Inter-simple Sequence Repeat Markers Research Articles

Molecular Variation in Some Taxa of Genus Astragalus L. (Fabaceae) in the Iraqi Kurdistan Region

Astragalus L. is one of the main genera of blossoming plants, and its diversity of species and forms is well known. The Astragalus L. taxa make a significant contribution to the mountainous and steppe ecosystems of the Kurdistan region of Iraq. Although the species within this genus have been the subject of several molecular studies, the evolutionary relationships among these species remain unidentified. Despite extensive research, little is known about the phylogenetic relationships among the various subgenera of Astragalus. This research is intended to investigate the molecular variation of 33 species of the genus Astragalus L. found in the Kurdistan area of Iraq. For molecular validations, three separate techniques (nuclear ribosomal DNA (rDNA), inter simple sequence repeats (ISSR), and conserved DNA-derived polymorphism (CDDP)) were used. With respect to Astragalus L. indentations, universal ITS1 and ITS4 gene sequencing was used, and the discovered sequences were subjected to BLAST searches in the NCBI database. A phylogenetic tree was generated with two main clades. Regarding detecting genetic diversity between the taxa, 24 molecular markers (14 ISSR and 10 CDDP) were used. High values of polymorphic materials and gene diversity were detected. ISSR markers had an average of 22.71 polymorphic bands per primer, while CDDP markers had the highest mean values for polymorphic information content (0.37), Shannon’s information index (0.27), expected heterozygosity (0.19), and unbiased expected heterozygosity (0.23). Cluster and principal coordinate analyses divided the Astragalus L. taxa into four main groups using the two molecular data sets. According to the results of the molecular variance analysis, the highest variation was detected within sections, with values of 92.01 and 89.48% for ISSR and CDDP markers, respectively. These outcomes suggest the effectiveness of molecular markers and the ITS region in determining and identifying genetic correlations between Astragalus species.

The potential of gamma irradiation on antioxidant capacity and genomic alterations in Calendula officinalis

There are lines of evidence that ionizing radiations such as gamma rays can cause different biological effects on plants. Marigold (Calendula officinalis L.) is a member of the family Asteraceae. It possesses profound amounts of active ingredients. The aim of this study was to evaluate the changes imposed upon different dose levels of gamma radiation on some features of Calendula officinalis such as antioxidant activity, total phenolic compounds and flavonoid contents, antibacterial activity and genomic alterations. Calendula officinalis seeds were exposed to different doses of Gamma radiation (0, 10, 15, 20 and 25 GY). Total phenolics, flavonoids, antioxidant activity (measured by DPPH assay) using methanolic extracts of plants and antibacterial activity measured by the disc diffusion assay showed significant differences to the control samples. The samples treated with 10 GY gamma rays showed the highest total phenol and flavonoid contents. Antioxidant activity significantly differed between Gamma rays dose levels and it was the highest at 25 GY. Four bacterial strains including E. coli, Bacillus subtilis and Pseudomonas aeroginosa were used for the antibacterial assay. Extracts from plants treated with 25 GY gamma rays showed the highest antibacterial activity against the 4 bacterial strains. Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were used to study the genetic variation. The polymorphism information content (PIC) for RAPD primers ranged from 3% to 13% and ranged from 6 to 13% for ISSR primers. Results indicated that ISSR markers were more efficient than RAPD markers, as they detected 25.57% polymorphic DNA bands compared to 21.31% polymorphism for RAPD markers.

Population structure and mixed reproductive strategies in Bipolaris maydis from single and multiple corn cultivars in Fujian Province, China.

