Search Results (11)

Blueberries (Vaccinium spp.) are valued for their nutritional benefits but face challenges in germplasm identification, phylogenetic analysis, and breeding due to their complex genetic background. Long Terminal Repeat Retrotransposons (LTR-RTs), major drivers of plant genetic diversity, offer a basis for the Inter-Retrotransposon Amplified Polymorphism (IRAP) system, which excels in germplasm identification, diversity assessment, and relatedness studies. Here, we developed a blueberry IRAP system using Ty1-copia reverse transcriptase sequences. From 25 core primers, we obtained 266 polymorphic loci (average PIC = 0.866). These IRAP markers fingerprinted 112 accessions and revealed relationships through Nei’s diversity index (H = 0.361), Shannon’s index (I = 0.533), AMOVA (9.33% among regions; 90.67% within populations; Nm = 1.50), UPGMA dendrograms (three clusters at 0.615 similarity), and PCoA, indicating weak geographic structure across Guiyang, Qiandongnan, and Bijie consistent with Nm = 1.50 (homogenizing gene flow). The dendrogram and PCoA indicate among-accession heterogeneity with weak geographic structuring across Guiyang, Qiandongnan, and Bijie, consistent with the AMOVA and gene-flow estimates. We also built a Molecular IDs database for differentiation. IRAP proved highly efficient for identification and analysis, matching SSR/SNP polymorphism levels while offering advantages like low-cost agarose gel resolution for detecting subtle clonal variants in polyploids—outperforming SSRs in field triage and complementing SNPs’ high throughput. This supports IP protection and breeding. Together with established SSR/SNP platforms, this IRAP approach can support IP protection and breeding as a complementary, cost-effective option. Full article

This study investigated interspecific and intraspecific polymorphism in Rheum (Polygonaceae) from Kazakhstan using the inter-primer binding site (iPBS) retrotransposon marker system. The results revealed considerable variation in the level and nature of genetic polymorphism both within and among Rheum species and ecopopulations across different regions of Kazakhstan. Rh. compactum and the ecopopulation Rh. tataricum from the Zhambyl Region (ZH) exhibited the lowest levels of polymorphism, supporting their designation as conservation priorities. Genetic differentiation analysis among species and ecopopulations identified clear distinctions, resulting in the formation of well-defined clusters with high bootstrap support. Minimal genetic distances were observed between the two ecopopulations of Rh. tataricum, along with a high degree of intraspecific genetic homogeneity in Rh. compactum and Rh. nanum. A distinct genetic divergence between Rh. compactum and the other taxa was detected, reinforcing its status as a separate species rather than a synonym of Rh. altaicum. The iPBS markers proved effective for investigating genetic variation in Rheum, offering valuable insights for future studies aimed at understanding the evolutionary history of the genus. Full article

The species belonging to the Rhododendron genus are well-known for their colorful corolla. Molecular marker systems have the potential to elucidate genetic diversity as well as to assess genetic fidelity in rhododendrons. In the present study, the reverse transcription domains of long terminal repeat retrotransposons were cloned from rhododendrons and used to develop an inter-retrotransposon amplified polymorphism (IRAP) marker system. Subsequently, 198 polymorphic loci were generated from the IRAP and inter-simple sequence repeat (ISSR) markers, of which 119 were derived from the IRAP markers. It was shown that in rhododendrons, IRAP markers were superior to the ISSRs in some polymorphic parameters, such as the average number of polymorphic loci (14.88 versus 13.17). The combination of the IRAP and ISSR systems was more discriminative for detecting 46 rhododendron accessions than each of the systems on their own. Furthermore, IRAP markers demonstrated more efficiency in genetic fidelity detection of in-vitro-grown R. bailiense Y.P.Ma, C.Q.Zhang and D.F.Chamb, an endangered species recently recorded in Guizhzhou Province, China. The available evidence revealed the distinct properties of IRAP and ISSR markers in the rhododendron-associated applications, and highlighted the availability of highly informative ISSR and IRAP markers in the evaluation of genetic diversity and genetic fidelity of rhododendrons, which may facilitate preservation and genetic breeding of rhododendron plants. Full article

