Simple Sequence Repeat Molecular Markers Research Articles

Genome-Wide Analysis of the NBS-LRR Gene Family and SSR Molecular Markers Development in Solanaceae

The Solanaceae family occupies a significant position, and the study of resistance genes within this family is extremely valuable. Therefore, our goal is to examine disease resistance genes based on the high-quality representative genomes of Solanaceae crops, and to develop corresponding Simple Sequence Repeat (SSR) molecular markers. Among nine representative Solanaceae species, we identified 819 NBS-LRR genes, which were further divided into 583 CC-NBS-LRR (CNL), 54 RPW8-NBS-LRR (RNL), and 182 TIR-NBS-LRR (TNL) genes. Whole genome duplication (WGD) has played a very important role in the expansion of NBS-LRR genes in Solanaceae crops. Gene structure analysis showed the striking similarity in the conserved motifs of NBS-LRR genes, which suggests a common ancestral origin, followed by evolutionary differentiation and amplification. Gene clustering and events like rearrangement within the NBS-LRR family contribute to their scattered chromosomal distribution. Our findings reveal that the majority of NBS-LRR family genes across all examined species predominantly localize to chromosomal termini. The analysis indicates the significant impact of the most recent whole genome triplication (WGT) on the NBS-LRR family genes. Moreover, we constructed Protein–Protein Interaction (PPI) networks for all 819 NBS-LRR genes, identifying 3820 potential PPI pairs. Notably, 97 genes displayed clear interactive relationships, highlighting their potential role in disease resistance processes. A total of 22,226 SSRs were detected from all genes of nine Solanaceae species. Among these SSRs, we screened 43 NBS-LRR-associated SSRs. Our study lays the foundation for further exploration into SSR development and genetic mapping related to disease resistance in Solanaceae species.

Intergeneric Transfer of Simple Sequence Repeat Molecular Markers for the Study of Chaenomeles as Fruit Crop Breeding Material

The genus Chaenomeles, part of the subfamily Maloideae within the Rosaceae family, comprises five recognized species and has long been valued for its ornamental qualities. However, the use of Chaenomeles japonica as a fruit crop is relatively recent, with its introduction into targeted breeding activities only occurring in the 1950s. Due to this, genetic information on the genus remains limited, and the application of molecular markers in crop breeding and further development have been narrow, relying primarily on non-specific marker applications in germplasm analysis. One potential solution is the transfer of molecular markers between genera, specifically from the related Maloideae genera. This study aimed to test the transferability of SSR markers developed for Malus to Chaenomeles, and to analyze the structure of available Chaenomeles germplasm. By including 74 Chaenomeles genotypes, 95 SSR markers originally developed for Malus were tested, with 25 proving effective for characterizing Chaenomeles germplasm. These adapted SSR markers successfully differentiated among Chaenomeles species, including Chaenomeles japonica, Chaenomeles speciosa, Chaenomeles cathayensis, and hybrids like Chaenomeles × superba and Chaenomeles × californica. The markers demonstrated high stability and repeatability, indicating their suitability for large-scale genetic research, species composition assessment, and breeding material evaluation. Given the limited studies on SSR markers in Chaenomeles, this research lays the foundation for further exploration, potentially expanding into the genetic diversity assessment and trait screening for breeding. As genetic research on Chaenomeles is still in its early stages, the development of additional markers will be crucial for advancing this crop.

Molecular Insights into the Reproductive Patterns and Genetic Structure of Wheat Stripe Rust in Ili, Xinjiang.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a globally significant fungal disease that seriously threatens wheat yield, particularly in China. This study investigates the genetic structure and reproductive patterns of Pst populations in Ili, Xinjiang, using 12 pairs of Simple Sequence Repeat (SSR) molecular markers. Analyses of 79 Pst isolates from either spring or winter wheat areas in Ili revealed three primary genetic clusters, indicating notable differences between populations associated with spring and winter wheat. The STRUCTURE results, complemented by UPGMA and PCoA analyses, highlight significant genetic diversity within these populations, with evidence of genetic recombination and sexual reproduction in certain areas. Pst populations in Ili exhibit a mixed mode of reproduction, predominantly sexual in Qapqal and Xinyuan D and primarily asexual within the spring wheat populations. The gene flow analysis underscores extensive inter-population communication, which facilitates the spread and adaptation of the pathogen across diverse wheat-growing environments. This study marks the first documentation of sexual reproduction in Pst within Xinjiang, providing new insights into its spread and genetic variation. These findings suggest that sexual reproduction may play a role in the regional adaptation and evolution of Pst, impacting future management strategies for wheat stripe rust in Xinjiang and potentially in broader Central Asian contexts.