Bipolaris maydis is the pathogenic microorganism of southern corn leaf blight, a persistent biotic constraint responsible for substantial yield losses of corn worldwide. In the present study, 96 isolates from six representative fields growing single and multiple sweet corn cultivars in Pingnan, Fuqing, and Jian'ou in Fujian Province, which are characterized by different geographical characteristics and cropping patterns, were genetically analyzed using inter-simple sequence repeat (ISSR) markers to assess the impact of geographical origins and corn cultivars on B. maydis population differentiation. B. maydis isolates originated from diverse regions possessed higher genetic variety than those from single and multiple sweet corn cultivars. Phylogenetic analysis showed that the isolates from single and multiple sweet corn cultivars were randomly grouped into different clusters, with those from the same location tending to form clusters. A greater genetic differentiation among different geographical populations than between those from single and multiple sweet corn cultivars was observed by pairwise comparison. Hierarchical analysis indicated that among-population variation was higher when comparatively analyzed B. maydis populations from different locations than in those from single and multiple sweet corn cultivars. In conclusion, these results suggest that geographical origin acts a more considerable role in genetic differentiation of B. maydis than corn cultivar. Two divided genetic clusters were detected in the B. maydis populations from single and multiple sweet corn cultivars at the three locations in Fujian Province, with major genetic variation being derived within populations. The high haplotypic diversity and expected mating type ratio of 1:1 in combination with significant linkage disequilibrium suggested that a mixed reproductive strategy occurs in the B. maydis population in Fujian Province. This study will enrich the information on the role that geographical origins and corn cultivars play in the population structure of the pathogen as well as the reproductive strategies in B. maydis population in Fujian Province.

Genetic characterization of superior durian (Durio zibethinus L.) accessions in Batang District, Central Java, Indonesia based on ISSR markers

Abstract. Amrullah MI, Rahayu ES, Puwantoyo E, Maharani RI, Solichin, Sriyadi, Hadiprasetya TY, Retnoningsih A. 2023. Genetic characterization of superior durian (Durio zibethinus L.) accessions in Batang District, Central Java, Indonesia based on ISSR markers. Biodiversitas 24: 4811-4819. Durian (Durio zibethinus L.) has the highest level of genetic diversity in the genus of Durio. The genetic diversity of D. zibethinus in Batang District, Central Java, Indonesia needs to be explored to obtain data on superior durian accessions that are adaptive in the area. This study aimed to analyze the genetic diversity of 40 superior durian accessions from 13 locations in Batang District using 10 Inter Simple Sequence Repeat (ISSR) primers. Genomic DNA was isolated from leaves using a modified CTAB method. PCR products were electrophoresed on 2% agarose and yielded 161 ISSR alleles with a percentage of 100% polymorphic alleles. The level of genetic diversity based on Nei's gene diversity and Shannon's Information index are 0.277 and 0.434, respectively. The durian accessions studied have a similarity coefficient of 0.22-0.86 and are divided into two main clusters. Siwatu 1 and Siwatu 2 accessions have the highest genetic similarity coefficient (0.86), while Butternuts and Watu Tembogo 1 accessions show the lowest genetic similarity coefficient (0.05). Specific alleles were found in 11 durian accessions. The molecular characterization results show the high genetic diversity of superior durian accessions in Batang District and add to the list of local superior durian accessions in Indonesia.

Enhancement of some barley (Hordeum vulgare L.) resistance for nematode (Heterdra avanae) using DNA fingerprinting analysis