This study investigated the genetic diversity and population structure of 63 genotypes from Turkish bread wheat germplasm using iPBS-retrotransposons primers. The thirty-four iPBS primers produced a total of 1231 polymorphic bands, ranging from 8 (iPBS-2375) to 60 (iPBS-2381) alleles per marker, with an average number of 36.00 alleles. The polymorphism information content (PIC) per marker varied between 0.048 (iPBS 2087) and 0.303 (iPBS 2382), with an average of 0.175. The numbers of effective alleles (ne), genetic diversity of Nei (h), and Shannon’s information index (I) value were calculated as 1.157, 0.95, and 0.144, respectively. The greatest genetic distance (0.164) was between Eastern Anatolia Agricultural Research Institute genotypes and Çukurova Agricultural Research Institute genotypes. The unweighted pair-group method with arithmetic mean (UPGMA) dendrogram placed the 63 wheat genotypes into three clusters. The percentage of genetic diversity explained by each of the three main coordinates of the basic coordinate analysis was determined to be 44.58, 12.08, and 3.44, respectively. AMOVA (Analysis of Molecular Variance) showed that the variation within populations was 99% and that between populations was 1%. The result of genetic structure analysis suggests that the greatest value of K was calculated as 3. The F-statistic (Fst) value was determined as 0.4005, 0.2374, and 0.3773 in the first to third subpopulations, respectively. Likewise, the expected heterozygosity values (He) were determined as 0.2203, 0.2599, and 0.2155 in the first, second, and third subpopulations, respectively. According to the information obtained in the study, the most genetically distant genotypes were the G1 (Aksel 2000) and G63 (Karasu 90) genotypes. This study provided a deep insight into genetic variations in Turkish bread wheat germplasm using the iPBS-retrotransposons marker system. Full article

Ambrosia beetles, Anisandrus dispar Fabricius, Xylosandrus germanus Blandford, and Xyleborinus saxesenii Ratzeburg (Coleoptera: Curculionidae: Scolytinae) are among the most significant hazelnut pests in Turkey. The control of these pests is difficult and expensive due to their biology. The present study aimed to isolate entomopathogenic fungi (EPF) from A. dispar, X. germanus, and X. saxesenii individuals that were obtained from the main hazelnut production areas of Turkey, characterize the EPF isolates using internal transcribed spacer (ITS)-DNA sequencing and iPBS profiling, and determine the efficacy of the isolates against A. dispar, X. germanus, and X. saxesenii under laboratory conditions. Phylogenetic analyses based on ITS revealed that the 47 native isolates were Beauveria bassiana (11), B. pseudobassiana (8), Cordyceps fumosorosea (6), Cordyceps farinosa (1), Akanthomyces lecanii (13), Purpureocillium lilacinum (3), Clonostachys rosea (2) and Metarhizium anisopliae (3). For the first time, the primer binding site (PBS) marker system, based on retrotransposons, was used to discriminate successfully among the EPF species. Some isolates of B. bassiana, B. pseudobassiana, C. fumosorosea, A. lecanii, and M. anisopliae caused 100% mortality of the beetle species within 7 to 9 days. The findings of this study indicated that some isolated entomopathogenic fungi provide an essential basis for the development of bioproducts, as well as a promising alternative method for controlling these ambrosia beetles. Full article