Genetic diversity and fingerprinting of Elaeagnus angustifolia based on SSR molecular markers

DNA fingerprinting can reveal the genetic diversity of Elaeagnus angustifolia germplasm resources and clarify the source and genetic background of E. angustifolia germplasm, which are the preconditions for the breeding of new varieties, the identification and protection of germplasm resources, and the comprehensive development of the E. angustifolia industry considering both ecological and economic benefits. We employed 11 pairs of primers with high polymorphism, clear bands, and high reproducibility to analyze the genetic diversity of 150 E. angustifolia germplasm accessions from Gansu and Beijing by the simple sequence repeat (SSR) molecular markers. We then employed the unweighted pair-group method with arithmetic means (UPGMA) to perform the cluster analysis based on genetic distance and analyzed the genetic structure of the 150 germplasm accessions based on a Bayesian model in Structure v2.3.3. The genetic diversity analysis revealed the mean number of alleles (Na) of 7.636 4, the mean number of effective alleles (Ne) of 2.832 6, the mean Shannon genetic diversity index (I) of 1.178 1, the mean Nei's gene diversity index (H) of 0.582 1, the mean observed heterozygosity (Ho) of 0.489 9, the mean expected heterozygosity (He) of 0.584 0, the mean polymorphism information content (PIC) of 0.535 4, and the mean genetic similarity (GS) of 0.831 5. These results suggested that the E. angustifolia germplasm resources we studied exhibited significant genetic differences and rich genetic diversity. The cluster analysis revealed that the tested materials can be classified into 3 groups, with the main genetic distance (GD) of 0.422 9. The clustering results were not completely consistent with the geographic origin. The population structure analysis classified the germplasm accessions into 2 populations. We used 8 pairs of primers with high PIC to construct the fingerprints of 150 E. angustifolia germplasm accessions. The present study successfully constructs the DNA fingerprints and clarified the genetic relationship of the E. angustifolia germplasm resources in Gansu and Beijing, providing a theoretical basis for germplasm resource identification, breeding of elite varieties, application in gardening, and molecular-assisted breeding of E. angustifolia.

Species delimitations in the Campomanesia xanthocarpa group (Myrtaceae): insights from molecular markers and taxonomy

Different views on recognising taxa associated with the Campomanesia xanthocarpa group (Myrtaceae) demonstrate the difficulties in clearly delimiting species. Studies using Inter Simple Sequence Repeats (ISSR) molecular markers were carried out on 201 individuals from 13 populations of C. xanthocarpa Mart. ex O.Berg, C. adamantium (Cambess.) O.Berg, C. costata M.Ibrahim & Landrum and C. littoralis D.Legrand in an attempt to improve understanding of species boundaries between these species. SplitsTree, analysis of molecular variance (AMOVA), principal component analysis (PCA), Neighbour-Joining (NJ) dendrogram and STRUCTURE showed inconsistencies between morphological and genetic data in these taxa. Therefore C. adamantium and C. xanthocarpa are treated as distinct taxa in this study, as are C. costata, C. littoralis and C. rhombea O.Berg that were previously considered part of C. xanthocarpa. Structured populations in C. adamantium were not congruent with taxonomic data or poorly supported in the data analysed. These were maintained as a single polymorphic species and new integrative approaches are necessary to improve understanding of taxon boundaries. We present a taxonomic treatment based on these decisions. This study contributes to the systematic treatment of Campomanesia and encourages specific delimitation studies to resolve remaining taxonomic issues within the genus.

Simple Sequence Repeat Marker-Based Genetic Diversity and Chemical Composition Analysis of Ancient Camellia sinensis in Jiulong County, Sichuan Province, China.

