Inter-retrotransposon Amplified Polymorphism Research Articles

Population structure and genotypic variation of Crataegus pontica inferred by molecular markers

Information about the natural patterns of genetic variability and their evolutionary bases are of fundamental practical importance for sustainable forest management and conservation. In the present study, the genetic diversity of 164 individuals from fourteen natural populations of Crataegus pontica K.Koch was assessed for the first time using three genome-based molecular techniques; inter-retrotransposon amplified polymorphism (IRAP); inter-simple sequence repeats (ISSR) and start codon targeted (SCoT) polymorphism. IRAP, ISSR and SCoT analyses yielded 126, 254 and 199 scorable amplified bands, respectively, of which 90.48, 93.37 and 83.78% were polymorphic. ISSR revealed efficiency over IRAP and SCoT due to high effective multiplex ratio, marker index and resolving power. The dendrograms based on the markers used and combined data divided individuals into three major clusters. The correlation between the coefficient matrices for the IRAP, ISSR and SCoT data was significant. A higher level of genetic variation was observed within populations than among populations based on the markers used. The lower divergence levels depicted among the studied populations could be seen as evidence of gene flow. The promotion of gene exchange will be very beneficial to conserve and utilize the enormous genetic variability.

Towards the identification of retrotransposon-based and ISSR molecular markers associated with populations resistant to ZYMV in melon

Melon (Cucumis melo L.) is one of the most important commercial vegetable crops grown in Iran. Very few studies on the genetic structure and diversity of melon landraces of Iran are available in the literature. In addition, it is susceptible to a number of diseases causing reduction in both productivity and quality of the crop. In this study we applied inter retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP) and inter simple sequence repeat (ISSR) molecular markers to investigate genetic diversity and its association with populations resistant to ZYMV in 11 Iranian melon populations and 12 commercial lines. Significant differences (P≤0.01) were detected among populations for reaction to ZYMV infection. No symptoms observed on inbred line PI414723, while variety Charentais T showed the highest value of virus infection (1.87). Based on five IRAP, 15 REMAP and 20 ISSR primers, a total of 656 reproducible and scorable loci were generated, among them 75.41% were polymorphic. Population structure analysis using STRUCTURE software identified K=10 as the reliable value for the number of clusters. Associations between molecular markers and populations resistant to ZYMV were tested using mixed linear model (MLM) approach that accounts for population structure. Highly significant associations were found for seven REMAP and four ISSR markers affecting ZYMV resistance (P≤0.01). This study provides evidence that using natural germplasms, the diversity can be enhanced for marker-trait associations that can be validated in segregating populations and exploited through marker-assisted selection.

Genetic diversity ofSorghumhalepense(L.) Pers. in Iran as revealed by IRAP markers

Sorghum halepensegrows in a vast range of ecological regions of Iran. In this study, inter-retrotransposon amplified polymorphism (IRAP) markers were used to assess the genetic diversity of 38 accessions ofS. halepenseand two accessions ofSorghum bicolor(used as out groups) collected from different regions of Iran. In total, 180 DNA fragments were amplified from eight combinations of IRAP primers, from which 178 (98.9%) were polymorphic. The IRAP-based trees and two-dimensional plot of principal coordinate analysis demonstrated six different groups corresponding to their geographical origin in Iranian germplasm ofS. halepense: (1) in the south-west region; (2) in the west along the Zagros Mountains; (3) in the north-west of the country; (4) in the centre of the country; (5) and (6) in the northern region along the eastern and western coast of Caspian Sea. The most variable populations were found in the centre and the west of Iran. The results showed high gene flow among different regions, although the south-western accessions were well differentiated from those growing in other regions. The accessions collected from western coast of Caspian Sea were differentiated from neighbouring regions in both morphological characters and IRAP data. The measured genetic distances were independent of geographical distances. This survey demonstrates high genetic dynamism in Iranian germplasm ofS. halepenseand indicates that the present germplasm is of great value in terms of sampling for new alleles for crop improvement.

