Amplified Polymorphism Markers Research Articles

DNA barcode and sequence related amplified polymorphism markers reveal phylogenetic relationship among Pinus species representing closed lineage divergence

DNA barcode and sequence related amplified polymorphism markers reveal phylogenetic relationship among Pinus species representing closed lineage divergence

Induced Mutations in Gaillardia pulchella Foug Plants by Chemical Mutagen and Detection Variation by (SRAP) Sequence-Related Amplified Polymorphism Markers

Induced Mutations in Gaillardia pulchella Foug Plants by Chemical Mutagen and Detection Variation by (SRAP) Sequence-Related Amplified Polymorphism Markers

Genetic evaluation of F2 and F3 interspecific hybrids of mung bean (Vigna radiata L. Wilczek) using retrotransposon‐based insertion polymorphism and sequence‐related amplified polymorphism markers

Mung bean (Vigna radiata L. Wilczek) is a self‐pollinating and indispensable pulse crop in Indonesia. While low yield productivity is a major concern, genetic improvement is possible through interspecific hybridization. However, interspecific hybridization is relatively infrequent and produces low recombination exchanges, significantly limiting crop breeding efficiency. Thus, a comprehensive study is needed of the selection and genetic diversity evaluation of progenies in advanced generations derived from interspecific hybridization using a specific molecular marker. This study aims to confirm the heterozygosity in the F2 population and assess the genetic diversity in F3 mung bean populations resulting from interspecific hybridization between the mung bean and common bean. We designed the retrotransposon‐based insertion polymorphism (RBIP) marker by identifying the syntenic regions in the flanking sequences of retrotransposon insertion in common bean and mung bean. The RBIP marker can be applied to distinguish the heterozygote progenies from the homozygote progenies. Six combinations of sequence‐related amplified polymorphism (SRAP) primers were used in the genotyping of F3 mung bean progenies. The SRAP marker showed a high degree of polymorphism of up to 100%, while high genetic variation was observed within the population (71%) of mung bean progenies. The F3.4 population had the greatest number of genotypes and displayed the highest number of effective alleles, private alleles, and percentage of polymorphic loci, suggesting the existence of high genetic diversity within this population. These genetic diversity data are exceptionally critical for future genetic research since it has potentially high yield production. The genomic and marker‐assisted selection studies will support the major goals of the mung bean breeding program.

Induction of genetic variability with gamma radiation and detection of DNA polymorphisms among radiomutants using sequence-related amplified polymorphism markers in Gaillardia pulchella Foug. plants

Background Developing novel ornamental varieties with improved floral characterization is the main aim of floriculture. Biotechnological techniques linked to classical breeding methods have been applied for modifying flower color. Objective This investigation was carried out in the nursery of the Ornamental Horticulture Department, Faculty of Agriculture, Cairo University, Egypt, during two successive generations, 2019/2020 and 2020/2021, to assess the effects of gamma irradiation (γ) on vegetative growth, flowering parameters, abnormalities, and induced changes at the DNA level between two mutative generations (MG1 and MG2) of Gaillardia pulchella Foug. plants. Materials and methods Seeds of G. pulchella (local red) were irradiated at Atomic Energy Commission-united irradiation-Gamma, The Egyptian Atomic Energy Authority (EAEA), Nasr City, Cairo, Egypt, by six doses of γ-irradiation (10, 20, 30, 40, 50, and 60 Gy), using Gamma-1 type cobalt60, at a dose rate of 1.107 KGy/h. Results and conclusion The results revealed that low gamma doses (10 and 20 Gy) had significant effects on vegetative growth, that is, plant height and the number of branches, as compared with the control, giving the tallest plants with the highest number of branches. The high doses (50 and 60 Gy) delayed flowering compared with untreated plants and other gamma doses. In contrast, low doses induced early flowering and increased the number of flowers. All doses of gamma rays induced mutants in leaf morphology, inflorescence color, shape, and deformation; the largest number of these mutants was obtained from a high dose of 60 Gy. On the contrary, sequence-related amplified polymorphism analysis produced 32 loci, of which 12 (37.50%) were polymorphic. Jaccard’s coefficients of dissimilarity ranged from 0.69 to 0.96. In a dendrogram constructed depending on genetic identity coefficients, the mutants were classified into three major groups: the first group (I) was composed of 10-, 20-, 30-, and 40-Gy mutants. The second group (II) included 50- and 60-Gy mutants. The third group (III) contained only the control. Therefore, it was concluded that treatment of G. pulchella seeds with gamma rays led to the induction of a sufficient number of mutations. In addition, the sequence-related amplified polymorphism marker is considered to be an important tool in the identification of mutants. Consequently, these mutants can be used in breeding programs to improve G. pulchella plants.

