Sequence-related Amplified Polymorphism Markers Research Articles

Assessment of Genetic Diversity and Relationships among Gypsophila and Silene Species from Turkey based on SRAP Markers

Gypsophila (Gypsophila L.) is a member of the Caryophyllaceae family and its genus consists of approximately 150 species. Some of several species are grown commercially for a variety of uses herbal medicine, and food. Its most common use is as cut flower worldwide. Gypsophila species are native and widely distributed in Turkey that is the main genetic resource center. In this study, firstly Gypsophila L. genotypes were collected from native areas in Turkey. Secondly, genetic diversity using molecular markers were provided valuable information for breeding programs and strategies of germplasm conservation. Sequence-related amplified polymorphism (SRAP) as a molecular markers were used to determine diversity and relationships among 41 Gypsophila (Caryophyllaceae) genotypes including 13 species (G. viscosa, G. simonii, G. venusta, G. bicolor, G. simulatrix, G. bitlisensis, G. germanicopolitana, G. perfoliata, G. arrostii, G. eleganas, G. paniculata and G. aucheri) and 2 Silene types (S. vulgaris and Silene spp.) as outgroups. As results, twenty primer combinations were produced 153 scorable fragments, and also all markers were showed 100% polymorphism for 43 genotypes. The significance of the resulting dendrograms was verified calculating the cophenetic correlation r values (r ≥ 0.80) for SRAP markers. The Gypsophila and Silene species were clearly grouped according to subspecies and by region. Results indicated that SRAP markers were useful for investigating diversity and relationships among Gypsophila germplasm. Additionally, this data could be used for development of new Gypsophila varieties in the breeding programme.

Determination of genetic diversity of edible-seeded watermelon genotypes using SRAP markers

The watermelon (Citrullus lanatus L.) is one of the most commonly grown and consumed vegetables in the world. Some genotypes of watermelon, which have significant variations, have a snack potential due to their seed characteristics. In this study, SRAP (Sequence Related Amplified Polymorphism) marker technique was used to determine the genetic relationship between some edible-seeded watermelon genotypes. A total of 166 bands were obtained in 24 genotypes and the polymorphism rate was calculated as 97.4%. Four main clusters were observed in the cluster analysis. It was determined that genotypes 2 and 7 clustered separately from the others. Structure analysis revealed that the genotypes consisted of two subpopulations. It was concluded that the edible-seeded watermelon genotypes can be genetically differentiated by the SRAP techniques. The results of this study can be used in breeding strategies for the improvement of the edible-seeded watermelon cultivars.

The development and utilization of two SCAR markers linked to the resistance of banana (Musa spp. AAA) to Fusarium oxysporum f. sp. cubense race 4

Banana (Musa spp.) production worldwide is seriously threatened by Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc). The best way to control this disease is to grow resistant cultivars. However, it requires large-scale field evaluations and labor- and time-consuming to obtain disease-resistant germplasm. Development of early, reliable, and reproducible selection strategies are considered as the efficient approach which could speed up the selection procedure. In this study, two pairs of sequence-related amplified polymorphism (SRAP) primers related to banana Foc resistance/susceptibility were screened from 100 pairs of random primers. Correspondingly, two pairs of sequence characterized amplified region (SCAR) markers (namely SC4-F/SC4-R and SC14-F/SC14-R, respectively) were successfully generated from these two SRAP markers using 30 cultivars either resistant or susceptible to Foc. Both SCAR markers were located in mitochondrion genome and showed discriminatory power of 96.67% and 100%, respectively. Mitochondrial proteins possibly play a very important role in banana resistance to Foc. In additional, these two SCAR markers were employed simultaneously to screen potential resistant germplasm from 53 accessions with unknown resistance to Foc, and the results revealed a consistency of 83.0% with each other, further indicating their high reliability and reproducibility. These results suggest that both SCAR markers could be used in molecular marker-assisted selection for banana germplasm resistant to Fusarium.