Background Heterodera avenae, the cereal cyst nematode or European cyst nematode, is a plant pathogen and an obligate parasite of cereal crops including barley, oats, wheat, and rye. Cereal crops infected with this nematode are more susceptible to infection by fungal diseases such as Rhizoctonia root rot. Objective The main objective of the present study was to map Heterodera avenae resistance and to compare seven different species. This study also aimed to increase the efficiency and precision of standard procedures for testing the resistance of barley toward root-lesion nematodes. Materials and methods The genetic variability analysis of seven barley genotypes, of Egypt was achieved using 7 Inter simple sequence repeat (ISSR) primers. Phylogenetic relationships of seven accessions of (Hordeum vulgare L.) collected from different region of Egypt were assessed. The soil was sterilized in an autoclave of each pot was planted in the comparison experiment, as well as in the treatment experiment with nematode Heterdra avanae infected soil brought from an infected field, and this soil was added to the treated pots. Also (ISSR) molecular marker technique was used for DNA fingerprinting and assessing genetic diversity and phylogenetic relationships in barley germplasm. Results and conclusion A significant correlation was observed between the Jaccard’s dissimilarity matrices based on ISSR markers, as revealed by Mantel test using the Pearson correlation coefficient (r = 0.69; P < 0.05). The results showed that ISSR primers produced 37 bands their size ranged between 100-2000 bp with (87.5%). polymorphism percentage. Polymorphic information content PIC was 0.74 for ISSR. Unweighted Pair Group Method with Arithmetic (UPGMA), Dendrogram was divided into two clusters by morphological traits and ISSR analysis. Genetic similarity matrix was examined with Jaccard’s coefficient, maximum similarity was found between Giza126 and Giza127 (99%) with morphological analysis both and lowest similarity between Giza123 and Giza126 (6%) with ISSR analysis. Determination of genetic diversity between barley is of major importance for characterization of barley germplasm, breeding programs and conservation purposes. Morphological traits and ISSR analysis are effective tools for detecting genetic variations. The results showed that H. vulgare have high ratio of variation. This study may be considered as reference study for further studies on H. vulgare and may contribute to species concept and breeding programs.

DNA barcodes, ISSR, RAPD and SCAR markers as potential quality control tools for molecular authentication of black and white mulberry

Morus species, especially black mulberry (Morus nigra L.), are well known for their nutritive and economic values. Black mulberry is often a subject for deliberate and undeliberate substitution with the morphologically similar white mulberry (Morus alba L.). In the current study, the genetic diversity of Morus nigra L. and Morus alba L. was assessed using different genetic profiling and fingerprinting techniques namely namely DNA barcoding, Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR). DNA barcoding was implemented using 2 plastid loci (matK, and rbcL-1) and 2 nuclear spacers (ITS and ITS2) aiming at accurate authentication of the studied species. DNA barcoding, targeting the selected loci succeeded to identify and authenticate the studies Morus species but failed to differentiate them, owing to their close genetic resemblance. Out of 52 screened RAPD primers, 27 were able to produce reproducible and clear profiles with 115 amplified fragments of which 37 were polymorphic accounting for 32.17% polymorphism. The number of amplified bands varied from 2 to 7 ranging in size from 100 to 700 bp. Moreover, 55 ISSR primers were evaluated, 108 fragments were produced, using 20 primers, of which 28 were polymorphic accounting for 25.92% polymorphism with size range of 200–800 bp. Sequence Characterized Amplified Region (SCAR) marker was developed based on reproducible banding pattern obtained by RAPD primer (OPG-03), for the purpose of accelerating the initial screening of Morus batches and enabling the preventative rejection of adulterated samples. The polymorphic band obtained was sequenced and specific primers were designed to develop a SCAR marker of approximately 558 bp exclusively for M. nigra, allowing detection of down to 1 ng, of M. nigra. The SCAR marker showed 100% success in differentiating authentic M. nigra and M. alba samples. In addition, the application of the developed SCAR marker was extended to distinguish M. nigra from its four common adulterants namely Ficus carica L., Fragaria vesca L., Ficus racemosa L. and Vitis vinifera L.. The proposed protocol was successfully implemented for the evaluation of 47 commercial M. nigra samples collected from different Egyptian locations.

The biodiversity of Aspergillus flavus in stored rice grain leads to a decrease in the overall aflatoxin B1 production in these species

Aspergillus flavus is a significant fungus that poses a threat to food safety by producing mycotoxins in various crops. In this study, A. flavus isolates were obtained from storage rice collected from seven provinces in southern China, and their AFB1 production, biosynthesis genes presence, and diversity were detected. Results showed that 56 out of the 81 A. flavus isolates produced detectable levels of AFB1, and 71 isolates (87.6 %) possessed aflR gene in their AF synthesis gene cluster, while only 41 isolates (50.6 %) had the ver-1 gene present. Genetic diversity analysis using inter-simple sequence repeats (ISSR) markers revealed seven main clusters among the isolates and the genetic similarity coefficients of 81 A. flavus isolates ranged from 0.53 to 1.00. Additionally, coculture assays were conducted using two toxigenic and two atoxigenic isolates from the same grain depot to investigate the effect of intraspecific inhibition on AFB1 production and to assess the AFB1 contamination risk of storage rice. The in situ results demonstrated that the atoxigenic isolates effectively inhibited the AFB1 contamination of toxigenic isolates. These findings provide insight into the genetic diversity of A. flavus isolates populations and highlight the potential food safety hazards of them in stored rice grain in China.