Genetic Diversity and Relationships within Citrus Species Based On Sequence-Related Amplified Polymorphism Markers (Sraps)

Genetic Diversity and Relationships within Citrus Species Based On Sequence-Related Amplified Polymorphism Markers (Sraps)

Biological Activity and NMR-Fingerprinting of Balkan Endemic Species Stachys thracica Davidov.

Stachys thracica Davidov is a Balkan endemic species distributed in Bulgaria, Greece, and Turkey. In Bulgaria, it is classified as “rare” and is under the protection of the Bulgarian biodiversity law. The aim of our study was to develop an efficient protocol for ex situ conservation of S. thracica and to perform comparative NMR-based metabolite profiling and bioactivity assays of extracts from in situ grown, in vitro cultivated, and ex vitro acclimated plants. Micropropagation of S. thracica was achieved by in vitro cultivation of mono-nodal segments on basal MS medium. Ex vitro adaptation was accomplished in the experimental field with 83% survival while conserved genetic identity between in vitro and ex vitro plants as shown by the overall sequence-related amplified polymorphism marker patterns was established. Verbascoside, chlorogenic acid, and trigonelline appeared the main secondary metabolites in in situ, in vitro cultivated, and ex vitro acclimated S. thracica. High total phenolic and flavonoid content as well as antioxidant and radical scavenging activity were observed in in situ and ex vitro plants. Further, the anti-inflammatory activity of S. thracica was tested by hemolytic assay and a high inhibition of the complement system was observed. Initiated in vitro and ex vitro cultures offer an effective tool for the management and better exploitation of the Stachys secondary metabolism and the selection of lines with high content of bioactive molecules and nutraceuticals.

Biosystematics, fingerprinting and DNA barcoding study of the genus Lallemantia based on SCoT and REMAP markers

Lallemantia is a medicinally important plant in the world. Due to interspecific hybridization and horizontal gene transfer, spices relationship and delimitation on the genus Lallemantia is difficult based on different molecular markers. Therefore, selecting the appropriate marker can be important. Fingerprinting techniques continue to be used for genomic profiling for the characterization of germplasm and the establishment of the identity of varieties/hybrids/parental sources of aromatic and medicinal plants. For this, we need to produce detailed information on genetic diversity available in Lallemantia as well as investigate spices relationship and delimitation. Therefore, the present study was performed on Lallemantia species in Iran. We used the start codon targeted and retrotransposon-microsatellite amplified polymorphism molecular marker for our genetic investigation with the following aims: 1- To reveal the species delimitation and species relationship in Lallemantia, and 2- To investigate discriminating power of the start codon targeted and retrotransposon-microsatellite amplified polymorphism markers by Gst and NM analysis. The results obtained revealed that the start codon targeted marker is the best to show the relationships between species while the retrotransposon-microsatellite amplified polymorphism marker is the best for species delimitation. we found the loci with the high value of Gst (1.00) in start codon targeted and retrotransposon-microsatellite amplified polymorphism markers that can be used in barcoding and fingerprinting of L. royleana.