Retrotransposons account for more than one-third of the pig reference genome. On account of the genome variability in different breeds, structural variation (SV) caused by retrotranspos-on-generated deletion or insertion (indel) may have a function in the genome. Litter size is one of the most important reproductive traits and significantly impacts profitability in terms of pig production. We used the method of bioinformatics, genetics, and molecular biology to make an analysis among different pig genomes. Predicted 100 SVs were annotated as retrotransposon indel in 20 genes related to reproductive performance. The PCR detection based on these predicted SVs revealed 20 RIPs in 20 genes, that most RIPs (12) were generated by SINE indel, and eight RIPs were generated by the ERV indel. We selected 12 RIPs to make the second round PCR detection in 24 individuals among nine pig breeds. The PCR detection results revealed that the RIP-A1CF-4 insertion in the breed of Bama, Large White, and Meishan only had the homozygous genotype but low to moderately polymorphisms were present in other breeds. We found that RIP-CWH43-9, RIP-IDO2-9, RIP-PRLR-6, RIP-VMP1-12, and RIP-OPN-1 had a rich polymorphism in the breed of Large White pigs. The statistical analysis revealed that RIP-CWH43-9 had a SINE insertion profitable to the reproductive traits of TNB and NBA but was significantly affected (p < 0.01) and (p < 0.05) in the reproductive traits of litter birthweight (LW) in Large White. On the other hand, the SINE insertion in IDO2-9 may be a disadvantage to the reproductive traits of LW, which was significantly affected (p < 0.05) in Large White. These two RIPs are significant in pig genome research and could be useful molecular markers in the breeding system. Full article

Beans are legumes that play extremely important roles in human nutrition, serving as good sources of protein, vitamins, minerals, and antioxidants. In this study, we tried to elucidate the genetic diversity and population structure of 40 Turkish bean (Phaseolus vulgaris L.) local varieties and 5 commercial cultivars collected from 8 different locations in Erzurum-Ispir by using inter-primary binding site (iPBS) retrotransposon markers. For molecular characterization, the 26 most polymorphic iPBS primers were used; 52 bands per primer and 1350 bands in total were recorded. The mean polymorphism information content was 0.331. Various diversity indices, such as the mean effective allele number (0.706), mean Shannon’s information index (0.546), and gene diversity (0.361) revealed the presence of sufficient genetic diversity in the germplasm examined. Molecular analysis of variance (AMOVA) revealed that 67% of variation in bean germplasm was due to differences within populations. In addition, population structure analysis exposed all local and commercial bean varieties from five sub-populations. Expected heterozygosity values ranged between 0.1567 (the fourth sub-population) and 0.3210 (first sub-population), with an average value of 0.2103. In contrary, population differentiation measurement (Fst) was identified as 0.0062 for the first sub-population, 0.6372 for the fourth subpopulations. This is the first study to investigate the genetic diversity and population structure of bean germplasm in Erzurum-Ispir region using the iPBS-retrotransposon marker system. Overall, the current results showed that iPBS markers could be used consistently to elucidate the genetic diversity of local and commercial bean varieties and potentially be included in future studies examining diversity in a larger collection of local and commercial bean varieties from different regions. Full article

In this study, the molecular, biochemical and agro-morphological characterization of genotypes belonging to hawthorn species collected from Bolu province of Turkey was performed. Inter-priming binding sites (iPBS) markers based on retrotransposons were used for the first time in the molecular properties of hawthorn genotypes in the world. The marker system provided very useful information for revealing the genetic variation of the genotypes. Six iPBS markers amplified 68 fragments, of which 65 were polymorphic (95.59%) with an average of 10.83 polymorphic bands per primer. The polymorphism and resolving power per primers ranged from 0.12 to 0.42 and from 0.78 to 8.11 with the average being 0.32 and 5.95, respectively. Pomological properties of Crataegus tanacetifolia, such as fruit pomology and core weight were determined to higher than those of Crataegus monogyna. Citric acid was determined as the most predominant organic acid, followed by malic and succinic acid in the genotypes of both species. The highest citric acid content (26.745 mg 100 g⁻¹) was noted for 14BL09 genotype. The vit. C content was recorded ranging from 2.681 to 9.621 mg 100 g⁻¹. Catechin, chlorogenic, caffeic and rutin contents were varied between 4.140–51.393 mg, 2.254–42.361 mg, 0.624–4.407 mg, and 1.241–10.029 mg per 100 g of fruits, respectively. As a result, it has been determined that twenty-five genotypes belonging to different hawthorn species are important genetic resources to be evaluated in horticultural breeding studies in terms of their physical and biochemical contents. Full article