Genetic fidelity assessment of in vitro-regenerated plants of Albizia julibrissin using SCoT and IRAP fingerprinting

A protocol was established for callus induction and plant regeneration of Albizia julibrissin Durazz., a multipurpose tree. Calli were induced on hypocotyl explants excised from 10- to 14-d-old in vitro seedlings cultured on Murashige and Skoog (MS) medium supplemented with α-naphthaleneacetic acid (NAA) alone or in combination with 6-benzylaminopurine (BA) or 6-furfurylaminopurine (kinetin). The highest frequency of organogenic callus (82.2 ± 3.6%) was obtained on MS medium with 10.8 μM NAA and 4.4 μM BA. Calli were then cultured on MS medium with BA or zeatin, singly or in combination, for shoot regeneration. Calli cultured on MS medium with 13.2 μM BA and 4.6 μM zeatin produced the highest frequency of adventitious shoot regeneration (75.3 ± 6.3%). Maximum rooting of shoots (73.3 ± 5%) was achieved using half-strength MS medium with 4.9 μM indole-3-butyric acid. The genetic fidelity of 12 plants acclimatized to the greenhouse was assessed based on analyses of start codon targeted (SCoT) polymorphism and inter-retrotransposon amplified polymorphism (IRAP). The 14 SCoT and 7 IRAP adapted primers produced 71 and 34 scoreable fragments, of which 33 (46%) and 12 (35%) were polymorphic, respectively. The in vitro-raised plants exhibited 0.129–0.438 genetic distance from the mother plant and 0.000–0.788 distance from one another according to the SCoT and IRAP analyses. Although the culture method described here may not be suitable for clonal propagation of elite genotypes, it can be used for conservation of this plant.

Analysis of Genetic Diversity in 21 Genotypes of Indian Banana Using RAPDs and IRAPs Markers

Table top banana (AAA) and cooking type plantines (BBB/ABB) are cultivated commercially for high yield and lucrative market value. Morphological similarities among the banana clones make identification difficult under field conditions. Random amplified polymorphic DNA (RAPD) and inter-retrotransposon amplified polymorphism (IRAP), were used to characterize genetic variations among 21 banana germplasm. IRAP primers were designed to determine ‘AA’ and ‘BB’ specific markers on the basis of repetitive and genome-wide dispersed long terminal repeat (LTR) retrotransposons. RAPD markers successfully detected genetic variation between genotypes. IRAP markers amplified either by a single primer or a combination of primers, based on LTR orientation, successfully amplified different retrotransposons dispersed in the Musa genome. The average level of polymorphism exhibited by RAPD and IRAP markers were 71.47 % and 81.3 % respectively that suggests substantial genetic variations among the tested varieties. All the 12 table-top varieties were clustered together while four cooking varieties i.e. Bantala-I, Bantala-II, Dakhkhnisagar and Athiakol with ‘BB’ formed a distinct group. These results suggested that IRAP markers were found more robust than RAPD markers to study the intra-group genetic diversity between table top and cooking banana.

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.

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

Transferability of barley retrotransposon primers was investigated to analyze population structure in St. John's wort (Hypericum perforatum L.) based on inter-retrotransposon amplified polymorphism (IRAP). Seven long terminal repeat (LTR) retrotransposon primers derived from the barley genome were used to detect genetic polymorphism in eight Iranian populations and three cultivars (Helos, New Stem, and Topaz) of H. Perforatum based on IRAP analysis. Nine possible LTR primers/primer combinations successfully amplified fragments from the H. Perforatum genome. In total, 311 bands of 100-3000 base pairs were amplified, of which 244 were polymorphic. The number of polymorphic fragments ranged from 10 (Nikita/5'LTR-2) to 57 (3'LTR), with an average of 27.11. Principal coordinate analysis (PCoA) could clearly differentiate samples of wild populations and cultivars. Based on analysis of molecular variance (AMOVA), among populations variance explained 58% of total molecular variation. This study demonstrates that IRAP markers can be utilized not only to determine the relationships of Hypericum populations and cultivars, but also as a tool for selection of suitable populations for breeding programs.

SIRE1Retrotransposons in Barley (Hordeum vulgareL.)

