefly describes the general aspects of retrotransposon-based molecular markers and also outlines our method for screening LTR sequences suitable for genetic analyses.(http://www.ddbj.nig.ac.jp/).

Retrotransposon-based molecular markers for assessment of genomic diversity

Retrotransposons (RTs) are major components of most eukaryotic genomes. They are ubiquitous, dispersed throughout the genome, and their abundance correlates with genome size. Their copy-and-paste lifestyle in the genome consists of three molecular steps involving transcription of an RNA copy from the genomic RT, followed by reverse transcription to generate cDNA, and finally, reintegration into a new location in the genome. This process leads to new genomic insertions without excision of the original element. The target sites of insertions are relatively random and independent for different taxa; however, some elements cluster together in 'repeat seas' or have a tendency to cluster around the centromeres and telomeres. The structure and copy number of retrotransposon families are strongly influenced by the evolutionary history of the host genome. Molecular markers play an essential role in all aspects of genetics and genomics, and RTs represent a powerful tool compared with other molecular and morphological markers. All features of integration activity, persistence, dispersion, conserved structure and sequence motifs, and high copy number suggest that RTs are appropriate genomic features for building molecular marker systems. To detect polymorphisms for RTs, marker systems generally rely on the amplification of sequences between the ends of the RT, such as (long-terminal repeat)-retrotransposons and the flanking genomic DNA. Here, we review the utility of some commonly used PCR retrotransposon-based molecular markers, including inter-primer binding sequence (IPBS), sequence-specific amplified polymorphism (SSAP), retrotransposon-based insertion polymorphism (RBIP), inter retrotransposon amplified polymorphism (IRAP), and retrotransposon-microsatellite amplified polymorphism (REMAP).

LTR-retrotransposon activation, IRAP marker development and its potential in genetic diversity assessment of masson pine (Pinus massoniana)

Activation of retrotransposon is the pivotal factor for the genesis of genetic polymorphism. Retrotransposon-based molecular markers are excellent tools for detecting genetic diversity and genomic changes associated with retrotransposon activity. The scarcity of retrotransposon long terminal repeat (LTR) sequence limits the application of retrotransposon-based molecular marker systems. In this study, retrotransposon 3′-LTR segments were firstly isolated and characterized from the masson pine genome using a genome walking strategy, subsequently inter-retrotransposon amplified polymorphism (IRAP) markers were explored for genetic diversity assessment. These were shown to have clearly distinguishable amplification bands and high levels of polymorphism for masson pine. Dendrogram of our IRAP data highlighted that IRAP markers for individual elements are distinguishable and will shed light on the usage in genetic diversity studies of the masson pine. Transcription activation of Ty1-copia and Ty3-gypsy group retrotransposons in masson pine was investigated with exposure to various abiotic stresses. The insertional polymorphism and the transposition activation were detected by IRAP. Results revealed that none of the analyzed materials in the course of 2-month trials displayed fingerprint changes.

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

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.