Phenological, morphological and genetic characterization of local grapevine (Vitis labrusca L.) genotypes grown in the Black Sea Region in Northern Turkey

Vitis labrusca has become widely naturalized in the Black Sea region of Northern Turkey. The aim of this work was to evaluate the morphological, phenological, and genetic characteristics of V. labrusca accessions grown in the Black Sea region during the last three growing seasons. Local genotypes were described according to the Organisation Internationale de la Vigne et du Vin (OIV) ampelographic descriptor, including shoot length (cm), mature leaf size, bunch length and width, berry length and width, berry weight, number of berries, Total Soluble Solids (TTS) and titratable acidity. Additionally, phenological data, including bud burst, flowering, veraison and harvest date, were recorded. The accessions were characterized at the molecular level, and genetic relationships were assessed by means of Inter Simple Sequence Repeat (ISSR) markers. Using 6 ISSR primers, seventy-seven bands were obtained, of which 69 were polymorphic with a mean polymorphic rate of 88.68%. These ISSR primers produced polymorphism information content (PIC) values ranging from 0.48 to 0.5. The genetic similarity ranged from 0.08 to 0.83 among the genotypes. According to the dendrogram based on the ISSR analysis, Accessions 8 and 5 were genetically related, with a coefficient of similarity of 0.83, while Accession 3 was the most distantly related genotype, with a coefficient of similarity of 0.08. These results demonstrated that ISSR markers can be used for genetic diversity analysis among V. labrusca genotypes. Our results also described characteristics of new V. labrusca genotypes that could be valuable for future Marker-Assisted Selection (MAS) and grapevine breeding.
 Key words: Diversity, foxy species, Inter-Simple Sequence Repeat markers (ISSRs), Breeding, polymorphism

Genetic Uniqueness and Genetic Structure of Populations of Picea obovata Ledeb. and Larix sibirica Ledeb. in the Northern and Middle Urals

Establishing sustainable plantations with genetic diversity equivalent to that of natural populations is vital for successful reforestation efforts. In this study, we present an innovative approach for selecting populations suitable for reforestation, taking into account their genetic uniqueness using Inter Simple Sequence Repeats (ISSR) markers. Our investigation focused on six populations of Picea obovata Ledeb and six populations of Larix sibirica Ledeb, collected from the Northern and Middle Urals. We found that the indicators of genetic diversity were significantly higher in L. sibirica compared to P. obovata, while the number of rare alleles was greater in Siberian spruce (R = 19). Among the P. obovata populations, the Cherdyn’s forestry exhibited notably high genetic diversity, and for L. sibirica, the Gainy’s forestry stood out in this regard. Moreover, the genetic subdivision of the six P. obovata populations (GST = 0.331) was higher than that of the six L. sibirica populations (GST = 0.177). To ensure optimal seed selection considering the genetic originality coefficient (GOC) and population differentiation, we recommend utilizing the P. obovata population from Gainy’s forestry with a GOC of 0.554 and the L. sibirica population from Cherdyn’s forestry with a GOC of 0.372. These populations harbor typical alleles characteristic of the research region, making them ideal candidates for seed selection. Furthermore, the specific alleles identified can serve as valuable markers for determining the geographic origin of P. obovata and L. sibirica wood, aiding in efforts to trace the sources of these species in forestry and trade practices.

