SSR Molecular Markers Research Articles

SSR loci information analysis in transcriptome of Cordyceps sinensis

To analysis the SSR loci information in the transcriptome of Cordyceps sinensis and develop SSR molecular markers,MISA(MicroSatellite) software was used to analyze the microsatellites information from 16 875 unigene sequences and SSR primer designed by Primer 3. 0. In total,5 899 SSRs were detected in 4 252 unigene with the distribution frequency of 34. 99%,which was represented by 74 repeat motifs and SSR loci occurred per 7 952 bp in length. In the SSRs,the mono-nucleotide was the most abundant repeat motif(42. 5%),followed by tri-nucleotide(34. 48%),C/G and CCG/CGG were the dominant repeat motifs,respectively. The number of repetitions of the six SSR repeat types was concentrated on 5 to 12 times,and the length was mostly less than 24 bp. A total of 12 282 pairs of primers were screened and selected 20 pairs of primers for validity detection randomly,10 pairs of primers amplified the expected specific bands,and primer P1 has significant polymorphism. Moreover,it was found that unigene containing SSR loci is mainly related to genetic and environmental functions after GO and KEGG annotation. In conclusion,these SSR loci in the transcriptome of O. sinensis are high in frequency,rich in primitive types,high in polymorphism,and highly available,which will provides abundant candidate molecular markers for its genetic diversity analysis,resource identification protection,and gene function research.

Classification and phylogenetic relationship of 10 fig varieties by RAPD and SSR molecular markers

In this experiment, 24 fig varieties were analyzed by RAPD and SSR. Results showed that 80 loci were amplified by 9 RAPD primers, including 70 polymorphic loci. The polymorphic percentage was 87.50%. A total of 34 allelic variations were detected in 10 pairs of SSR primers, 29 of which were polymorphic bands, and the percentage of polymorphic sites was 85.29%. Correlation analysis of the two markers of genetic identity showed significant correlation, indicating that the two markers were highly consistent in the analysis of fig genetic diversity. Cluster analysis revealed that the RAPD markers showed that the 24 fig varieties had a genetic similarity coefficient of 0.7 and could be divided into four groups. SSR markers showed that the 24 fig varieties can be divided into four groups at the genetic similarity coefficient of 0.66. The results show that the two molecular markers are suitable for the genetic diversity analysis of fig, and they are more reliable when combined than when used alone.

High genetic differentiation of grapevine rootstock varieties determined by molecular markers and artificial neural networks

The genetic differentiation of grapevine rootstock varieties was inferred by the Artificial Neural Network approach based on the Self-Organizing Map algorithm. A combination of RAPD and SSR molecular markers, yielding polymorphic informative loci, was used to determine the genetic characterization among the rootstock varieties 420-A, Schwarzmann, IAC-766 Campinas, Traviú, Kober 5BB, and IAC-572 Jales. A neural network algorithm, based on allelic frequency, showed that the individual grapevine rootstocks (n = 64) were grouped into three genetically differentiated clusters. Cluster 1 included only the Kober 5BB rootstock, Cluster 2 included rootstocks of the varieties Traviú and IAC-572, and Cluster 3 included 420-A, Schwarzmann and IAC-766 plants. Evidence from the current study indicates that, despite the morphological similarities of the 420-A and Kober 5BB varieties, which share the same genetic origin, two new varieties were generated that are genetically divergent and show differences in performance.

Genetic Diversity Among Old Local Grape Cultivars in South of Syria

This investigation was carried out in Sweida governorate of Syria from 2014 to 2015. The purpose of this investigation was to estimate the genetic diversity among 17 old local grape cultivars using morphological traits and SSR molecular markers. Principal Component Analysis (PCA) of morphological traits revealed that four main components were accountable for 50.34 % of variance, with Eigen values of 16.77%, 13.31%, 10.59% and 9.67%, respectively. While distribution of cultivars was found significantly dependent of first and second components, which separated Aswad Sharar and Derbly cultivars rather than other studied cultivars. Hierarchical cluster of morphological traits showed high diversity among studied cultivars. On the other hand, molecular characterization was conducted using eight informative SSR primer pairs, polymorphism was detected by seven SSR's primers. As a result, 18 polymorphic alleles were revealed with a polymorphism percentage of 100%, which reflected the genetic variation among studied cultivars. Genetic similarity was achieved, where 0.875 was the highest between Zeiny and Khedry cultivars, while the other two cultivars Ebeidy and AhmarMokamaa showed the lowest genetic similarity as 0.077. Cluster analysis of SSR markers grouped the studied cultivars into three clusters as per Jaccard coefficient. The first cluster grouped Ebeidy, Aswad Helwany and Derbly cultivars together, the second cluster contained two cultivars Beiady and Alb Atair, while the third cluster contained the remaining cultivars. Consequently, the results showed high diversity among studied cultivars, and some morphological traits were useful for cultivar discrimination.