Genetic Variation among Aeluropus lagopoides Populations Growing in Different Saline Regions

Aeluropus lagopoides is a halophytic grass growing in different sabkhas of Saudi Arabia. In this study, 14 inter-simple sequence repeat (ISSR) and 15 sequence-related amplified polymorphism (SRAP) molecular markers were selected to investigate the genetic diversity within and among five natural populations of A. Lagopiodes. The genetic diversity varied within and among populations. ISSR markers were slightly more efficient than SRAP markers in evaluating genetic diversity. Average polymorphism information content, effective number of alleles, Nei’s genetic diversity, and Shannon’s information index values of ISSR markers were higher than SRAP. Analysis of molecular variance revealed about 40% genetic variation among the population and 60% within the population. Overall, the genetic diversity was lowest in Jouf (40%), while the Qaseem populations were the highest (60%). Jizan populations were highly dissimilar to other regions. A Mantel test indicated a positive correlation between geographic and genetic distance. The cluster analysis showed three groups; the first group comprises Jouf and Salwa populations, the second group comprises Qareenah and Qaseem, and the third group comprises the Jizan population. This observation matched the geographic distribution of the species. These findings can help in the conservation of a diverse population of A. lagopoides in saline regions as well as rehabilitation of these degraded unique habitats.

Sequence-related Amplified Polymorphism and Target Region Amplification Polymorphism Markers-based Profiling of Sodium Azide and Ethyl Methanesulfonate-derived Black Rot-resistant Dendrobium sp. ‘Earsakul’ Mutants from In Vitro Mutagenesis and Selection

To reveal the applicability of sequence-related amplified polymorphism (SRAP) and target region amplification polymorphism (TRAP) markers to mutant genotyping and marker identification for resistance to black rot (Phytophthora palmivora) in orchids (Dendrobium sp. ‘Earsakul’), we fingerprinted four nonmutagenized controls and 12 black rot-resistant mutants obtained with in vitro sodium azide (NaN3) and ethyl methanesulfonate (EMS) mutagenesis and in vitro selection using culture filtrate of P. palmivora. Each of the 20 SRAP and TRAP primer combinations yielded 375 and 384 scorable DNA bands, respectively, of which 94 (24.42%) and 88 (22.91%) were polymorphic, respectively. Mantel’s test cophenetic correlation coefficients of SRAP, TRAP, and SRAP/TRAP were 0.750, 0.921, and 0.861, respectively, indicating the efficiency of these markers, especially TRAP and SRAP/TRAP, for Dendrobium sp. ‘Earsakul’ mutant characterization. Moreover, the correlations between the matrices of cophenetic correlation values for the dendrograms of SRAP with TRAP, SRAP with SRAP/TRAP, and TRAP with SRAP/TRAP were 0.399, 0.566, and 0.793, respectively, and the dendrograms based on SRAP vs. TRAP and SRAP vs. SRAP/TRAP, with lower correlations, had more variations, i.e., the number of clusters, the members of clusters, and the placement of the materials, than the ones based on TRAP vs. SRAP/TRAP. Among the three dendrograms, all nonmutagenized controls were clustered together, whereas all the highly resistant and the most resistant mutants were distributed separately as individuals. Interestingly, the four SRAP and TRAP markers were significantly associated with black rot resistance. Overall, our results will be useful for facilitating future Dendrobium sp. ‘Earsakul’ breeding programs.

Genetic Diversity and Structure of Quercus petraea (Matt.) Liebl. Populations in Central and Northern Romania Revealed by SRAP Markers

The genetic variability of five populations of Quercus petraea originating from the Transylvania and Maramureș regions of Romania was investigated in this study to provide insights into the species’ adaptability, population dynamics, and potential for preservation in the face of environmental challenges. To achieve this, sequence-related amplified polymorphism (SRAP) markers, in conjunction with a set of 18 primer combinations, were employed. The outcomes of the analysis revealed a range of polymorphisms spanning from 69.78% to 85.75%. Additionally, the assessment of genetic diversity using Shannon’s information index (I) yielded values ranging between 0.2887 and 0.3955, while Nei’s gene diversity (He) exhibited a spectrum from 0.1833 to 0.2582. The analysis of genetic variability, conducted via molecular variance (AMOVA), unveiled that 9% of the genetic variation was attributable to differences among the populations, while a substantial 91% resided within the populations. A further investigation of the population structure revealed that the construction of a UPGMA dendrogram based on Nei’s genetic distances elucidated the presence of two principal genetic clusters, a finding that was reinforced by a Principal Coordinate Analysis (PCoA). The genetic diversity revealed by Quercus petraea using SRAP molecular markers offers promising potential for upcoming breeding programs to identify optimal genitors, facilitating the development of well-adapted oak populations in the Transylvania and Maramureș regions.