Genetic Diversity of the Endemic Species Phanera sirindhorniae in the Mekong Basin of Thailand Based on ISSR Markers

Phanera sirindhorniae, an endemic species to the Mekong Basin’s upper northeastern region in Thailand, is notable for its therapeutic properties in alleviating pain and discomfort. The objective of this study was to assess the genetic diversity of P. sirindhorniae derived from four natural sources, specifically Sakon Nakhon, Nakhon Phanom, Bueng Kan and Mukdahan provinces, utilizing Inter-Simple Sequence Repeat (ISSR) markers. A total of 51 samples were analyzed, and 10 primers exhibited distinct, robust amplified fragments and polymorphism. The amplified fragment sizes ranged from 170 to 1,300 base pairs, identifying a total of 113 amplified fragments, of which 107 (94.69 %) displayed polymorphism. Polymorphic information content (PIC) values spanned between 0.112 and 0.429, while Nei’s gene diversity ranged from 0.2088 ± 0.2184 to 0.2994 ± 0.1912. Assessment of genetic diversity within and among populations revealed the total genetic diversity (Ht = 0.3443 ± 0.0225) and the genetic diversity within populations (Hs = 0.2617 ± 0.0161). The variability among populations (Gst = 0.2401) indicated a significant degree of gene flow (Nm = 1.580). The Analysis of Molecular Variance (AMOVA) results supported this, with 74 % of genetic differentiation occurring within populations and 26 % among populations. Using the Neighbor-Joining (NJ) generated from Nei’s genetic distance-based clustering analysis, Dendrogram construction successfully classified 2 distinct groups. The analysis revealed that P. sirindhorniae from Nakhon Phanom, and Bueng Kan constituted 1 group, whereas P. sirindhorniae from Mukdahan, and Sakon Nakhon formed another. These findings provide essential data for developing genetic conservation initiatives for this valuable genetic resource. HIGHLIGHTS This study presents the inaugural analysis of genetic diversity in wild Phanera sirindhorniae populations, a species designated as endangered, utilizing Inter-Simple Sequence Repeat (ISSR) markers. A group of 10 Inter Simple Sequence Repeat (ISSR) primers showed values for Polymorphism Information Content (PIC), with (AG)8YC (PIC= 0.445) standing out. These results highlight their potential for use in the investigation of genetic diversity. The examination of P. sirindhorniae resulted in the identification of 2 distinct genetic groups, which have the potential to inform and facilitate the development of genetic conservation strategies for this crucial genetic resource. GRAPHICAL ABSTRACT

Genetic structure of Trifolium pratense populations in a cityscape.

Urban grasslands provide numerous ecosystem services, and their maintenance should be based on naturally regenerating plant populations. However, the urban environment is challenging for preserving viable populations, mostly because of their high fragmentation and small size, which can lead to genetic drift. We examined red clover (Trifolium pratense) in a medium-size city in Central Europe to test the cityscape effect on within- and among-population genetic diversity. We used eight inter-simple sequence repeat markers to examine the genetic structure of 16 populations, each represented by eight individuals. The isolation by resistance was analysed using a least cost patch approach, focusing on gene flow via pollinators. We found great variation among T. pratense populations, with no discernible geographic pattern in genetic diversity. We linked the diversity to the long history of the city and high stochasticity of land use changes that occurred with city development. In particular, we did not find that the Odra River (ca. 100 m wide) was a strong barrier to gene transfer. However, notable isolation was present due to resistance and distance, indicating that the populations are threatened by genetic drift. Therefore, gene movement between populations should be increased by appropriate management of urban green areas. We also found that small urban grassland (UG) patches with small populations can still hold rare alleles which significantly contribute to the overall genetic variation of T. pratense in the city.