Genome survey analysis and SSR loci mining of Bupleurum falcatum

Buplewrum falcatum is a traditional Chinese medicine,which is mainly used for the treatment of cold and liver protection. B. falcatum is dominantly cultivated in Japan as well as planted in China,Korea and other countries and regions. In order to determine the appropriate sequencing strategy,the genome survey before large-scale genome sequencing is needed. This survey can provide information about the size and complexity of the whole genome of the target species. In the present study,the next generation sequencing technology( Illumina Hiseq 2000) was used to analyze the genome size and complexity of B. falcatum. In addition,SSR loci were analyzed from the sequenced data. Primer 3 was used to design specific primers and 33 pairs of primers were randomly selected for PCR with template DNA of B. falcatum,and the PCR system and optimal annealing temperature were screened. A total of 288. 64 G genome sequence data was obtained,and the estimated genome size of B. falcatum was 2 119. 58 Mb. The measured genome data depth was138×; the rate of heterozygosity was 1. 84%; and the ratio of repeat sequence was 83. 89%. It is speculated that the genome of B. falcatum is complex. The preliminary assembly was performed with K-mer = 41,and the contig N50 was 224 bp,the total length 896. 97 Mb,the scaffold N50 313 bp,and the total length was 922. 67 Mb. A total of 91 377 SSR sequences were detected in the sequenced genome data which were distributed in 70 809 unigenes.The main type is dinucleotide repeats,with 49 680 sequences,accounting for70. 16%. Among the 33 pairs of primers randomly synthesized according to the obtained SSR sequences,21 pairs were successfully amplifying the target sequences. The results will be helpful for later large scale genome sequencing and SSR molecular markers development for germplasm identification and trait mapping.

Genetic diversity of mutant napiergrass using Expressed Sequence Tag Simple Sequence Repeat (EST-SSR)

Abstract. Mansyur, Karti PMH, Abdullah L, Husni A, Lestari P. 2019. Genetic diversity of mutant napiergrass using Expressed Sequence Tag Simple Sequence Repeat (EST-SSR). Biodiversitas 20: 2403-2409. Napiergrass is one of the tropical grasses which has a very important role in developing ruminant livestock, its productivity is high and its nutritional content is quite good. Plant breeding to produce new varieties that have better productivity continues. One of them is through mutation breeding and in vitro culture. The purpose of this research was to look at the genetic diversity among napiergrasses using the Expressed Sequence Tag Simple Sequence Repeat (EST-SSR). This study used 14 SSR molecular markers. The results showed that mutant DNA of napiergrass can be clearly amplified by all the EST-SSR primers used. The average number of alleles was 4.57, the average frequency of the main allele was 42%, and the average value of gene diversity was 0.66. While the PIC average value was 0.60. There were five markers that were very informative and have PIC values ​​above 0.7, among others, namely ICMP3045, ICMP3018, PSMP2090, PSMP2209, and PSMP2019. Phylogenetic analysis shows that 37 numbers of napiergrass mutants split into two main clusters at a coefficient of 0.56. The first cluster consists of 26 lines while the second cluster consists of 11 mutants. The parent napiergrass is in the first cluster. There are two pairs of mutants that have the same diversity, namely R20-11 with R 20-20-3 and R100-1 with R100-3.

Identification of Leaf Rust Resistance Genes in Selected Wheat Cultivars and Development of Multiplex PCR.

Ten leading wheat cultivars originating from the Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute (Poland) and the Department of Gene Bank (Czech Republic) were used to establish a field experiment in 2017 and 2018 at the Dłoń Experimental Farm. The analyzed wheat genotypes were characterized by diversified field resistance to leaf rust. Jubilatka, Thatcher and Sparta were the most resistant cultivars in field conditions in both 2017 and 2018. The aim of the work was to identify the Lr11, L13, Lr16 and Lr26 genes encoding resistance to leaf rust using molecular SSR markers (wmc24, wmc261, Xgwm630, Xwmc764 and P6M12) and to develop multiplex PCR conditions to accelerate identification of these genes. Markers of three leaf rust resistance genes have been identified simultaneously in these cultivars. Jubilatka, Thatcher and Sparta cultivars may serve as a good source of the analyzed leaf rust resistance genes. In addition, multiplex PCR conditions have been developed for the simultaneous identification of the Lr11 and Lr16 and Lr11 and Lr26 gene pairs.