The effect of plant growth regulators on micropropagation of Melientha suavis Pierre. and assessment of genetic fidelity of regenerants based on iPBS and SRAP markers

Abstract. Siringam T, Vanijajiva O. 2023. The effect of plant growth regulators on micropropagation of Melientha suavis Pierre. and assessment of genetic fidelity of regenerants based on iPBS and SRAP markers. Biodiversitas 24: 4628-4634. Melientha suavis Pierre, a significant deciduous edible plant species with high nutritional value and belonging to the Opiliaceae family, holds paramount importance for both agricultural and conservation purposes in its native Southeast Asia. However, the species faces challenges due to habitat fragmentation and negative anthropogenic impacts, leading to a decline in its population. This study aimed to explore the effects of various concentrations of plant growth regulators (cytokinin and auxin) on the shoot and root development of M. suavis, and to assess the genetic stability of micropropagated plants obtained from nodal explants. In vitro shoot regeneration and proliferation were conducted on Murashige and Skoog (MS) semi-solid medium, supplemented with 6-benzylaminopurine (BAP) or kinetin (Kn) at different doses. The optimal shoot length, shoot number, and leaf volume were observed in the modified MS medium with 1.0 mg/L BAP after an 8-week incubation period. Efforts to enhance the rooting of micropropagated shoots included the addition of auxins, such as ?-naphthalene acetic acid (NAA) or indole-3-butyric acid (IBA). However, the species exhibited recalcitrant behavior during the reproduction and rooting stages, as the rooting percentage did not correlate with the increase in auxin concentration. Interestingly, the highest root number and length were achieved in the MS medium without plant growth regulators after 8 weeks of incubation. To ensure genetic fidelity, regenerants were subjected to inter-primer binding site (iPBS) and sequence-related amplified polymorphism (SRAP) marker analysis. The results revealed no genetic variation between the micropropagated plants and the mother trees, confirming the production of genetically stable progeny. Overall, this protocol presents a promising alternative for profitable propagation and establishment of genetically constant progeny of M. suavis, with important implications for sustainable applications and germplasm conservation in Southeast Asia. Addressing the challenges faced by this valuable species through micropropagation and genetic fidelity assessment can contribute significantly to its preservation and utilization for agricultural and conservation initiatives.

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.

Development of SRAP markers to evaluate the genetic variability in Brachypodium distachyon complex

ABSTRACT Brachypodium distachyon has been accepted as a model grass species for genetics and molecular genomics in cereals since 2001. However, the genetic variability present in Brachypodium spp. continue being the aim of many research. Therefore, the aim of this work was to analyze the genetic variability present in different Brachypodium spp. from different countries and to find different open reading frames (ORFs) among them by using sequence-related amplified polymorphism (SRAP) markers. In our study, a total of 12 Brachypodium spp. accessions were selected from different countries. By using SRAP markers, the genetic variability was evaluated and some fragments were sequenced to obtain differential ORF information among genotypes. SRAP molecular markers revealed high variability among accessions being USA the accession that showed the most variability at the DNA level. The analysis of sequenced SRAP fragments from monomorphic and polymorphic fragments as well as those obtained from new primer combinations targeted coding regions into B. distachyon available genome. SRAP molecular marker showed not only to be an excellent tool for Brachypodium variability studies but also to provide additional information about differential amplification of open reading frames.

Evaluation in Genetic Variation of Krachai by Sequence Related Amplified Polymorphism (SRAP) and Random Amplified Polymorphic DNA (RAPD) Techniques