Retrotransposon-based markers revealed a repartition depending on geographical origin and breeding status of Tunisian pistachio species

Abstract Retrotransposon movements are considered to be an important factor in evolutionary processes and speciation as well as a source of genetic variation. In order to analyze genetic diversity and population structure in Tunisian pistachio species, nine inter-retrotransposon amplified polymorphism (IRAP) markers were used. As a result, eighty-six amplicons were produced among which 98.15 % were polymorphic. Mean numbers of the effective number of alleles (Ne), Shannon’s information index (I) and Nei’s genetic diversity (H) were respectively 1.529, 0.478, and 0.310. The average within-population genetic diversity (Hs) was 0.24 and the total diversity (Ht) was 0.3. The Tunisian pistachio populations exhibited high genetic differentiation (Gst =0.275) and gene flow (Nm = 1.888). The Analysis of Molecular Variance (AMOVA) indicated that variation was very high within populations (83 %). Phylogenetic tree using neighbor- joining (NJ) method and Principal Coordinates Analysis (PCoA) depicted that groupings of Tunisian varieties were made independently of the sex of the trees, but depending on their geographical origin and their breeding status. The modelbased Bayesian clustering (STRUCTURE) confirmed these observations. The inter-retrotransposons amplification polymorphism markers were significantly informative at the interspecific level. Findings reported in our study will be essential toward breeding for new pistachio genotypes with developed chemical and horticultural features.

Genetic divergence ofDeschampsia antarctica(Poaceae) population groups in the maritime Antarctic

AbstractWe used inter-simple sequence repeats and inter-retrotransposon amplified polymorphism markers to assess genetic variation in Deschampsia antarctica populations in the context of its uneven distribution in the northern and central maritime Antarctic. Genetic diversity and population structure and differentiation were assessed in nine populations from geographically isolated population groups of D. antarctica, including the South Shetland Islands, Anvers Island and the Argentine Islands regions. In total, 265 amplified DNA fragments were scored, of which 220 (83.0%) were polymorphic. The total sample showed low genetic diversity (unbiased expected heterozygosity = 0.081 and Shannon diversity index = 0.115) and high population differentiation (molecular variance among populations = 0.659). We also found a trend toward a decrease in genetic diversity and an increase in population differentiation toward the southern edge of the species range. Principal coordinates analysis of polymerase chain reaction data and Bayesian population structure analysis showed three main clusters, which included plants originating from three spatially isolated population groups. The unweighted pair group method with arithmetic mean clustering of populations based on Nei’s genetic distances was mainly in agreement with this pattern. Testing of isolation by distance using the Mantel test demonstrated a significant correlation between genetic and ln-transformed geographical distance (r = 0.703). The data obtained indicate that the geographically isolated D. antarctica populations in the maritime Antarctic might form genetic clusters within the total range.

Genetic Profiling of Sida rhombifolia Originated from Several Indonesian Ethnicities Based on Sequence-Related Amplified Polymorphism Markers

Sida rhombifolia is one of wild flowering plants that grows easily in many habitats with moderate humidity, with some usefulness in traditional medicine. Genetic characterization of Sida rhombifolia accessions originated from 12 ethnicities of Indonesia was analyzed based on Sequence-Related Amplified Polymorphism (SRAP) Markers. The genomic DNA were extracted from leaf samples and then were characterized by using the SRAP marker system according to Li and Quiros (2001). Nine pairs of SRAP primer resulted high polymorphic bands and were used in the genetic profiling. The data analysis was performed using GenAlEx to calculate genetic distance, Principal coordinate analysis, and Analysis of Molecular Variance (AMOVA), also using POPGENE to assess genetic diversity (Hs and Ht) and Nm to predict gene flow among populations. The coordinate analysis showed that the accessions originated from ethnicities along Wallacean line tend to differ genetically from most other locations. However, the results of analysis of molecular variance suggested that there were only slight differences (0.1%) found between ethnicities, while most genetic variances (99.9%) were found mostly among accessions within populations. The results suggested that there was an extensive genetic flow and plant spreading among Sida rhombifolia plant populations, resulting more homogenous genetic characters among most populations, while high diversity within population. The calculation of the number of migration (Nm = 1.7341) confirmed that the high rate of gene flow had occurred between populations.