Genetic variability among autotetraploid populations of banana plants derived from wild diploids through chromosome doubling using SSR and molecular markers based on retrotransposons

The development of banana cultivars resistant to diseases is the most viable way to minimize crop damages. However, this strategy is limited by the low fertility observed among commercial triploid cultivars, especially those of the Cavendish subgroup. Induced polyploidy has the potential to overcome sterility barriers and allows the development of triploid genotypes with fruit sensory profiles aligned with market demands. This work characterized agronomically five autotetraploid plant populations derived from diploids treated with colchicine. The experiment was conducted using an augmented block design, and 13 agronomic characteristics were evaluated during two production cycles. The sum of ranks proposed by Mulamba and Mock allowed the genotypes Pisang Lilin 8, Malbut 10, Niyarma Yik 2, Pisang Mas 3, and Thong Dok Mak 2 to be selected, which were superior for most of the agronomic characteristics evaluated. SSR and IRAP molecular markers detected variability in the autotetraploid populations, and the analysis of molecular variance supports that approximately 78% of identified variability was contained within the populations studied. Based on the results, it is inferred that the promising autotetraploids can be crossed with diploids to develop secondary triploid hybrids.

A multivariate approach for the ampelographic characterizations of Algerian grapevine genotypes (Vitis vinifera L.): Insights into conservation and commercialization

This study was conducted in three vegetation successive periods (2015, 2016, and 2017) to determine ampelographic characteristics of the 36 grapevine varieties grown in the Eastern Algerian germplasm collection by a total of 108 ampelographic criteria using OIV descriptors. The data were processed by multivariate statistical procedures. A number of factors have been well identified in the classification of grape varieties studied, some are quantitative in particular the length of veins from N1 to N5 (OIV601, OIV602, OIV603, OIV604, OIV611), length of petiole sinus to upper and lower lateral leaf sinus (OIV605, OIV606) and fruit production represented by the bunch size (OIV202, OIV203) and weight (OIV502), while the qualitative parameters related mainly to the density of hairs for the young shoot (OIV004), density of prostrate and erect hairs on and between main veins on lower side of blade young leaf (OIV053, OIV054, OIV055, OIV056, respectively) and density of prostrate hairs between the main veins on lower side of blade mature leaf (OIV084). The results obtained by all parameters together confirmed the synonymy between varieties already found previously by molecular SSR markers in particular between both varieties as Bouaber des Aures, Kabyle Aldebert; Ahmar Mechtras II, Ahmar Mechtras III; Farana Blanc, Farana de Mascara; Aneb Kabyle, Ahmed draa Mizen and between three cultivars Lekhzine, Ahchichene, Adari des Bibans. However, the problem of synonymy remains invalid between Louali and El wali, despite the close convergence between them, especially in ampelographic quantitative measured criteria.

Assessment of genetic diversity among local pea (Pisum sativum L.) accessions cultivated in the arid regions of Southern Tunisia using agro-morphological and SSR molecular markers

The pea (Pisum sativum L.) is arguably an important winter pulse crop and a fundamental source of proteins for human and animal nutrition. In Tunisia, pea cultivation is characterized by its instability, especially in the arid region of Southern Tunisia. We carried out an investigation of the agro-morphological and genetic diversity of 12 local pea accessions cultivated in the arid region. We analyzed 21 qualitative and 26 quantitative traits following the UPOV descriptors. Furthermore, 8 SSRs were employed to examine genetic polymorphism, differentiation, and population structure. Molecular and agro-morphological data distinguished all the accessions under investigation. A considerable phenotypic diversity among accessions was observed for many characters, including some related to agronomical performance. At the molecular level, all the SSRs were polymorphic, with an average of 0.44 PIC value per locus. Our work indicated the presence of a wide-ranging variation among the local pea accessions evaluated. The overall results indicated that the agro-morphological traits and SSR markers were reliable and effective for assessing the genetic diversity of phenotypic pea accessions.

Genetic Diversity of Torch Ginger (Etlingera elatior) Germplasm Revealed by ISSR and SSR Markers.