The ancient tea plant germplasm resources are rich in genetic diversity and provide an important basis for the genetic diversity in tea germplasm resources. To explore the genetic diversity of ancient tea plant germplasm resources in Jiulong County, Sichuan Province. 59 ancient tea tree germplasm resources were analyzed using simple sequence repeat (SSR) molecular markers and chemical composition analysis. The results showed that a total of 83 alleles were amplified by 23 pairs of SSR primers, with an average observed allele number (Na) of 3.6 and an effective allele number (Ne) of 2.335. The average Shannon information index (I) and the polymorphic information content (PIC) of the primers were 0.896 and 0.446, respectively. The results of the UPGMA cluster analysis showed that 59 ancient tea tree samples could be classified into five different subgroups. Based on the results of chemical composition analysis, two specific tea germplasm resources with high amino acid content, 10 excellent germplasm resources with tea polyphenol content over 20% and some other tea germplasm resources were identified. This study reveals that Jiulong's ancient tea tree germplasm exhibits significant genetic diversity and includes valuable tea tree planting resources. These findings provide a foundational framework for the conservation, detailed exploration and sustainable utilization of these resources.

Analysis of Fluorescently Labeled ISSR Markers to Reveal the Genetic Diversity of Cassava Varieties (Manihot esculenta Crantz) in the Kerala’s Tribal Area of India

The study Inter Simple Sequence Repeat (ISSR) molecular markers to genotype distinct cassava (Manihot esculenta Crantz) cultivars within tribal communities in Kerala, India. Fluorescent ISSR primers were labelled with 6-carboxyfluorescein and used for PCR amplification. The total number of bands produced was 72, of which 49 were found to be polymorphic markers; an average of 17 polymorphic bands was obtained per primer. The manuscript is a scientific validation of the traditional knowledge of tribal people regarding the diversity and wealth of cassava crops in the region, and this validation can therefore help in protecting the farmers right on a particular landrace that they cultivate. The technique used in the diversity analysis is a time-saving process as compared to conventional breeding programs for crop improvement. The data in the manuscript also supports similarity and differences of each variety to one another, which is analysed statistically with the molecular marker-based data generated. By examining genetic diversity at a high resolution, ISSR markers can provide valuable insights into the evolutionary dynamics of these cassava populations. This research contributes to the broader goal of enhancing agricultural sustainability and food security in tribal communities.

Identification and Fine Mapping of a Mutant pv‐nts Gene Responsible for Dwarf and Thin Stem of Snap Bean (Phaseolus vulgaris L.)

ABSTRACTPlant height is one of the most important traits in the breeding of snap bean, which determines the planting density and the resistance to failure, which in turn affects its yield and quality. Therefore, studying the molecular mechanism of plant height in snap bean is an important measure to realize the improvement of snap bean. We obtained a dwarf, thin‐stemmed mutant nts (normal to slim) from a dwarf variety of snap bean A18 via 60CO‐γ‐ray treatment. We conducted phenotypic observations, endogenous hormone content measurements and genetic analyses of the dwarfing thin‐stemmed mutant nts and explored gene localization and candidate gene screening for the mutant trait in snap bean. Compared with wild‐type A18, nts mutant exhibited various abnormal phenotypes such as dwarfing, reduced branching, thinner top stem, reduced plant width, reduced number of leaf area and thousand grain weight and increased content of hormones such as indole‐3‐acetic acid (IAA) in the top stem. Genetic analysis indicated that the mutant trait was controlled by a single recessive nuclear gene, and the mutant gene was named pv‐nts. pv‐nts was localized to a 361.1‐kb segment on chromosome 8 as revealed by bovine serum albumin (BSA) hybrid pool sequencing and simple sequence repeat (SSR) molecular markers. Phvul.008G106300 (encoding LAX2 protein) was identified as a candidate gene corresponding to pv‐nts via gene function annotation. Phvul.008G106300 was significantly upregulated in nts mutant compared with wild‐type A18, which was consistent with the results of endogenous IAA levels. Sequence analysis showed that the Phvul.008G106300 gene in nts had a base mutation that altered the protein structure, thus causing the dwarfed, thin‐stemmed phenotype of cauliflower. Taken together, these results contribute to a better understanding of the genetic basis of dwarfing traits in snap bean.

Development of SSR Markers and Evaluation of Genetic Diversity of Endangered Plant Saussurea involucrata.