Analysis of genetic variability in F2 interspecific hybrids of mung bean (Vigna radiata) using inter-retrotransposon amplified polymorphism marker system

Abstract. Fatmawati Y, Setiawan AB, Purwantoro A, Respatie DW, Teo CH. 2021. Analysis of genetic variability in F2 interspecific hybrids of mung bean (Vigna radiata) using inter-retrotransposon amplified polymorphism marker system. Biodiversitas 22: 4880-4889. Mung bean (Vigna radiata L. Wilczek) categorized as one of the pivotal annual crops of Vigna genera is commonly cultivated in rotation with the cereal crops during the drought season. Conversely, to ameliorate its stunted productivity, the interspecific hybridization technique has been introduced between the mung bean and the common bean to promote genetic improvement with the breeding projects in Indonesia. However, since mung bean is a self-pollinated crop and has a narrow genetic base, the selection and improvement of a specific trait using marker-assisted selection is more challenging. Hence, a precautionary investigation is imperative to evaluate the progenies resulting from interspecific hybridization using an ideal marker. This study aimed to investigate the genetic variability of the F2 population of the interspecific mung bean hybrids using retrotransposon-based markers, particularly Inter-Retrotransposon Amplified Polymorphism (IRAP) markers. In this study, we identified retrotransposon from the mung bean genome and determined the Long Terminal Repeat (LTR) sequence using the LTR Finder. The IRAP primers were designed from a conserved region of the LTR sequence. One hundred of the F2 interspecific hybrids generated from the crossing between mung bean and common bean were successfully discriminated by IRAP markers. The IRAP marker showed high heterozygosity and moderate Polymorphic Information Content (PIC) values. The IRAP markers were able to detect genetic variability in the F2 progenies resulting from the interspecific hybridization. Cluster analysis showed that 100 of the F2 progenies were grouped into three clusters. This study demonstrated that retrotransposon-based markers can offer an effective approach for evaluating the segregation in the F2 population of intercross hybrids in the mung bean.

Exploring Genetic Variability among and within Hail Tomato Landraces Based on Sequence-Related Amplified Polymorphism Markers

Landraces are valuable sources of genetic characteristics, which are of plant breeders’ interest to include in breeding programs for crop improvement. We assess the inter- and intra-genetic variability among 96 accessions representing three Hail tomato landrace using DNA-based marker sequence-related amplified polymorphism (SRAP). Seven SRAP primer combinations generated 55 alleles with a polymorphism of 100%, and an average of 7.86 polymorphic alleles per pair of primers. All primers showed an average of 0.68 polymorphic information content (PIC) value and discrimination power (DP) of 14.29. Principal coordinate analysis (PCoA) confirmed the clustering produced via the UPGMA similarity dendrogram allowed for the grouping of the 96 accessions according to its gene bank accession numbers and showed relatively good separation between landraces. A similarity value ranged from 0.04 to 1.0 among accessions of Hail 747, 0.05 to 1.0 in Hail 1072, and from 0.16 to 0.92 in Hail 548. These results showed the landraces harbor a wide range of genetic diversity at both inter and intra-variation levels. AMOVA showed that most of the genetic variation was because of differences within populations (87%). Tomato Hail landraces have well-differentiated genetic populations and admixtures, where Hail 747 formed their separate group, and both Hail 548 and Hail 1072 were admixed, and some accessions showed more diversity pattern. We have to take the SRAP technique’s effectiveness in the study of genetic variability among and within landraces into consideration in the tomato-breeding programs through marker-assessed selection.

Genetic diversity of ‘Bangle’ (Zingiber montanum (J.Koenig) Link ex A.Dietr.) inferred from sequence-related amplified polymorphism markers

Genetic diversity of ‘Bangle’ (Zingiber montanum (J.Koenig) Link ex A.Dietr.) inferred from sequence-related amplified polymorphism markers

Genetic diversity of quinoa (Chenopodium quinoa Willd.) germplasm as revealed by sequence-related amplified polymorphism markers

Genetic diversity of quinoa (Chenopodium quinoa Willd.) germplasm as revealed by sequence-related amplified polymorphism markers

Genetic mapping of the three-pistil gene Pis1 in an F2 population derived from a synthetic hexaploid wheat using multiple molecular marker systems