Krachais are local name of Thai herb which are identified within 2 genera, namely Bosenbergia (white or red krachai) and Kaempferia (black krachai). The rhizome of Bosenbergia rotunda (L.) Mansf. contains major aromatic compounds against COVID19 but its many morphological characteristics such as leaves, stems and rhizome are like other species in same genus or family. In this study, a total of 13 accessions containing 5 samples of B. rotunda, 2 samples of Boesenbergia spp. and 3 samples of Kaempferia parviflora including 3 samples of other species in same family as outgroups were analyzed and clustered using sequence-related amplified polymorphism (SRAP) and random amplified polymorphism DNA (RAPD) markers. The results showed that 8 SRAP primers (M1E1, M1E2, M1E7, M2E10, M3E9, M5E1, M5E2 and M6E10) could generate 79 polymorphism bands with an average of 92.15% whereas a total of 5 RAPD primers (OPY04, OPY02, OPY04, JAT11 and JAT12) could give 64 polymorphisms with 100% as a percentage of the polymorphism band. The PIC of the SRAP marker (0.470) has a higher value than the RAPD marker (0.264). The highest similarity coefficients within genus Boesenbergia of 1.000 and 0.952 were obtained from SRAP and RAPD markers, respectively. The UPGMA dendrogram of SRAP and RAPD information among krachai presented 2 and 4 groups, respectively. The cluster of Boesenbergia was separated from K. parviflora and other species in same family. Furthermore, the results also pointed that Boesenbergia sp. from Phayao is in correct genus and is B. pandurata (Roxb.) Schltr. because of having red leaf while Boesenbergia sp. from Chiang Rai showed confusion between SRAP and RAPD data. It was concluded that SRAP and RAPD have great potential for the study of genetic diversity of Boesenbergia and other species in family Zingiberaceae.

Molecular Characterization and Metabolite Profiling of Philippine Allium sativum Linn.: Ilocos Pink

Ilocos Pink garlic (IPG) is a local garlic variety found in Ilocos Norte, Philippines. Recently known for its moderate beta-adrenergic receptor inhibitory activity in vivo, there is still a limited number of studies describing its genetic and metabolite profile to distinguish it from other garlic varieties. In this study, genetic markers of IPG were identified using sequence-related amplified polymorphism (SRAP) analysis. Ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry followed by principal component analysis (PCA) was used to discriminate IPG’s metabolites from Ilocos Native garlic. Based on the degree of brown-stripe pigmentation on their outer skin, IPG samples can be classified into three – light, moderate, and heavy pigmentation. These subgroups were found to share seven SRAP marker pairs – namely,ME1-EM1 (at 300bp), ME1-EM4 (at 400bp), ME2-EM3 (500bp), ME3-EM1 (300bp), ME3-EM2(at 400bp), ME3-EM4 (at 200bp), and ME5-EM2 (at 300bp). Unique SRAP marker pairs were also observed between subgroups. PCA revealed Ilocos Native garlic to be discriminated from the IPG groups, but the marker matrix tool showed mere differences in concentrations except m/z247.129 at RT 1.40. Concentration-wise, nine markers may be proposed to discriminate IPG light from IPG moderate and heavy, seven of which are putatively identified as saponins. These findings suggest that SRAP markers can effectively discriminate IPG into subgroups, whereas metabolite profiling may provide little insight into the differences between IPG and Ilocos Native garlic.

Genetic diversity analysis and potential suitable habitat of Chuanminshen violaceum for climate change

To provide a scientific basis for the sustainable development of C. violaceum, we correctly identified the different germplasm resources and obtained excellent germplasm resources. In this study, MaxEnt was used to predict the distribution range of C. violaceum in China under current and future climate scenarios and explain the impact of environmental variables on its distribution. An SRAP (sequence-related amplified polymorphism) molecular marker was used to analyse the genetic diversity of the plant. The results showed the areas of the total, most, moderately and poorly suitable habitats of C. violaceum were 69.93 × 104 km2, 7.77 × 104 km2, 12.68 × 104 km2 and 49.49 × 104 km2, respectively. The most suitable habitat was concentrated in central and eastern Sichuan, and scattered in Chongqing and Hubei. Under SS1–2.6, SSP2–4.5 and SSP5–8.5 scenarios in 2050s and 2090s, the area of the most suitable habitat would decrease by 25.13%–34.88%. The centroid of the most suitable habitat would move to the west by 45.44 km (SSP1–2.6), 42.15 km (SSP2–4.5) and 37.72 km (SSP5–8.5) in the future. Annual precipitation (bio12), minimum temperature of the coldest month (bio6), precipitation of coldest quarter (bio19), temperature annual range (bio7), elevation (El) and mean UV-B of highest month (UV-B3) were identified as the dominant environmental variables related to the distribution of C. violaceum. A total of 374 bands were amplified by 37 primer pairs, of which 283 bands were polymorphic, and the polymorphic percentage was 75.67%. The analysis of molecular variance showed higher percentages of genetic variation within the population. All the accessions could be distinguished by SRAP markers. The cluster analysis results showed that 63 accessions were classified into 7 groups, which were correlated with the geographical distribution of the accessions to some degree. The accessions from Langzhong and Qingbaijiang had higher diversity. These results suggest that strategic transplantation of C. violaceum from particular geographic locations could help make the species more resilient to climate change and slow the contraction of the species' distribution.