Genetic diversity analysis of Bitti (Vitex cofasssus), native species Indonesia based on Inter Simple Sequence Repeat (ISSR) marker

Bitti (Vitex cofassus) is a native species in Indonesia and is a superior wood in South Sulawesi. This type is a hardwood that is sought after and exported in large enough quantities. A narrow genetic base requires joint efforts to develop plant varieties, so it is necessary to carry out selection activities to obtain a superior diversity of traits. The most advanced method in assessing genetic diversity is a molecularly based approach using the Inter Simple Sequence Repeat (ISSR) marker. Germplasm exploration was carried out in Pattiroang Village, Kajang District, Bulukumba Regency, South Sulawesi Province. A total of 30 samples were extracted using the Genomic DNA Mini Kit (plant) method with modifications. Ten primers tested obtained six primers that produced bright polymorphic bands, namely UBC 820, UBC 822, UBC 823, UBC 824, UBC 827, and UBC 830. The highest He value is in the UBC 824 primary with a PIC of 0.48, while the lowest He values is in the UBC 827 primer with a PIC value of 0.15. The visualization of the dendrogram shows two large clusters, each consisting of a diverse number of individuals. It indicates a relatively moderate kinship between the types of V. cofassus.

Molecular insight into genetic differentiation, population structure and banding pattern analysis of Bambara groundnut (Vigna subterranea [L.] Verdc.) linked with inter simple sequence repeats (ISSR).

A set of 44 selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions was sampled from 11 distinct populations of four geographical zones to assess the genetic drift, population structure, phylogenetic relationship, and genetic differentiation linked with ISSR primers. The amplification of genomic DNA with 32 ISSR markers detected an average of 97.64% polymorphism while 35.15% and 51.08% polymorphism per population and geographical zone, respectively. Analysis of molecular variance revealed significant variation within population 75% and between population 25% whereas within region 84% and between region 16%. The Bidillali exposed greater number of locally common band i.e., NLCB (≤ 25%) = 25 and NLCB (≤ 50%) = 115 were shown by Cancaraki while the lowest was recorded as NLCB (≤ 25%) = 6 and NLCB (≤ 50%) = 72 for Roko and Maibergo, accordingly. The highest PhiPT value was noted between Roko and Katawa (0.405*) whereas Nei's genetic distance was maximum between Roko and Karu (0.124). Based on Nei's genetic distance, a radial phylogenetic tree was constructed that assembled the entire accessions into 3 major clusters for further confirmation unrooted NJ vs NNet split tree analysis based on uncorrected P distance exposed the similar result. Principal coordinate analysis showed variation as PC1 (15.04%) > PC2 (5.81%). The current study leads to prompting the genetic improvement and future breeding program by maximum utilization and better conservation of existing accessions. The accessions under Cancaraki and Jatau are population documented for future breeding program due to their higher genetic divergence and homozygosity.

Morpho-molecular exploration and selection of elite genotypes from indigenous Syzygium cumini L. Skeels (jamun) diversity of North-Western Indian Himalayas

AbstractEfficiently distinguishing various Syzygium cumini L. Skeels (jamun) accessions holds practical significance for selection purposes. This study concentrated on 15 superior genotypes of jamun from the North Western Indian Himalayas, selected for their pivotal horticultural traits. Drawn from a pool of 82 collected genotypes and assessed across two consecutive years (2019 and 2020), these genotypes underwent morphological evaluations utilizing a randomized block design replicated thrice. Concurrently, random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers were employed for molecular analysis. Substantial variations surfaced among genotypes, both in morphological traits and fruit biochemistry. Notably, tree 43 exhibited promise across multiple horticultural facets, encompassing fruit weight, length, pulp weight, pulp-to-seed ratio and pulp percentage. Conversely, tree 49 excelled in elevated levels of total soluble solids, total sugar and reducing sugar. While principal component analysis and cluster analysis unveiled modest genetic variability, RAPD and ISSR markers unveiled pronounced molecular-level polymorphism. Agglomerative hierarchical clustering delineated the genotypes into five distinct clusters. Cluster I encompassed two genotypes, cluster II embraced five while the largest group, cluster III, included six genotypes. Clusters IV and V highlighted individual genotypes, trees 43 and 54 respectively. In the molecular analysis, UPGMA clustering yielded two primary clusters, spotlighting the noteworthy similarity between genotypes trees 49 and 52 whereas, trees 40, 43, 44 and 48 stood distinct. The observed genetic diversity stands as a valuable resource with substantial potential to enrich diverse breeding initiatives. These salient genetic variations underscore the richness within the studied population, offering a valuable asset for focused future pursuits.