Sireviruses are genera of copia LTR retrotransposons with a unique genome structure among retrotransposons. Barley (Hordeum vulgare L.) is an economically important plant. In this study, we used mature barley embryos, 10-day-old roots and 10-day-old leaves derived from the same barley plant to investigate SIRE) retrotransposon movements by Inter-Retrotransposon Amplified Polymorphism (IRAP) technique. We found polymorphism rates between 0-64% among embryos, roots and leaves. Polymorphism rates were detected to be 0-27% among embryos, 8-60% among roots, and 11-50% among leaves. Polymorphisms were observed not only among the parts of different individuals, but also on the parts of the same plant (23-64%). The internal domains of SIRE1 (GAG, ENV and RT) were also analyzed in the embryos, roots and leaves. Analysis of band profiles showed no polymorphism for GAG, however, different band patterns were observed among samples for RT and ENV. The sequencing of SIRE1 GAG, ENV and RT domains revealed 79% similarity for GAG, 96% for ENV and 83% for RT to copia retrotransposons. Comparison between barley retrotransposons and SIRE1 in barley indicated that SIRE1-GAG, ENV and RT might be diverge earlier from barley retrotransposons. SIRE1 sequences were compared with SIRE1 in barley, results showed the closest homologues were SIRE1-ENVand SIRE1-RTsequences, and SIRE1-GAG sequences was a sister group to sequences of Glycine max. This study is the first detailed investigation of SIRE1 in barley genome. The obtained findings are expected to contribute to the comprehension of SIRE1 retrotransposon and its role in barley genome.

Endophytic fungi from the genus Colletotrichum are abundant in the Phaseolus vulgaris and have high genetic diversity.

To evaluate the diversity of endophytic fungi from the leaves of the common bean and the genetic diversity of endophytic fungi from the genus Colletotrichum using IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism) analyses. The fungi were isolated by tissue fragmentation and identified by analysing the morphological features and sequencing the internal transcribed spacer (ITS) regions and the rDNA large subunit (LSU). Twenty-seven different taxa were identified. Colletotrichum was the most commonly isolated genera from the common bean (32.69% and 24.29% of the total isolates from the Ouro Negro and Talismã varieties, respectively). The IRAP and REMAP analyses revealed a high genetic diversity in the Colletotrichum endophytic isolates and were able to discriminate these isolates from the phytopathogen Colletotrichum lindemuthianum. Fungi from the genus Colletotrichum are abundant in the Phaseolus vulgaris endophytic community, and the IRAP and REMAP markers can be used to rapidly distinguish between C. lindemuthianum and other Colletotrichum members that are frequently found as endophytes. This is the first report of the diversity of endophytic fungi present in the common bean and the use of IRAP and REMAP markers to assess the genetic diversity of endophytic fungi from the genus Colletotrichum.

Genetic differentiation in Quercus infectoria from northwest of Iran revealed by different nuclear markers

The aim of the present study was to examine the genetic variability of natural populations of Quercus infectoria, based on inter-retrotransposon amplified polymorphism (IRAP), inter-simple sequence repeat (ISSR), and start codon targeted (SCoT) markers, in view of long-term conservation plans. A total of 150 accessions from ten populations of this species were sampled from northwest of Iran. Eighteen ISSR, ten IRAP, and ten SCoT primers generated a total of 466 unambiguous and repeatable bands, from which 448 (96.14 %) were polymorphic for all markers. The polymorphism information content (PIC) values for IRAP, ISSR, and SCoT markers were 0.26, 0.35, and 0.37, respectively. Genetic similarity and distance analyses indicated the existence of high variability among the studied accessions, so that a pairwise Jaccard’s genetic similarity based on combined data ranged from 0.27 to 0.79. Cluster analysis for three different molecular types revealed that the accessions taken for the analysis can be divided into two distinct clusters. Molecular variance analysis revealed that more than 70 % of the variation resided within populations and less than 30 % could be attributed to variation among populations, possibly due to gene flow between populations and life history traits. These data provide valuable information for natural resource conservation.