Estimating genetic diversity among durum wheat (Triticum durum desf.) landraces using morphological and SRAP markers

The durum wheat (Triticum turgidum L. ssp. durum Desf.) Landraces are a valuable source of natural germplasm for enhancing the genetic diversity of existing durum wheat cultivars. The study analyzed the genetic diversity of twenty-two durum wheat landraces including eight local Saudi landraces and fourteen introduced landraces using sixteen morphological descriptors and sequence-related amplified polymorphism (SRAP) markers. The results showed significant differences between the analyzed agro-morphological parameters and a large degree of genetic variation across the tested landraces. Principle components analysis (PCA) was used to determine agro-morphological relationships among different traits. The first six principal components (PCs) accounted for 78.47 % of the cumulative variability among 22 landraces. The PC1demonstrated variability in coleoptile anthocyanin coloration, straw pith, culm neck glaucosity, flag leaf glaucosity, ear glaucosity, and length of awn at tip relative to length of ear. Wheat landraces (L8, L14, L497, L569, L590, L594, L600, L601, and L602) showed increased diversity in dry region and contributed to PC1. A couple landraces had higher plant height (L12, L598, and L654), heading days (650, 656), and ear length (L12, L594, and L650) respectively. The dendrogram generated from the standardized morphological data separated the twenty-two durum wheat genotypes mainly into two clusters. The landraces 14, 600 and 602 grouped into separate cluster with strong correlation to ear glaucosity. Genetic diversity of these landraces was also evaluated using eight SRAP markers, with 482 amplified fragments and an average polymorphic information content (PIC) of 0.27. The dendrogram based on SRAP markers separated into two clusters with some diversified landraces (L8, 594, 602, 977, and L650). The Mantel test found no significant correlation (phenotypic or genetic) between 22 wheat durum landraces (r = 0.013, p = 0.84, =0.05). The results demonstrated the power of morphological and SRAP markers for detecting diversity among durum wheat landraces in the semi-arid region of Saudi Arabia. Thus, study provides insights into wheat diversity for better in-situ and ex-situ conservation and paves the road for their use in a Saudi durum wheat breeding program.

Assessment of Genetic Diversity and Genetic Structure of Saussurea medusa (Asteraceae), a "Sky Island" Plant in the Qinghai-Tibet Plateau, Using SRAP Markers.

Saussurea medusa Maxim. is a typical "sky island" species and one with the highest altitude distributions among flowering plants. The present study aimed at analyzing the genetic diversity and population structure of 300 S. medusa accessions collected from 20 populations in the Qilian Mountains in the northeastern Qinghai-Tibet Plateau (QTP), using sequence-related amplified polymorphism (SRAP) markers. A total of 14 SRAP primer combinations were employed to analyze genetic diversity and population structure across all accessions. Out of 511 amplified bands, 496 (97.06%) were polymorphic. The populations in the eastern Qilian Mountains had significantly higher genetic diversity than those in the central and western groups. Population structure analysis revealed greater genetic differentiation among populations with a Gst of 0.4926. UPGMA-based clustering classified the 300 S. medusa accessions into 3 major clusters, while the Bayesian STRUCTURE analysis categorized them into 2 groups. Correlation analyses showed that the genetic affinity of the populations was based on differences in geographical distance, moisture conditions, and photothermal conditions between the habitats. This study represents the first comprehensive genetic assessment of S. medusa and provides important genetic baseline data for the conservation of the species.