The wheat spike mutant 'three-pistil' (TP) exhibits normal external morphology but produces two additional pistils per floret. Much attention has been paid to this natural mutation because elucidation of its genetic foundation potentially paves a way to increase the number of grains per spike for breeding. Our previous studies roughly mapped the causal locus of TP on chromosome 2D. In this study, we performed genetic mapping of the three-pistil gene Pis1 in an F2 population derived from a cross of TP and synthetic hexaploid wheat of which chromosome 2D was from Aegilops tauschii. Segregation analysis in the F2 population confirmed the dominance of the Pis1 locus. Bulked segregant analysis with three DNA marker systems revealed a total of 18 markers genetically linked with Pis1. Successive genetic linkage analysis of the F2 individuals using the 18 markers identified two sequence-related amplified polymorphisms markers, Me5-eM33 and Me26-eM33, flanked the Pis1 locus at distances of 0.6 and 1.7 cM, respectively. Integration of the genetic linkage and previously discovered DNA markers associated with Pis1 revealed a potential location of the Pis1 locus between Me5-eM33 and a KASP marker M75. Thus, the constructed partial genetic linkage map is useful for the isolation of Pis1 and marker-assisted breeding in wheat.

Environmentally induced phenotypic plasticity and DNA methylation changes in a wild potato growing in two contrasting Andean experimental gardens.

DNA methylation can be environmentally modulated and plays a role in phenotypic plasticity. To understand the role of environmentally induced epigenetic variation and its dynamics in natural populations and ecosystems, it is relevant to place studies in a real-world context. Our experimental model is the wild potato Solanum kurtzianum, a close relative of the cultivated potato S. tuberosum. It was evaluated in its natural habitat, an arid Andean region in Argentina characterised by spatial and temporal environmental fluctuations. The dynamics of phenotypic and epigenetic variability (with Methyl Sensitive Amplified Polymorphism markers, MSAP) were assayed in three genotypes across three growing seasons. These genotypes were cultivated permanently and also reciprocally transplanted between experimental gardens (EG) differing in ca. 1000 m of altitude. In two seasons, the genotypes presented differential methylation patterns associated to the EG. In the reciprocal transplants, a rapid epigenomic remodelling occurred according to the growing season. Phenotypic plasticity, both spatial (between EGs within season) and temporal (between seasons), was detected. The epigenetic and phenotypic variability was positively correlated. The lack of an evident mitotic epigenetic memory would be a common response to short-term environmental fluctuations. Thus, the environmentally induced phenotypic and epigenetic variation could contribute to populations persistence through time. These results have implications for understanding the great ecological diversity of wild potatoes.

Sequence-related amplified polymorphism markers – a tool for litchi breeders in Africa

Litchi represents an economically important crop in South Africa – however, the local industry is based on only five cultivars. In order to expand the gene pool and to extend the harvest season, new cultivars have been imported. Currently, cultivars are identified based on morphological characteristics, but these are not always reliable. Molecular markers provide a tool to supplement morphological characterisation, particularly in cases in which confusion exists. The present study reports on the application of sequence-related amplified polymorphism (SRAP) markers in litchi for assessment of genetic relationships and molecular characterisation. The results provide evidence for separation of cultivars based on maturation period and fruit characteristics. The SRAP markers provide a tool for molecular characterisation that can be readily used by researchers with limited budgets, which is common in many developing countries.
 Significance:
 
 We report on the application of SRAP markers as a tool for litchi breeders in resource constrained countries.
 The tested molecular markers allowed for genotyping (molecular characterisation) of litchi cultivars and selections.
 The markers also revealed relationships between genetic and morphological (phenotypic) characteristics.