Fifty-seven accessions of torch ginger (Etlingera elatior) collected from seven states in Peninsular Malaysia were evaluated for their molecular characteristics using ISSR and SSR markers to assess the pattern of genetic diversity and association among the characteristics. Diversity study through molecular characterization showed that high variability existed among the 57 torch ginger accessions. ISSR and SSR molecular markers revealed the presence of high genetic variability among the torch ginger accessions. The combination of different molecular markers offered reliable and convincing information about the genetic diversity of torch ginger germplasm. This study found that SSR marker was more informative compared to ISSR marker in determination of gene diversity, polymorphic information content (PIC), and heterozygosity in this population. SSR also revealed high ability in evaluating diversity levels, genetic structure, and relationships of torch ginger due to their codominance and rich allelic diversity. High level of genetic diversity discovered by SSR markers showed the effectiveness of this marker to detect the polymorphism in this germplasm collection.

Seleksi Pendonor Serbuk Sari Sifat Kuantitas Endosperma Skor Tinggi pada Kelapa dalam Kopyor

Endosperm quantity in kopyor coconut determines the quality of kopyor coconut. However, data of the best parental based on their progeny test is unavailable yet. In this study, we employed polycross approach and SSR molecular marker to estimate general combining ability of the best pollen contributor for the breeding purpose of this trait. Totally 151 kopyor coconuts were collected from the naturally open-pollinated population of kopyor Tall coconut Agom Lampung. The harvested nuts were rated for their endosperm quantity (scored 1-9). The analysis identified 31 paternal trees of the 53 progenies. The TJ-185 with the highest GCA has been considered as a promising paternal tree for development of high endosperm quantity of kopyor coconut.Keywords: combining ability, molecular marker, paternal trees, polycross, tall coconut

Metabolite profiles of essential oils and SSR molecular markers in Juniperus rigida Sieb. et Zucc. from different regions: A potential source of raw materials for the perfume and healthy products

Juniperus rigida Sieb. et Zucc. (J. rigida) is the traditional Chinese medicine with therapeutic effect of rheumatoid arthritis and dropsy. The essential oils showed unique industrial production potential including flavoring, cosmetics and household products. However, current research on J. rigida were mainly focused on their morphological features with few consideration of breeding quality evaluation and production development. This study combined metabolite profiles with SSR molecular marker which correlated with essential oils to estimate the differentiation between chemotypes and genotypes of J. rigida to evaluate the breeding quality for further production development. The chemotypes were evaluated by GC–MS fingerprint combined with chemometrics, in which the J. rigida derived from Fugu (S2), Jinhua (S8) and Fengcheng (S10) owned the best quality due to their rich volatile compositions and strong bioactivity. The J. rigida from 10 origins were assorted into three quality clusters and 8 essential oils compositions were selected as the indicated compounds that contributed to the quality evaluation of J. rigida. In addition, 23 pairs of SSR molecular marker primer sequences were developed and the PCA analysis results also divided J. rigida into three categories. Correlation analysis showed the metabolites content differed from genetic diversity. The ylangene, α-farnesene, neryl isobutyrate, and α-guaiene were the indicating compounds for the selection of high-quality J. rigida origin. These results may further provide theoretical basis for the quality evaluation of J. rigida and give some insights into the source application and industrial product development as well.

Evaluation of genetic diversity within sweet cherry accessions of Czech genetic resources by molecular SSR markers

Sweet cherry is a vegetatively propagated, perennial plant with high level of heterozygosity and ancient breeding history. Therefore, it is necessary to keep, conserve and evaluate known genetic resources for future breeding programs and fruit production stability. In present, the utilization of DNA molecular genetic methods is the best suitable method for evaluation of individual accessions, so that we eliminated duplications and characterized genetic relationships. Recently, there are many different molecular methods but the most reliable are SSR markers. In our work, we used PCR primer combinations for 20 SSR and 2 EST-SSR markers for analyses of 82 current, old and local sweet cherry cultivars from Czech genetic resources of the Research and Breeding Institute of Pomology in Holovousy. In total, 113 polymorphic markers were amplified which we used for hierarchical cluster analysis of genetic variability. The resulting dendrogram corresponded with genealogical and geobotanical characteristics of individual accessions which were divided into five clusters. The breeding history of several known accessions was also proved.