Revealing genetic diversity of tulips in Turkey with inter-simple sequence repeat markers

Revealing genetic diversity of tulips in Turkey with inter-simple sequence repeat markers

Evaluation of the Genetic Diversity of Greek Garlic (Allium sativum L.) Accessions Using DNA Markers and Association with Phenotypic and Chemical Variation

The genetic diversity of 27 garlic accessions (local varieties/landraces) was investigated using five simple sequence repeat (SSR) and six inter-simple sequence repeat (ISSR) markers. The SSR genotyping revealed 26 different alleles, while 84 polymorphic bands were produced using the ISSR markers. The average polymorphism information content (PIC) was 0.471 and 0.465 for the SSR and the ISSR markers, respectively. Compared to ISSRs, SSR markers revealed a higher level of redundancy, indicating potential duplicates among the accessions. The analysis of molecular variance (AMOVA) based on both marker systems showed that most of the molecular diversity was attributable to differences within accessions, rather than among them. UPGMA, STRUCTURE, and Principal Coordinate Analysis (PCoA) based on the SSRs produced similar clustering results, although not in agreement with those produced by the ISSR markers. Fisher’s exact tests and multinomial logistic regression analyses identified significant associations between the chemical compounds, the morphological traits of the bulb, and specific SSR and ISSR loci. Our results provide a molecular basis for understanding the genetic diversity of Greek garlic landraces, which could be useful for the conservation and sustainable management of this crop. Potential markers fostering the selection of genotypes in garlic breeding have also been revealed.

Genetic stability analysis associated with salt stress and salicylic acid in fenugreek (Trigonella foenum-graecum) plants

Abstract. Alhasnawi AN. 2023. Genetic stability analysis associated with salt stress and salicylic acid in fenugreek (Trigonella foenum-graecum) plants. Biodiversitas 24: 3601-3608. Salt damage to plants has been attributed to a combination of many factors like the accumulation of toxic metal ions or osmotic stress. This study attempted to understand the mitigating effects of the salicylic acid (SA) treatment on the salt-stressed seed germination ability of the fenugreek plants (Trigonella foenum-graecum); SA pre-treatment along with the salt tolerance capacity have also been tested. The effects of salinity and applied SA on biochemical traits and genetic stability of plantshave been estimated in this study. Respective molecular and biochemical changes occurring in plants as well as genetic analysis have been performed. The results indicated that exogenous application of SA(0.4 mmol) improved the biochemical traits in the seedlings. The evaluation of the genetic stability of the plants was also conducted. Whereas DNA marker-based genetic stability estimates are considered a reliable, accurate, and advanced technique.The Inter-Simple Sequence Repeats (ISSR) analysis has been performed with the help of 7 ISSRs primers. The 6 ISSRs primers generated 54 fragments in total, with an average of 4.5 bands for every primer. The ISSR did not reveal any polymorphic bands. Finally, it has been concluded that exogenous SA can be effectively used as a potential growth regulator for improving the biochemical traits and salinity stress tolerance of the fenugreek plants and stimulating its medicinal properties. Furthermore, ISSR markers were seen to be a good tool as potential diagnostic markers for testing the genetic stability of plants.