Retrotransposon insertional polymorphism in sunflower (Helianthus annuus L.) lines revealed by IRAP and REMAP markers

Retrotransposons are ubiquitous components of plants genomes, making them useful molecular markers for genetic diversity studies. We used inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) markers to assess genetic diversity and survey activity of LTR retrotransposon elements in 106 sunflower (Helianthus annuus L.) genotypes from different research centers. We found 118 (out of 128) and 113 (out of 120) polymorphic loci using 14 IRAP and 14 REMAP primers, respectively. The Mantel test between IRAP and REMAP cophenetic matrices revealed low correlation (r = 0.55) between them. Dice similarities based on combined (IRAP + REMAP) data ranged from 0.34 to 0.93 among (“11 × 12” and “F1250/03”) and (“HA335B” and “TMB51”) genotypes, respectively. Classification of genotypes using the Dice similarity matrix derived from IRAP+REMAP data based on the un-weighted pair-group method using the arithmetic average algorithm resulted in nine distinct groups. The studied genotypes were divided into seven groups considering their origins (research centers). Classification of genotypes can be useful to assess the genetic variation and gene flow between and within research centers. Analysis of molecular variance based on IRAP+REMAP data revealed a higher level of genetic variation within (94%) than between (6%) research centers. A high amount of gene flow was detected among USDA, ASGROW, and ENSAT groups. Because environmental factors have no influence on molecular markers, the construction of heterotic groups based on retrotransposon markers will be useful for the selecting of parents with a high probability of producing superior hybrids.

Sukkula retrotransposon insertion polymorphisms in barley

Tissue culture could be considered as one of the stress factors that affect the activation of retrotransposons. In this study, mature barley embryos (Hordeum vulgare L., cv. Tokak 157/37) were cultured for callus formation. Sukkula (a non-autonomous retrotransposon) polymorphism was investigated in calli with different culturing time (40- and 80-day-old), which was derived from the same embryo in MS medium supplemented with 3 mg/L of Dicamba. Polymorphism was detected using Inter-Retrotransposon Amplified Polymorphism (IRAP) and Inter-Primer Binding Site Amplification (iPBS) techniques with two different Sukkula-specific primers. Noncultured five mature embryos were used as a control. While up to 14% polymorphism rate was observed in the case of noncultured embryos, 61 and 0% polymorphism rates were observed with IRAP analyses for 40- and 80-day-old calli, respectively. iPBS analysis revealed the polymorphism ratio up to 29% in noncultured material, and up to 58 and 70% in 40- and 80-day-old callus materials, respectively. In addition, there were 50 and 74% polymorphism rates between 40- and 80-day-old calli by IRAP and iPBS analyses, respectively. The results obtained showed that tissue culture conditions and callus age affected Sukkula retrotransposon movements, and all individuals did not present the same effect.

Genetic variability and structure of Quercus brantii assessed by ISSR, IRAP and SCoT markers

Persian oak (Quercus brantii Lindl.) is one of the most important woody species of the Zagros forests in Iran. Three molecular marker techniques: start codon targeted (SCoT), inter-simple sequence repeat (ISSR) and inter-retrotransposon amplified polymorphism (IRAP) markers were compared for fingerprinting of 125 individuals of this species collected from different geographical locations of north-west of Iran. A total of 233 bands were amplified by 18 ISSR primers, of which 224 (96.10%) were polymorphic, and 126 polymorphic bands (97.65%) were observed in 129 bands amplified by 10 IRAP primers. Besides, 118 bands were observed for all 10 SCoT primers, of which 113 were polymorphic (95.71%). Average polymorphism information content (PIC) for ISSR, IRAP and SCoT markers was 0.30, 0.32 and 0.38, respectively, and this revealed that SCoT markers were more informative than IRAP and ISSR for the assessment of diversity among individuals. Based on the three different molecular types, cluster analysis revealed that 125 individuals taken for the analysis can be divided into three distinct clusters. The Jaccard's genetic similarity based on the combined data ranged from 0.23 to 0.76. These results suggest that efficiency of SCoT, IRAP and ISSR markers was relatively the same in fingerprinting of individuals. All molecular marker types revealed a low genetic differentiation among populations, indicating the possibility of gene flow between the studied populations. These results have an important implication for Persian oak (Q. brantii) germplasm characterization, improvement, and conservation.