Evaluation of the growth, yield traits and the genetic diversity of some Brassica napus genotypes under Egyptian conditions

BackgroundCanola (Brassica napus L.) is considered an alternate oilseed plant. Therefore, this study aimed to evaluate some growth parameters, yield, chemical parameters and genetic diversity among thirteen canola genotypes including a collection of Chinese, German, French, and local genotypes under Egyptian conditions.ResultTrapper genotype recorded the highest values of plant height (47.12 and 89.75 cm) and dry weight/plant (8.54 and 28.19 dry weight/plant) at 60 and 90 days from sowing, respectively. Data from the field experiments showed that significant differences were recorded among tested genotypes for all yield and its component parameters (i.e., plant height (cm), branches/no. plant, siliquas and seed weight (g/plant) and seed oil %. The genetic diversity and the relationships among the thirteen canola genotypes were evaluated utilizing sequence-related amplified polymorphism (SRAP) and simple-sequence repeats (SSRs) markers. The allelic frequency of the different SRAP and SSR markers tested has differed among the thirteen canola genotypes. The SRAP and SSR analyses showed 659 out of 742 and 15 out of 45 markers, respectively, were detected as polymorphic markers (88.8% and 33.33%) among the tested wheat cultivars In addition, the polymorphism information content (PIC), marker index (MI) and resolving power (RP) parameters were computed to assess the effectiveness of the markers. The results indicated the occurrence of a considerable genetic variation between Chinese, European and Egyptian genotypes.ConclusionThese markers are of considerable value and can be utilized to screen large canola populations. The results of the comparison between the two molecular markers showed that the most effective marker that showed the genetic diversity between canola genotypes was SRAP (88.8%) polymorphism. It could be concluded that the tested canola genotypes could be cultivated under the Egyptian condition with high performance especially Trapper, Agamax and Topas genotypes. Therefore, it could be suggested that these three genotypes seem to be promising for oil gap reduction and need further evaluation for the expansion under new reclaimed regions.

<i>Corrigendum to</i>: Assessing genetic diversity and population structure of Iranian melons (<i>Cucumis melo</i>) collection using primer pair markers in association with resistance to Fusarium wilt

We evaluated genetic diversity and population structure of Iranian melons (Cucumis melo L.) using combinations of 35 primer pairs: 15 Simple-Sequence-Repeats (SSR); 10 Inter-Simple-Sequence-Repeats (ISSR); and 10 Sequence-related amplified polymorphism (SRAP) markers in association with resistance to melon Fusarium wilt, caused by Fusarium oxysporum f. sp. melonis (FOM ). Genetic similarity was determined by simple matching coefficient (SSM) and dendrogram by clustering-analysis with unweighted pair groups using arithmetic averages (UPGMA). By combining ISSR-SSR-SRAP markers, a high degree of variation among the melons was detected. The mean polymorphism information content (PIC), marker index (MI), effective-number of alleles (I), expected heterozygosity (H), and Nei's gene diversity parameters were 0.392, 0.979, 1.350, 0.551 and 0.225, respectively. According to MI, PIC, I, H, and Nei indices evaluation, ISSR6, ISSR9, SRAP3, SRAP5, SSR3 and SSR6 had the best performance in genetic diversity of the related melons population. The 35 primers yielded a total of 264 bands, of which 142 showed polymorphism. Clustering of genotypes based on resistance to Fusarium wilt, and comparison with grouping on SSR, SRAP and ISSR marker revealed a significant compliance between disease severity and molecular marker dendrograms. Thus, increasing the number of molecular markers for genetic diversity provides a powerful tool for future agricultural and conservation tasks.

Comparative study and genetic diversity in Malva using srap molecular markers

The Malva genus has 25-40 species and it can be considered as an annual and/or biannual herb. Malva species are indicated with potential therapeutic as cicatrizing and analgesic by the Ministry of Health. The aim of this study was to analyze SRAP (Sequence-related amplified polymorphism) markers in a total of 70 accessions of Malva species, which included five species Malva neglecta Wallr., Malva pusilla Sm., Malva sylvestris L., Malva verticillata L., Malva nicaeensis All.. A total of 89 (Number of total loci) (NTL) DNA bands were produced through polymerase chain reaction amplifications (PCR) amplification of five Malva species. These bands were produced with the combinations of 5 selective primers. The total number of amplified fragments ranged from 10 to 27. The predicted unbiased gene diversity (UHe) varied between 0.077 (Malva sylvestris) and 0.382 (Malva pusilla). The genetic similarities between three species are estimated from 0.70 to 0.91. Neighbor-Joining tree results showed two major clusters. According to the SRAP (Sequence-related amplified polymorphism) markers analysis, Malva pusilla and Malva aegyptia had the lowest similarity. Our results provided great molecular identification of all assayed genotypes, which have shown that there is large quantity of genetic diversity among the Malva accessions. Objectives of the study were; a) to estimate genetic diversity; b) to evaluate population relationships using NJ approaches. Current results have implications in breeding and conservation programs.