Determination of Genetic Diversity of Tamarind (Tamarindus indica) Accessions in Eastern Region of Kenya Using Inter Simple Sequence Repeat (ISSR) Markers

There is scanty information on tamarind’s genetic diversity in Easter Kenya. The objective of this study was to determine the genetic diversity of 64 tamarind accessions from Eastern Kenya using 12 Inter Simple Sequence Repeat (ISSR) markers. DNA was extracted from the young apical leaves using modified CTAB method and amplified using standard PCR. The data collected were scored as presence (1) or absence (0) of bands then compared to the 100bp ladder and analyzed using GeneAlex and R softwares. Only seven primers produced reproducible bands. A total of 46 alleles were produced for the 7 loci with an average of 6.6 per loci. Polymorphic information content (PIC) varied from 0.72 to 0.89 and genetic diversity varied from 0.74 to 0.9. The ISSR markers revealed effective polymorphism of 40.87 to 99.46% and the band sizes varied from 100 to 1000 bp. Analysis of Molecular Variance (AMOVA) depicted high variation within the tamarind populations at 90% and the least variation of 10% among the population. The first 3 components of Principal coordinate analysis (PCoA) contributed 40.83% of the total variation. Hierarchical cluster analysis grouped the tamarind accessions into seven major distinct groups. Tamarind accessions were different within counties with minimal variations among counties, proving that genetic diversity exists among the tamarind accessions in the Eastern region of Kenya. High genetic diversity was evident among Embu accessions and least among Masinga accessions. Diversity in tamarind can be utilized in marker-assisted breeding and primer ISSR17899A and ISSRHB11 can be explored in studying genes that code for various traits in tamarind accessions.

Know thy enemy: Investigating genetic contributions from putative parents of invasive Nymphaea mexicana hybrids in South Africa as part of efforts to develop biological control

Hybridisation of alien invasive plants complicates efforts to develop biological control, because variations in the genetic makeup of the target plant can impact the survival of host specific agents that have evolved adaptations specific to the original host. To maximise the likelihood of success in a biological control program, potential agents should therefore be collected from populations in the region of origin that are genetically similar to plants in the invaded range. Molecular markers are useful tools to understand genetic contributions in hybrid populations, especially where morphological differentiation is difficult. Nymphaea mexicana Zuccarini (Nymphaeaceae) is an invasive alien plant in South Africa that is being targeted for biological control, but hybrids with intermediate morphological traits are also present at several sites. In this study, ISSR (inter simple sequence repeats) and ITS (internal transcribed spacer) markers were used to determine which Nymphaea species are likely to be putative parents of these hybrids, and morphological characters were also investigated to determine if genetic and morphological traits matched. Two major hybrid groups were identified, with one group clustering with Nymphaea odorata Aiton and the other clustering with Nymphaea alba L. A third, smaller group clustered with Nymphaea tetragona Georgi, whereas the remaining samples clustered with pure N. mexicana from the native range. Morphological features agreed with deductions drawn from molecular data. These results allow us to focus efforts to find compatible biological control agents and better understand the complicated genetic structure of N. mexicana and Nymphaea hybrids in South Africa.

Molecular characterization of Melanoxylon brauna (Fabaceae) matrices established in a multiclonal minigarden

Melanoxylon brauna is a tree species native to the Atlantic Forest that has great potential for reforestation and urban afforestation. Due to its exploitation, germination difficulties, and absence in afforestation projects, it is currently endangered. Therefore, this study aims to evaluate the diversity and genetic structure in M. brauna matrixes established in multiclonal minigardens through inter simple sequence repeat (ISSR) markers. Plant material of 59 individuals arranged in the multiclonal minigarden was collected for the analyses. Eleven ISSR primers were selected, which generated 183 fragments, among which 117 were polymorphic (63,93%). The efficiency of the markers was confirmed through the polymorphism information content (PIC) which resulted in an average value of 0.36, characterizing them as moderately informative. High genetic diversity was found based on the values of the number of observed alleles (AO = 2.00) and effective alleles (AE = 1.63), Nei's diversity index (H* = 0.36), Shannon index (I* = 0.54), and the formation of distinct groups by cluster analysis. Despite the alleles being well distributed among individuals, revealing high genetic diversity, Bayesian inference revealed only one genetic group (K = 1). The ISSR markers proved to be efficient in the characterization of the genetic diversity in M. brauna individuals, and the population of the multiclonal minigarden can be used as a source of propagules for seedling production. However, actions such as the expansion of the genetic diversity through the introduction of plants from different origins can increase the adaptive potential of the minigarden and future established populations.