Morpho-taxonomical and molecular assessment of Musa genotypes from north-east India by morphological and inter-retrotransposon amplified polymorphism markers

The states of north-eastern region of India are home to several wild and cultivated bananas. There is a dearth of information on the genetic diversity of Musa resources of the region to assist in crop improvement programmes. Twenty-five genotypes of Musaceae accessions including one Ensete species maintained at Institute of Bioresources and Sustainable Development (IBSD), Imphal, were characterized based on 60 morpho-taxonomic characters and seven inter-retrotransposon amplified polymorphism (IRAP) primer combinations. The morphological data were presented in the form of hierarchical clusters and principal components. Hierarchically, the Musa genotypes can be grouped into distinctive clusters, and while the first four principal components could explain 58.66 % of variation of the total morphological traits studied. A total of 337 amplicons were generated using 12 IRAP primer combinations with an average percentage polymorphism of 96.12. The molecular markers used in this study could reveal intra- and inter-group diversity among the genotypes with similarity coefficients ranging from 0.16 to 0.90. It could also differentiate the clusters of all the edible cultivated Musa genotypes from the wild/semi-wild ancestors. Thus, the chosen parameters seem to be especially important in the varietal or genotype identifications.

Cold-induced genetic instability in micropropagated Pistacia lentiscus L. plantlets

Genetic stability of plants during in vitro propagation and conservation is one of the important aspects of plant biotechnology. In the present study, micropropagated P. lentiscus L. shoot cultures, which are cultivated for the mastic resin, have been cold stored up to 12 months at 4 °C in the dark for different durations (2, 4, 6, 8, 10 and 12 months) and genetic alterations in cold storage conditions were evaluated. Growth parameters such as proliferation rate, shoot numbers per explant, shoot lengths and shoot forming capacity were also calculated. Since the highest proliferation rate (100 %) was obtained in 6 month-stored shoot cultures without any severe influence of cold stress on proliferation ability, amplified fragment length polymorphism (AFLP) and inter-retrotransposon amplified polymorphism (IRAP) marker systems were used to determine genetic stability in the plantlets after this storage period. Totally, 702 scorable bands were produced by 10 AFLP primer pairs. Genetic similarity value of the non-stored (control) plant and cold-stored clones ranged from 0.66 to 0.84 with a mean of 0.74. In the case of IRAP, 159 bands were produced by 8 IRAP primers. Genetic similarity value of the non-stored plant and cold-stored clones varied from 0.65 to 0.83 and the average genetic similarity value was determined as 0.72. The genetic similarity indices revealed that genetic variability was similar in both techniques. Our results showed that tissue culture and especially cold storage of P. lentiscus L. may result transposons activation, thus could cause genetic instability.

Genetic diversity of maize germplasm assessed by retrotransposon‐based markers

Maize is one of the most important crops and also a model for grass genome research. Transposable elements comprise over 78% of the maize genome and their ability to generate new copies makes them good potential markers. Interretrotransposon-amplified polymorphism (IRAP) and retrotransposon microsatellite amplified polymorphism (REMAP) protocols were used for the first time in maize to study the genetic variability between maize cultivars. Ten PCR primers were selected based on a systematic analysis of the sequence conservation in the extremities of different high copy number transposable elements, whereas one primer was chosen based on a microsatellite sequence. Of the 16 primer combinations tested, 14 produced polymorphic bands. These markers were used to identify genetic similarity among 20 maize cultivars selected by their different kernel oil content. Genetic similarity analysis was performed based on the polymorphic band profiles and dendrograms were developed by the unweighted pair-group method with arithmetic averages. Clustering technique revealed that samples were grouped into three clusters that differed in their kernel oil content and size, and in their relative embryo size. In the current investigation, there is evidence that IRAP/REMAP may be useful as markers in maize.

Genome Classification of Musa cultivars from Northeast India as Revealed by ITS and IRAP Markers

Genome classification of 38 banana cultivars found in northeast India was successfully carried out using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of the internal transcribed spacer (ITS) region and inter-retrotransposon amplified polymorphism (IRAP) techniques. The RsaI digestion of the ITS region revealed the composition of A genome in 32 cultivars and B genome in 29 cultivars. With the gypsy-IRAP marker, 33 cultivars were identified to be composed of B genome. The AluI digestion of the 420-bp PCR amplification product using copia-IRAP primer resulted in the identification of the ABB genome in 17 cultivars. Overall, the data obtained from 36 cultivars using the molecular markers were in accordance with the initial classification based on morphological characters except in two cultivars. The present findings provide the reliable information on the genome classification and the status of the existing banana genetic resources from the northeastern Indian region, which could be utilized in improvement and conservation programs.