Bamboo, a non-timber grass species, known for exceptionally fast growth is a commercially viable crop. Long terminal repeat (LTR) retrotransposons, the main class I mobile genetic elements in plant genomes, are highly abundant (46%) in bamboo, contributing to genome diversity. They play significant roles in the regulation of gene expression, chromosome size and structure as well as in genome integrity. Due to their random insertion behavior, interspaces of retrotransposons can vary significantly among bamboo genotypes. Capitalizing this feature, inter-retrotransposon amplified polymorphism (IRAP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there are no transposon based markers reported from the bamboo genome and particularly using IRAP markers on genetic diversity. Phyllostachys genus of Asian bamboo is the largest of the Bambusoideae subfamily, with great economic importance. We report structure-based analysis of bamboo genome for the LTR-retrotransposon superfamilies, Ty3-gypsy and Ty1-copia, which revealed a total of 98,850 retrotransposons with intact LTR sequences at both the ends. Grouped into 64,281 clusters/scaffold using CD-HIT-EST software, only 13 clusters of retroelements were found with more than 30 LTR sequences and with at least one copy having all intact protein domains such as gag and polyprotein. A total of 16 IRAP primers were synthesized, based on the high copy numbers of conserved LTR sequences. A study using these IRAP markers on genetic diversity and population structure of 58 Asian bamboo accessions belonging to the genus Phyllostachys revealed 3340 amplicons with an average of 98% polymorphism. The bamboo accessions were collected from nine different provinces of China, as well as from Italy and America. A three phased approach using hierarchical clustering, principal components and a model based population structure divided the bamboo accessions into four sub-populations, PhSP1, PhSP2, PhSP3 and PhSP4. All the three analyses produced significant sub-population wise consensus. Further, all the sub-populations revealed admixture of alleles. The analysis of molecular variance (AMOVA) among the sub-populations revealed high intra-population genetic variation (75%) than inter-population. The results suggest that Phyllostachys bamboos are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the usability of IRAP markers in determining the inter-species variability of Asian bamboos. Full article

Laurel is a medicinally important plant and is known to the world for its essential oil. Turkey is the main market in the laurel leaf trade by sharing about 90% of the world trade. Here we made an effort to elucidate genetic diversity and population structure of 94 Turkish laurel genotypes collected from 26 provinces and four geographical regions using inter-primer binding site (iPBS) retrotransposon markers. A total of 13 most polymorphic primers were selected which yielded 195 total bands, of which 84.10% were found polymorphic. Mean polymorphism information content (PIC) was (0.361) and diversity indices including mean effective number of alleles (1.36), mean Shannon’s information index (0.35) and overall gene diversity (0.22) revealed the existence of sufficient amount of genetic diversity in the studied plant material. Most diversity was found in genotypes collected from the Mediterranean region. Analysis of molecular variance (AMOVA) revealed that most of the variation (85%) in Turkish laurel germplasm is due to differences within populations. Model-based structure, principal coordinate analysis (PCoA) and neighbor-joining algorithms were found in agreement and clustered the studied germplasm according to their collection provinces and regions. This is a very first study exploring the genetic diversity and population structure of laurel germplasm using iPBS-retrotransposon marker system. We believe that information provided in this work will be helpful for the scientific community to take more interest in this forgotten but the medicinally important plant. Full article

Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is the wild ancestor of all cultivated tetraploid and hexaploid wheats and harbors a large amount of genetic diversity. This diversity is expected to display eco-geographical patterns of variation, conflating gene flow, and local adaptation. As self-replicating entities comprising the bulk of genomic DNA in wheat, retrotransposons are expected to create predominantly neutral variation via their propagation. Here, we have examined the genetic diversity of 1 Turkish and 14 Israeli populations of wild emmer wheat, based on the retrotransposon marker methods IRAP and REMAP. The level of genetic diversity we detected was in agreement with previous studies that were performed with a variety of marker systems assaying genes and other genomic components. The genetic distances failed to correlate with the geographical distances, suggesting local selection on geographically widespread haplotypes (‘weak selection’). However, the proportion of polymorphic loci correlated with the population latitude, which may reflect the temperature and water availability cline. Genetic diversity correlated with longitude, the east being more montane. Principal component analyses on the marker data separated most of the populations. Full article