Population Structure and Genetic Diversity of Sweet Cassava Accessions from the Midwestern, Southeastern and Southern Regions of Brazil

Abstract The objective of this work was to screen sweet cassava accessions collected in smallholding areas in the Midwestern, Southeastern and Southern regions of Brazil, using 15 SSR molecular markers, to determine population structure and genetic diversity. Polymorphism was detected in every loci analyzed, with mean of 6.33 alleles per locus, and mean polymorphism information content (PIC) of 0.6057, pointing out that the primers were highly informative. The observed heterozygosity ranged from 0.0709 (SSRY 101) to 0.9398 (GA 12), with a mean of 0.6511, and mean genetic diversity of 0.6578, ranging from 0.3592 (GA 136) to 0.8116 (SSRY 21). The most dissimilar combinations observed were BGM526PR-BGM596MS, BGM526PR-BGM622MS and BGM526PR-BGM629MS. The traditional cassava cultivars assessed were divided into four distinct groups: two with cultivars from the South, one from the Southeast and one from the Midwestern region of Brazil. The variances among and within groups determined by the analysis of molecular variance were 44 and 56%, respectively. The PhiPT parameter (analogue to Fst) of 0.44 indicates high differentiation among groups. Broad genetic diversity was found among the traditional sweet cassava cultivars assessed, and the most divergent groups were formed by cultivars from the South and the Midwestern regions of Brazil.

Validation of SSR Molecular Markers Linked to Drought Tolerant in Some Wheat Cultivars

The present study was carried out to conduct drought tolerance in three wheat cultivars including susceptible (Gemmiza7) and tolerant (Sakha93 and Sahel1). Molecular characterization was done by 26 SSR markers located on chromosome7 which was associated with drought tolerance in many previous studies. 26 SSR markers were polymorphic and thus showed 100% polymorphism. The number of alleles per locus varied from 2 to 3 alleles with an average (2.62). The polymorphism information content (PIC) value ranged from 0.34 to 0.59, with a mean of 0.51. The discrimination power (Dp) value ranged between 0.67 and 0.78 with an average of 0.71 per locus and Heterozygosity (He) value varied from 0.44 to 0.67 with an average of 0.59. The genetic relationships estimated by the polymorphism of SSR markers revealed a greater level of genetic variability in wheat cultivars of wide adaptability and applicability. Whereas an average of combined probability value for the SSR markers was 6.15 x 10-16, suggests the capability of the marker system to distinguish identity and purity of wheat cultivars. In addition to the SSR markers revealed various bands that were either absent or present within tolerant cultivars (Sakha93 and Sahel1) which were altogether absent in susceptible cultivar (Gemmiza7). Also, SSRs of diagnostic and curatorial importance were discerned as ‘stand-alone’ molecular descriptors for barcoding the application of DNA sequences of standardized genetic markers for the identification of wheat cultivars. However, the genetic information in this study could provide useful information to address breeding programs and germplasm resource management.

Identification and characterization of SSR, SNP and InDel molecular markers from RNA-Seq data of guar (Cyamopsis tetragonoloba, L. Taub.) roots

BackgroundGuar [Cyamopsis tetragonoloba, L. Taub.] is an important industrial crop because of the commercial applications of the galactomannan gum contained in its seeds. Plant breeding programmes based on marker-assisted selection require a rich resource of molecular markers. As limited numbers of such markers are available for guar, molecular breeding programmes have not been undertaken for the genetic improvement of this important crop. Hence, the present work was done to enrich the molecular markers resource of guar by identifying high quality SSR, SNP and InDel markers from the RNA-Seq data of the roots of two guar varieties.ResultsWe carried out RNA-Seq analysis of the roots of two guar varieties, namely, RGC-1066 and M-83. A total of 102,479 unigenes with an average length of 1016 bp were assembled from about 30 million high quality pair-end reads generated by an Illumina HiSeq 2500 platform. The assembled unigenes had 86.55% complete and 97.71% partially conserved eukaryotic genes (CEGs). The functional annotation of assembled unigenes using BLASTX against six databases showed that the guar unigenes were most similar to Glycine max. We could assign GO terms to 45,200 unigenes using the UniProt database. The screening of 102,479 unigenes with MISA and SAMtools version 1.4 softwares resulted in the identification of 25,040 high-confidence molecular markers which consisted of 18,792 SSRs, 5999 SNPs and 249 InDels. These markers tagged most of the genes involved in root development, stress tolerance and other general metabolic activities. Each of the 25,040 molecular markers was characterized, particularly with respect to its position in the unigene. For 71% of the molecular markers, we could determine the names, products and functions of the unigenes. About 80% of the markers, from a random sample of molecular markers, showed PCR amplification.ConclusionsWe have identified and characterized 25,040 high confidence SSR, SNP and InDel molecular markers in guar. It is expected that these markers will be useful in molecular breeding programmes and will also be helpful in studying molecular mechanisms of root development, stress tolerance and gum synthesis in guar.