Assessment of genetic diversity among Indian potato (Solanum tuberosum L.) collection using microsatellite and retrotransposon based marker systems

Potato (Solanum tuberosum) is an important non-cereal crop throughout the world and is highly recommended for ensuring global food security. Owing to the complexities in genetics and inheritance pattern of potato, the conventional method of cross breeding for developing improved varieties has been difficult. Identification and tagging of desirable traits with informative molecular markers would aid in the development of improved varieties. Insertional polymorphism of copia-like and gypsy-like long terminal repeat retrotransposons (RTN) were investigated among 47 potato varieties from India using Inter-Retrotransposon Amplified Polymorphism (IRAP) and Retrotransposon Microsatellite Amplified Polymorphism (REMAP) marker techniques and were compared with the DNA profiles obtained with simple sequence repeats (SSRs). The genetic polymorphism, efficiency of polymorphism and effectiveness of marker systems were evaluated to assess the extent of genetic diversity among Indian potato varieties. A total of 139 polymorphic SSR alleles, 270 IRAP and 98 REMAP polymorphic bands, showing polymorphism of 100%, 87.9% and 68.5%, respectively, were used for detailed characterization of the genetic relationships among potato varieties by using cluster analysis and principal coordinate analysis (PCoA). IRAP analysis resulted in the highest number of polymorphic bands with an average of 15 polymorphic bands per assay unit when compared to the other two marker systems. Based on pair-wise comparison, the genetic similarity was calculated using Dice similarity coefficient. The SSRs showed a wide range in genetic similarity values (0.485–0.971) as compared to IRAP (0.69–0.911) and REMAP (0.713–0.947). A Mantel’s matrix correspondence test showed a high positive correlation (r=0.6) between IRAP and REMAP, an intermediate value (r=0.58) for IRAP and SSR and the lowest value (r=0.17) for SSR and REMAP. Statistically significant cophenetic correlation coefficient values, of 0.961, 0.941 and 0.905 were observed for REMAP, IRAP and SSR, respectively. The widespread presence and distinct DNA profiles for copia-like and gypsy-like RTNs in the examined genotypes indicate that these elements are active in the genome and may have even contributed to the potato genome organization. Although the three marker systems were capable of distinguishing all the 47 varieties; high reproducibility, low cost and ease of DNA profiling data collection make IRAP and REMAP markers highly efficient whole-genome scanning molecular probes for population genetic studies. Information obtained from the present study regarding the genetic association and distinctiveness provides an useful guide for selection of germplasm for plant breeding and conservation efforts.

IRAP and REMAP-based assessment of genetic diversity in chickpea collection from Iran

Retrotransposons (RTN) make a significant contribution to the size, organization and genetic diversity of their host genomes. Several RTN families have been identified in chickpea (Cicer arietinum L.) and other closely related species. In the current research, integration activity and insertional polymorphism of the RTNs CARE1, Tms1Ret1, TPS and LORE were studied in 64 chickpea accessions collected in Iran using inter retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) techniques. Results indicated that all RTNs studied, are transpositionally active in chickpea genome and amplified scorable and polymorphic banding pattern. Among the RTN families used, the highest percentage of polymorphic loci (PPL) was produced by TPS family (81.82%). Totally, 129 loci were amplified using 18 IRAP and REMAP primers which 83 (64.34%) were polymorphic. The Dice genetic similarity coefficients among accessions ranged from 0.84 (accessions Tj48 and Ba4) to 0.98 (accessions Ka30 and Urm61), averaging 0.93. The parameters of expected heterozygosity (He), Shannon?s information index (I) and number of effective alleles (Ne) were the highest for Urmia accessions. Cluster analysis based on UPGMA algorithm and Dice similarity coefficient categorized the 64 accessions in 7 main groups. The mean Fst values of all groups except for groups IV and VII, were lower than 0.20, demonstrating no clear differentiation among the groups, no genetic structure of the studied chickpea collection and probably occurrences of gene flow among the origins. In conclusion, although RTN-based markers were able to differentiate the chickpea accessions but the measured relative genetic similarity among accessions were not correlated with geographical distances between places of their origins.