Genetic Diversity among Eight Species of Willow (Salix spp.) from Iran Based on SRAP Markers

This study reports the application of sequence-related amplified polymorphism (SRAP) technique in characterization of 8 species of Salix (spp) from Iran by screening 22 primer combinations (PCs). Twenty two SRAP primer combinations could amplify 116 scorable loci, of which 107 bands were polymorphic. The amplified DNA fragments were used for calculation and statistical analysis. The Complete linkage cluster was performed and dendrogram drawn with the help of NTSYS pc 2.02 software which revealed two main clusters and several sub-clusters. This investigation showed that genetic distance was relatively significant among these species. The Jaccard similarity coefficient ranged from 0.18 to 0.55. The results also propose that the SRAP marker is a useful tool for evaluation of genetic diversity and relationships among different Salix species.

Assessment of Genetic Diversity of Local Coffee Populations in Southwestern Saudi Arabia Using SRAP Markers

Coffea arabica, a member of the Rubiaceae family, is the most commercially important species of the genus Coffea. It has been grown on the mountain terraces of southwestern Saudi Arabia for centuries. At present, the species is subject to increased genetic erosion due to the abandonment of many gardens by their owners and the increasingly dry climate. The current study was carried out to determine the genetic diversity of 56 local coffee accessions collected from the southern regions of Saudi Arabia using 30 sequence-related amplified polymorphism (SRAP) markers. Six SRAP markers showed polymorphism among the 56 accessions. A total of 1125 bands, with an average of 187.5, was produced from all six SRAP primers. The polymorphic information content (PIC) ranged from 74.8 to 97.7, with an average of 91.4 for all studied SRAP markers. The high polymorphism percentage seen in this study, along with the high number of alleles produced and the high PIC values of the primers used, demonstrate that the SRAP approach was an effective molecular technique for assessing genetic diversity in the studied populations. The structural analysis showed a sharp peak, with no ambiguity, demonstrating the highest delta K value at K = 3 and K = 6, and the coffee accessions could be grouped into three and six main populations, respectively. The PCoA, cluster analysis, and structural population analysis results suggest considerable genetic diversity among coffee populations growing on the southwestern mountain terraces of Saudi Arabia. The 56 accessions were segregated into five groups, mostly according to geographic distribution. The accessions from the southern districts of Jazan region mostly clustered in groups 2 and 4, while the accessions from the northern districts of Al-Baha and Assir regions formed separate groups. Based on these analyses, accessions KSA1R, KSA6R, KSA21, KSA25, KSA37, KSA38, KSA42, KSA59, KSA60, KSA62, and KSA63 were the most divergent. The genotypes should be conserved for use in coffee-breeding programs to improve the agronomic value of the crop, broaden the genetic base of C. arabica in Saudi Arabia and increase environmental resilience. Additional molecular and functional genomics studies are necessary to further elucidate how this germplasm has evolved and enhance the value of local Arabica coffee diversity in the Kingdom.

Performance prediction of F1 crosses in eggplant (Solanum melongena L.) based on morphological and molecular divergence

Identifying potential F1 hybrid combinations based on the parental diversity can increase the breeding efficiency and saves the opportunity cost of time. In this work, the genetic diversity between eggplant genotypes was measured by Mahalanobis D2 statistics and Sequence Related Amplified Polymorphism (SRAP) molecular markers. The genetic distances (GD) were correlated with heterosis and trait wise mean performance of F1 crosses generated in a line ? tester mating design for prediction of F1 performance for agronomically important traits. The cluster analysis performed based on the Mahalanobis D2 distance grouped all the eleven genotypes into two clusters and three clusters were formed based on the SRAP marker data. The polymorphic information content value generated by the 30 SRAP marker combinations ranged from 0.09 to 0.77 with a mean value of 0.38. For yield, the F1 combinations exhibited the mid parent heterosis ranged from 3.99% to 83.34% and the heterobeltiosis from -35.67% to 57.19%. GD based on both phenotypic values and molecular marker data successfully predicted the heterotic patterns in the number of fruits per plant and other fruit morphological traits such as fruit length and fruit breadth which is a significant outcome of the study. A multiple linear regression model that included GD, GCA and SCA was more significantly correlated with heterosis for fruit yield than any genetic parameter alone.