The conservation biology field underscores the importance of understanding genetic diversity and gene flow within plant populations and the factors that influence them. This study employs Simple Sequence Repeat (SSR) molecular markers to investigate the genetic diversity of the endangered plant species Saussurea involucrata, offering a theoretical foundation for its conservation efforts. Utilizing sequencing results to screen SSR loci, we designed and scrutinized 18 polymorphic microsatellite primers across 112 samples from 11 populations in the Bayinbuluke region. Our findings reveal high genetic diversity (I = 0.837, He = 0.470) and substantial gene flow (Nm = 1.390) among S. involucrata populations (China, Xinjiang), potentially attributed to efficient pollen and seed dispersal mechanisms. Principal Coordinate Analysis (PCoA) indicates a lack of distinct genetic structuring within the Bayinbuluke populations. The cluster analysis using STRUCTURE reflected the genetic structure of S. involucrata to a certain extent compared with PCoA. The results showed that all samples were divided into four groups. To safeguard this species, we advocate for the in situ conservation of all S. involucrata populations in the area. The SSR markers developed in this study provide a valuable resource for future genetic research on S. involucrata.

Genome-wide association study of the loci and candidate genes associated with agronomic traits in Amomum villosum Lour.

Amomum villosum Lour. (A. villosum) is a valuable herbaceous plant that produces the famous traditional Chinese medicine Amori Fructus. Identifying molecular markers associated with the growth of A. villosum can facilitate molecular marker-assisted breeding of the plant. This study employed 75 A. villosum accessions as the test material and utilized 71 pairs of polymorphic simple sequence repeat (SSR) molecular markers to genotype the population. The study analyzed the association between SSR markers and phenotypic traits through the linkage imbalance and population structure analysis. Candidate genes associated with the molecular markers were also identified. The results showed that the phenotypic diversity index range of the 12 agronomic traits was 4.081-4.312 and conformed to a normal distribution. Moreover, 293 allelic variations were detected in the 75 accessions, with an average of 5.32 amplified alleles per loci, ranging from 3 to 8. The maximum number of amplified alleles for AVL12 was 8. The population structure and cluster analysis indicated that the accessions could be divided into two subgroups. Using the mixed linear model (MLM) model of population structure (Q)+kinship matrix (K) for association analysis, three SSR molecular markers significantly associated with the agronomic traits were detected. Fluorescence quantification was used to analyze the expression levels of six candidate genes, and it was found that three of the genes were differentially expressed in phenotypically different accessions. This study is the first to use SSR markers for genome-wide association study (GWAS) mapping and identification of the associated agronomic traits in A. villosum. The results of this study provide a basis for identifying genetic markers for growth traits for marker-assisted breeding in A. villosum.

Quantitative Trait Loci Mapping and Association Analysis of Solanesol Content in Tobacco (Nicotiana tabacum L.)

Solanesol, which accumulates predominantly in the leaves of tobacco plants, has medically important bioactive properties. To investigate the genetic basis of solanesol in tobacco (Nicotiana tabacum), the solanesol contents of 222 accessions, 206 individuals from an N. tabacum Maryland609 (low-solanesol) × K326 (high-solanesol) F2 population and their corresponding F1 self-pollinations, were determined using ultra-performance liquid chromatography. Genome-wide quantitative trait locus (QTL) and association analysis were performed to identify QTLs and markers associated with solanesol content based on simple sequence repeat molecular markers. A total of 12 QTLs underlying solanesol content were mapped to seven linkage groups (LGs), with three of the QTLs (QTL3-1, QTL21-6, and QTL23-3) explaining 5.19–10.05% of the phenotypic variation. Association analysis revealed 38 significant marker-trait associations in at least one environment. The associations confirmed the QTLs located on LG3, LG10, LG14, LG21, and LG23, while new elite makers were located on 11 additional LGs, each explaining, respectively, 5.16–20.07% of the phenotypic variation. The markers LG14-PT54448, LG10-PT60114-2, LG10-PT60510, LG10-PT61061, and LG-21PT20388 may be useful for molecular-assisted selection of solanesol content in tobacco leaves. These results increase our understanding of the inheritance of solanesol-associated genes and will contribute to molecular-assisted breeding and further isolation of regulatory genes involved in solanesol biosynthesis in tobacco leaves.