Germplasm collection, genetic diversity and on-farm conservation of cowpea [Vigna unguiculata (L.) Walp.] landraces from Apulia region (southern Italy)

Cowpea [Vigna unguiculata (L.) Walp.] is a major tropical pulse in a number of countries and especially in sub-Saharan Africa where this species was domesticated. Although as niche product, a remarkable number of cowpea landraces are cultivated in the Mediterranean basin, primarily for human consumption of the grains and fresh pods. In this study, within the frame of a regional project devoted to the safeguard and management of local horticultural genetic resources, some germplasm explorations were carried out in Apulia region (southern Italy) to collect, among other crops, cowpea landraces still present in the area and promote on-farm conservation of this traditional material. A second objective was to investigate the efficiency of SSR markers in detecting genetic polymorphism in cowpea landraces from a restricted geographical area. In total, 13 samples of V. unguiculata were gathered, 12 of cultivar group unguiculata and 1 of cultivar group sesquipedalis. Genetic diversity and phylogenetic relationships among 13 Apulian accessions, 9 samples from various provenances and 1 var. spontanea accession were evaluated using SSR molecular markers. A set of 19 SSR primer pairs successfully identified closely related accessions and were able to separate the different cultivar groups of V. unguiculata.

Genotyping of Albania olive (Olea europaea) germplasm by SSR molecular marker

The increasing interest in olive varieties with high productivity and quality is the basis of modern olive growing. The molecular characterization of olive varieties is essential to maximize the genetic diversity in the in situ and ex situ collections of the olive germplasm. The importance of studies aimed at identification and selection of genotypes that meet the requirements for plant nursery certification, for oils traceability and to preserve genotypes that are not widespread from risks of extinction, is evident. In this context, DNA fingerprinting represents a valid tool because the productivity and quality of olive oil are intrinsic characteristics of the original varieties. To date, the Albanian olive-growing heritage has been little studied and the number of varieties has not yet been well defined. As a consequence, it doesn’t a precise characterization of the Albanian genetic entities. The aim of this work was to contribute in clarifying the identity of the Albanian olive cultivars, using the SSR molecular markers. We have genotyped olive trees at the level of nine nuclear microsatellite loci or SSR, pre-selected among those present in the literature and we have identified 38 unique genotypes. It has not been possible to establish a clear correlation between clustering of plants, depending on molecular profiles, and the geographical distribution of origin or maturation period or the intended use of drupes. However, our results show a high genetic diversity and a high discrimination capacity of the tested SSR markers.

Assessment of genetic diversity of selected <em>Capsicum chinense</em> and <em>C. frutescens</em> accessions derived through morphological and molecular characterization

Capsicum chinense and C. frutescens are common cultivated and consumed chilli species in some parts of Sri Lanka. Thirteen Capsicum accessions were characterized by morphological and molecular means to assess genetic diversity in plants by randomized complete block design with two replicates during yala 2016 and maha 2016/17 at the Field Crops Research and Development Institute, Mahailluppallama. Twelve morphological characters were analysed using analysis of variance (ANOVA) and multivariate methods. ANOVA revealed significant differences among genotypes for most of the tested traits. Principal component (PC) analysis explained more than 71% of total variability for the first 3 components among the traits of genotypes evaluated. Plant height, width, days to 50% flowering, pods per plant and yield were positively correlated with PC1. Dendrogram based on morphological and SSRs analyses showed two and three clusters respectively at 0.1 similarity levels and both analysis showed comparable results. A total of 45 alleles were detected in 15 microsatellite markers (M1 to M15) across the 13 Capsicum accessions. Out of these 15 SSR loci, 14 loci showed polymorphism. Genetic diversity ranged from 0.00 to 0.75 with an average of 0.51. High allelic richness was observed in M 10 and M 14. The PIC value varied from 0.13 to 0.70 with an average of 0.44. To date molecular characterization data of Capsicum accessions in Sri Lanka is limited. Therefore, this study will pave the way for a detailed characterization of C. chinense and C. frutescence accessions using morphological descriptors and SSR molecular markers.