Spathiphyllum‘un Geçici Daldırma Biyoreaktör Sistemi ile Mikroçoğaltımı

Türkiye, süs bitkileri yetiştiriciliği açısından elverişli koşulları, pazar ülkelere yakınlığı ve ucuz işgücüne sahip olması gibi sebeplerle avantajlı bir konuma sahiptir. Bir iç mekân bitkisi olan spathiphyllum talebini karşılamak amacıyla, klasik üretim yöntemlerine ek olarak biyoteknolojik yöntemlerden de yararlanılmaktadır. Son yıllarda bitkilerin Mikroçoğaltım‘ında klasik doku kültürü sistemleri ile beraber, geçici daldırma biyoreaktörler olarak adlandırılan sistemlerin de kullanımına başlanmıştır. Bu çalışma kapsamında, ticari olarak öneme sahip spathiphyllum ‘Chico‘ genotipinde, klasik doku kültürü ve geçici daldırma biyoreaktör sistemlerinden biri olan Plantform kullanılarak, Mikroçoğaltım ve köklendirme çalışmaları yürütülmüştür. Her iki sistemde kurulan Mikroçoğaltım denemelerinde 1 mg L-1 6-Benzilaminopürin (BAP) içeren Murashige ve Skoog (MS) besin ortamı, köklendirme denemelerinde ise 1 mg L-1 İndol-3-bütirik asit (IBA) içeren MS ortamı kullanılmıştır. Mikroçoğaltım ve köklenme sonuçlarının, her iki sistemde de başarılı olduğu tespit edilmiştir. Dizi İlişkili ÇoğaltılmışÌ§ Polimorfizm (SRAP) markırları ile yapılan DNA analizleri sonucunda da, çoğaltılan ve köklendirilen bitkilerde herhangi bir genetik açılımın olmadığı belirlenmiştir.

Genetic diversity and population structure of Meretrix petechialis in China revealed by sequence-related amplified polymorphism markers.

Genetic variation in nine stocks of Meretrix petechialis collected from China was analyzed using sequence-related amplified polymorphism (SRAP) markers. Eight primer pairs produced 132 polymorphic loci with an average of 16.5 loci per primer pair. A population from Jiangsu had the highest percentage of polymorphic loci at 27.27%, suggesting that these resources had a rich genetic diversity. The Nei’s gene diversity of the nine populations ranged from 0.0647 to 0.0793; a population from Shandong was the lowest and a population from North Korea the highest. The Shannon’s information index was between 0.1023 and 0.1202, with the lowest in the Shandong population and the highest in the Jiangsu population. The Nei’s unbiased genetic distance between the nine populations was 0.0243–0.0570 and the genetic similarity was 0.9446–0.9760; the genetic distance between Guangxi and Shandong populations was the furthest (0.0570) and the genetic distance between Shandong and Jiangsu populations was the closest (0.0243). Nei’s gene diversity analysis indicated that the genetic variance was mainly found within individual geographical populations, and the analysis of molecular variance revealed low but significant genetic differentiation among local and regional populations. The limited gene flow (Nm = 0.555) was inferred as a major reason for the extent of genetic differentiation in M. petechialis. The results obtained here indicated that M. petechialis have high degree of genetic diversity and the potential of further breeding with excellent germplasm resources. This study provides a scientific basis for the protection of germplasm resources and the breeding of M. petechialis.

Evaluating genetic diversity and structure of a wild hop (Humulus lupulus L.) germplasm using morphological and molecular characteristics

Humulus lupulus L., is an economically and ecologically important plant species, which has suffered habitat degradation throughout the Hyrcanian forests (Northern Iran). Towards conservation and exotic breeding germplasm assessment, we conducted a survey in the Hyrcanian forests: 15 wild populations (WPs) were located and 54 samples collected. Genetic diversity and population structure were assessed by scoring sequence-related amplified polymorphism markers (SSR, ISSR, and RAPD) and morphological features. Molecular marker analysis showed that RAPDs (232) and ISSRs (77) produced more polymorphic bands compared to SSRs (64) per marker. SSRs exhibited a higher PIC average value (0.64), than RAPDs (0.24) and ISSRs (0.54). Cluster analyses based on the SSR markers to a high degree discriminated WPs based on geographical regions and were more congruent with morphologic traits than the ISSR–RAPD-based clustering. The ΔK parameter of structure analysis showed five clusters. The grouping of the WPs based on the structure analysis was congruent with the SSR clustering to some extent. The results confirmed that SSR markers are effective tools to detect the genetic diversity in hops, but employing higher number of molecular markers (more SSRs), which have a higher polymorphism and prevalence in the genome, or application of NGS SNPs in the identification and genetic relationship of hop indigenous populations, is recommended.