Exploring the Genetic Landscape of Tilia Spp. with Molecular and Statistical Tools

Tree species with high ecological plasticity are recommended for use in urban green infrastructures. This study explores the genetic diversity of Tilia cordata, Tilia platyphyllos, and Tilia argentea, highlighting their contribution to urban landscapes. In this respect, the genetic variability of individuals from four populations of the Tilia genus has been analyzed using Inter Simple Sequence Repeats (ISSR) molecular markers, and some of their phenotypic characters were naked-eyed observed or determined by dendrometric measurements. Significant variability between the populations studied was determined. Cluster analysis identified two main groups: Tilia cordata I and Tilia cordata II populations formed the first cluster, and Tilia platyphyllos and Tilia argentea populations formed the second cluster. The results of the phenotypic analysis confirmed the genetic results separating the two populations of Tilia cordata from the populations of Tilia platyphyllos and Tilia argentea in relation to their visible morphological characters. Results obtained from dendrometric measurements analysis represent the foundation for further investigations on urban ecology. An essential potential practical use of the results: the establishment of more efficient ISSR primers to identify the Tilia species analyzed: UBC864, A12, UBC840, and A7 for Tilia cordata, A13 for Tilia platyphyllos and A7 for Tilia argentea has been demonstrated.

Genetic background of lily germplasm resources based on SSR markers

To study the genetic background of lily (Lilium spp.) germplasm resources, and accurately evaluate and select excellent germplasm for genetic improvement of lily, we analyzed the genetic background of 62 lily germplasm accessions from 11 provinces of China by using simple sequence repeat (SSR) molecular markers. The results showed that 15 out of 83 pairs of lily SSR primers were polymorphic. A total of 157 allelic loci were amplified, with the number of alleles per locus ranging from 5 to 19 and the average number of effective alleles per locus being 4.162 8. The average observed heterozygosity and expected heterozygosity were 0.228 2 and 0.694 1, respectively. The average polymorphic information content was 0.678 8. The average Nei's diversity index and Shannon's information index were 0.694 1 and 1.594 9, respectively, indicating that the tested lily germplasm had high genetic diversity. The 62 germplasm accessions were classified into 5 groups by the unweighted pair group method with arithmetic mean (UPGMA) and into 3 groups by the principal component analysis. The two analyses revealed a geographic correlation among different groups. The majority of lily germplasm accessions from the same source tended to cluster together. The population structure analysis classified the lily accessions into 4 populations and 1 mixed population. The above results provide a theoretical basis and genetic resources for the precise identification and breeding of lily germplasm resources.

Clustering Analysis of Natural D-borneol Resource Plants Based on Simple Sequence Repeat (SSR) Markers, Leaf Morphology, and Chemical Composition.

D-borneol is a double-loop monoterpene with a wide use in the pharmaceutical, food, and cosmetics industries. Natural D-borneol can be extracted from branches and leaves of D-borneol resource plants. With the widespread use of natural D-borneol, the identification of D-borneol resource plants and the protection of germplasm resources have become the focus of research. In this study, plant leaf morphology, chemical composition, and simple sequence repeat (SSR) molecular marker analysis were used to analyze and cluster 5 species of D-borneol resource plants and their closely related species. It was found that all three analysis methods could distinguish and cluster these D-borneol resource plants to some degree. The result of SSR analysis using capillary electrophoresis was the best, and it could distinguish Mei Pian tree from Yin Xiang as well as Longnao Zhang from An Zhang. The correlation analysis between SSR similarity matrix and leaf morphology analysis and between SSR similarity matrix and chemical composition similarity matrix revealed that they both had significant correlations (P < 0.0001) and the correlation (r = 0.588) between SSR and leaf morphology was a little higher than that (r = 0.519) between SSR and chemical composition. This indicated that the environment had a greater impact on the chemical composition than on leaf morphology. The research findings will offer efficient techniques to cluster natural D-borneol resource plants and establish a theoretical basis for their future development and utilization.

SSR Marker–Based Genetic Diversity and Relationship Analyses of Stephania tetrandra S. Moore

Stephania tetrandra S. Moore (family: Menispermaceae), a dioecious herbaceous vine and the only species in the subgenus Botryodiscia of the genus Stephania of the family Menispermaceae, is mainly distributed in hilly areas south of the Huaihe River in China and found in many provinces of China, showing a high genetic diversity. This paper aimed to study genetic diversity of and genetic relationship among individuals of S. tetrandra within China to provide a basis for evaluation, exploitation, and utilization of S. tetrandra by using simple sequence repeat (SSR) molecular markers. Our results show that effective products were amplified from the 26 screened SSR gene loci, a total of 183 alleles amplified (2–16 alleles amplified by each pair of primers). Among the 26 loci, 16 had a PIC value higher than 0.5, indicating a high level of polymorphism. For most of the loci, the number of effective alleles was lower than that of the observed alleles, and the observed heterozygosity was lower than the expected heterozygosity. The genetic differentiation coefficient (0.021–0.547) was lower than 0.05 (low level of genetic differentiation) for 7 loci and higher than 0.25 (very high level of genetic differentiation) for 2 loci, and had a value representing a medium level of genetic differentiation for the remaining 17 loci. The intra-population inbreeding coefficient had a positive value for 21 loci, suggesting the presence of inbreeding and homozygous excess. The gene flow value was bigger than 1, indicating that genetic drift and natural selection played an unimportant role in population genetic differentiation of S. tetrandra. Based on discriminant analysis of principal components and Bayesian Information Criterion, K-means clustering was performed on 620 samples. These samples were divided into 9 genetic clusters, whose similarity coefficients and genetic distances were 0.755–0.918 and 0.067–0.280, respectively, indicating that these clusters were highly similar and short-distanced. The Bayesian clustering analysis was implemented in the STRUCTURE software to analyze the genetic structure of S. tetrandra and it was found that the 620 samples could be clustered into 5 ancestor groups; the 9 clusters and 40 natural populations inherited genes from the 5 groups to varying degrees, but the proportion of genes inherited from the 5 groups by each cluster and natural population differed. S. tetrandra was characterized by the presence of population structure and pronounced genetic subdivision, which, together with the presence of gene flow, may indicate a relatively stable recent state of these populations.

Cross-Species Transferability of SSR Markers for Analyzing Genetic Diversity of Different Vicia species Collections

Legumes play an essential role in sustainable agriculture due to their ability to fix nitrogen and high protein content. Vicia is a relevant genus of the Fabaceae family that includes important crop species, such as V. faba and V. sativa, but also other species considered minor crops. They are mainly used as animal feed and usually cope resiliently with extreme conditions; therefore, they could play an essential role in sustainable agriculture under the present scenario of climate change and growing population. However, the scarcity of commercial cultivars limits their use. The Spanish National Plant Genetic Resources Center has collections of several species of the genus Vicia, including international landraces, which could be an essential source of biodiversity for breeding programs. These seed resources are underutilized due to the limited availability of characterization data, including the lack of molecular markers for these species. In this study, we analyzed the cross-transferability of SSR (simple sequence repeat) molecular markers from V. sativa and V. ervilia to distinct species of the genus Vicia. We also used heterologous validated markers for the genotypic characterization and genetic diversity analysis of almost 500 accessions of three undercharacterized Vicia collections: V. articulata (one-flower vetch), V. ervilia (bitter vetch), and V. narbonensis (narbon bean or French vetch). Subsequently, these molecular data were integrated with passport and agromorphological data to select representative varieties from these Vicia collections and establish core collections, with minimum loss of genetic diversity versus the Spanish total collections. The characterization of these legume collections is an essential step from an economic and ecological point of view to obtain selected Vicia varieties to be used in sustainable agriculture.

Effects of Different Media and Their Strengths in In Vitro Culture of Three Different Cistus creticus L. Populations and Their Genetic Assessment Using Simple Sequence Repeat Molecular Markers

Cistus creticus L. (rockrose), a species of ecological and medicinal significance, constitutes a valuable component of the Mediterranean ecosystem. The present study investigated the effect of the inorganic salt concentration of Murashige and Skoog medium (MS), woody plant medium (WPM), and Driver and Kuniyaki Walnut medium (DKW) at several strengths (1/8×, 1/4×, 1/2×, 1×, and 2×) on the in vitro growth and organogenesis of rockrose. Significant interactions were observed throughout the experiments between pairs of plant origins, medium types, and strengths, and we also examined the extent to which they affected the studied traits was examined. The types of nutrient medium affected all studied traits except shoot and root percentages. The maximum growth percentage (143.49%) was gained using full-strength WPM. The best performance in shoot percentage was obtained using MS (100%) at several strengths along with 1× WPM (100%). The topmost rooting percentage values (98.61%) were obtained using 1× WPM and 1/2× DKW. The highest number of shoots and roots were observed using full-strength MS (9.39) and half-strength WPM (6.49), respectively. The maximum values for shoot and root length were achieved using 1/2× MS (0.78 cm) and 1/8× WPM (1.55 cm), respectively. The origin of the plant material did not influence any studied trait. Moreover, the genetic relations among the populations used in the in vitro culture were assessed using simple sequence repeats (SSR) markers. Twenty-eight alleles were identified across all five STR loci. The different and effective alleles per locus were 5.60 and 4.72, respectively. The average observed and expected heterozygosity was estimated at 0.52 and 0.72, respectively. Shannon’s information index and the inbreeding coefficient (F) were assessed at 1.48 and 0.30, respectively, revealing a narrow genetic base and high genetic similarity among origins, suggesting that they belong to the same population.

TINJAUAN PUSTAKA SISTEMATIS: KARAKTERISASI KEANEKARAGAMAN GENETIK SPESIES JERUK (Citrus sp.) MENGGUNAKAN PENANDA SIMPLE SEQUENCE REPEAT (SSR)

Background: The biodiversity of citrus plants is very abundant and many are cultivated, creating various types. However, the high demand makes orange farmers feel overwhelmed. This is what causes some orange cultivars to become rare. Characterization of the genetic diversity of citrus germplasm at the molecular level is an important and crucial step that can assist in the breeding and conservation process. The aim of this literature review is to provide information regarding molecular markers regarding the application of SSR molecular markers to analyze the genetic diversity of citrus. Method: The method used is a systematic literature review with the literature sources used coming from articles taken from national journals and international journals indexed by Scopus. Results: The application of molecular markers using the SSR method is useful for identifying and characterizing the genetic diversity of citrus germplasm so that it can assist in breeding and conservation actions. SSR has many advantages both in terms of its use and the results obtained. Conclusion: One application of molecular markers is to analyze plant genetic diversity. Simple Sequence Repeat (SSR) molecular markers can help to analyze the characteristics and genetic diversity of oranges so that they can assist in plant breeding and conservation purposes.

Development and validation of genome-wide SSR molecular markers of Tapes dorsatus.

Tapes dorsatus is an economically important benthic animal in the Beibu Gulf of China. However, the deficiency of microsatellite markers has hindered the study of its genetics. The development of microsatellite markers will provide useful tools for genetic improvement, variety identification, phylogenetic analysis and resource conservation. Within the genome sequence, 145,008 simple sequence repeats (SSRs) were identified, and 29,691 primer pairs were designed successfully. A total of 100 primer pairs were randomly synthesized for testing, and 93 primers yielded products. Sixty highly polymorphic primers were used to reveal the genetic diversity of 50 T. dorsatus individuals. The average number of alleles (Na) of the population was 10.40; the average number of effective alleleswas 6.16, the average expected heterozygosity (He) was 0.82, and the average polymorphic information contentwas 0.80. The genetic structure of the population was detected, by which the population could be divided into three subpopulations. We identified 145,008 SSRs in the genome of T. dorsatus and designed 29,691 primer pairs in this study. Of 100 synthesized primers, 60 were highly polymorphic and used to reveal the genetic diversity and structure of the population. The SSR markers identified here will provide useful tools and a foundation for genetic diversity, linkage mapping and molecular marker-aided breeding in T. dorsatus.

Using RAPD and ISSR markers to assess genetic diversity and conservation of Bruguiera gymnorrhiza (L.) Lam. for sustainable management on Kerala's West Coast

In this genetic study focusing on Kerala’s west coast, particularly the southern region with diverse demographics and fluctuating salinity, we utilized random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) molecular markers to assess the genetic variation of the plant species Bruguiera gymnorrhiza, which is facing habitat loss in the region. The ISSR marker demonstrated a higher degree of polymorphism (13.6%) compared with RAPD (3.5%). The polymorphic information content averaged 0.484 for ISSR and 0.354 for RAPD. The B. gymnorrhiza samples from Alappuzha and Thrissur clustered together in both markers. Nei’s genetic diversity index (h) was determined to be 0.430 for RAPD and 0.453 for ISSR. The unweighted pair group with the arithmetic mean dendrogram, reflecting a greater degree of polymorphism, supports the conservation of B. gymnorrhiza throughout Kerala’s west coast. Additionally, the marker index was calculated as 0.506 for ISSR and 0.392 for RAPD, highlighting the efficacy of ISSR markers in assessing the genetic diversity of B. gymnorrhiza.