Comparison of RAPD and ISSR markers for genetic diversity analysis among different endangered Mangifera indica genotypes of Indian Gir forest region

The genetic variability and relationships among 20 Mangifera indica genotypes representing 15 endangered and 5 cultivars, obtained from Indian Gir forest region, were analyzed using 10 random amplified polymorphic DNA (RAPD) and 21 inter simple sequence repeat (ISSR) markers. RAPD markers were more efficient than the ISSR assay with regards to polymorphism detection. Also, the average numbers of polymorphic loci per primer, average polymorphic information content (PIC) and primer index (PI) values were more for RAPD than for ISSR. But, total number of genotype specific marker loci, Nei’s genetic diversity (h), Shannon’s information index (I), total heterozygosity (Ht), average heterozygosity (Hs) and mean coefficient of gene differentiation (Gst) were more for ISSR as compared to RAPD markers. The regression test between the two Nei’s genetic diversity indexes showed low regression between RAPD and ISSR based similarities but maximum for RAPD and RAPD + ISSR based similarities. The pattern of clustering of genotypes within groups was not similar when RAPD and ISSR derived dendrogram were compared. Thus, both the markers were equally important for genetic diversity analysis in M. indica.     

Population structure and genetic diversity in bottle gourd [Lagenaria siceraria (Mol.) Standl.] germplasm from India assessed by ISSR markers

Genetic diversity analysis was undertaken in 42 geographically distant genotypes accessions of bottle gourd (Lagenaria siceraria) from India northeastern (14) and northern region (28) using inter-simple sequence repeat (ISSR) markers. A total of 209 amplified bands were obtained from 20 ISSR primers used in this study, of which 186 were polymorphic with 89.00 % band polymorphism. Various parameters namely, observed number of alleles, effective number of alleles, Nei’s gene diversity/heterozygosity, resolving power, Shannon’s information index and gene flow were estimated under experiment. Jaccard’s similarity coefficient matrix was generated for pairwise comparisons between individual ISSR profiles and UPGMA cluster analysis based on this matrix showed clustering into six groups. Jaccard’s coefficient of similarity values ranged from 0.409 to 0.847, with a mean of 0.628 revealing a moderate level of genetic diversity. The Bayesian model-based approach to infer hidden genetic population structures using the multilocus ISSR markers revealed two populations among the 42 genotypes. This is the first report on the assessment of genetic variation using ISSR markers in this medicinal vegetable plant, and this study of diversity analysis will be helpful in analyzing future hybrid breeding strategy and devising effective germplasm exploration and conservation strategy.     

A Comparative Analysis of ISSR and RAPD Markers for Study of Genetic Diversity in Shisham (<Emphasis Type="Italic">Dalbergia sissoo</Emphasis>)

Shisham (Dalbergia sissoo) is one of the most preferred timber tree species of South Asia. Two DNA-based molecular marker techniques, intersimple sequence repeat (ISSR) and random amplified polymorphism DNA (RAPD), were compared to study the genetic diversity in this species. A total of 30 polymorphic primers (15 ISSR and 15 random) were used. Amplification of genomic DNA of 22 genotypes, using ISSR analysis, yielded 117 fragments, of which 64 were polymorphic. Number of amplified fragments with ISSR primers ranged from five to ten and varied in size from 180 to 1,900 bp. Percentage polymorphism ranged from 0 to 87.5. The 15 RAPD primers produced 144 bands across 22 genotypes, of which 84 were polymorphic. The number of amplified bands varied from five to 13, with size range from 180 to 2,400 bp. Percentage polymorphism ranged from 0 to 100, with an average of 58.3 across. RAPD markers were relatively more efficient than the ISSR assay. The mental test between two Jaccard’s similarity matrices gave r ≥ 0.90, showing very good fit correlation in between ISSR- and RAPD-based similarities. Clustering of isolates remained more or less the same in RAPD and combined data of RAPD and ISSR. The similarity coefficient ranged from 0.734 to 0.939, 0.563 to 0.946, and 0.648 to 0.920 with ISSR, RAPD, and combined dendrogram, respectively.     

ISSR Markers as a Tool for the Assessment of Genetic Diversity in Passiflora

Genetic variation among sweet, purple, and yellow passion fruit accessions was assessed using inter-simple sequence repeat (ISSR) markers. Eighteen ISSR primers were used to evaluate 45 accessions. The number of polymorphic bands per primer varied from 4 to 22, with 12.4 bands per primer on average. Nei's genetic distance between accessions ranged from 0.04 to 0.35. Clustering using the neighbor-joining method resulted in the formation of 11 major clusters. It was not possible to classify the accessions according to their geographic origin, showing that there is no structure in the gene bank. The overall mean Shannon-Weaver diversity index was 0.32, indicating good resolution of genetic diversity in passion fruit germplasm using ISSR markers. Our results indicate that ISSR can be useful for genetic diversity studies, to provide practical information for parental selection and to assist breeding and conservation strategies.     

Population structure and virulence analysis of <Emphasis Type="Italic">Alternaria carthami</Emphasis> isolates of India using ISSR and SSR markers

Alternaria leaf spot caused by Alternaria carthami is one of the most devastating diseases of safflower. Diversity among 95 isolates of A. carthami was determined using virulence assays, enzyme assays, dominant (ISSR) and co-dominant (SSR) markers. Collections and isolations were made from three major safflower producing states of India. The virulence assays categorised the population into four groups based on level of virulence. Estimation of activities of cell wall degrading enzymes (CWDE) yielded concurrent results to virulence assays with maximum CWDE activities in most virulent group. Eighteen ISSR primers were used and 23 polymorphic microsatellite markers were developed to assess the genetic diversity and determine the population structure of A. carthami. Analysis of ISSR profiles revealed high genetic diversity (Nei’s Genetic diversity index; h?=?0.36). Microsatellite markers produced a total of 56 alleles with an average of 2.43 alleles per microsatellite marker and Nei’s genetic diversity index as h?=?0.43. Unweighted Neighbor-joining and population structure analysis using both the marker systems differently arranged the isolates into three clusters. Distance analysis of the marker profiles provided no evidence for geographical clustering of isolates, indicating that isolates are randomly spread across India, signifying high potential of the fungus to adapt to diverse regions. Microsatellite markers clustered the isolates in consonance to the virulence groups in the dendrogram. This implies that the fungus has a high potential to adapt to resistant cultivars or fungicides. The information can aid in the breeding and deployment of A. carthami resistant varieties, and in early blight disease management in all safflower growing regions of the world.     

Genetic diversity in <Emphasis Type="BoldItalic">Astragalus argaeus</Emphasis>, a critically endangered species from Turkey

Astragalus argaeus is critically endangered endemic species growing only on Erciyes Mountain in Kayseri. Inter simple sequence repeat (ISSR) markers were chosen to detect the genetic diversity in four populations of A. argaeus. Ten primers were used to assess the diversity among 96 genotypes collected from the four localities in Erciyes Mountain. A total of 78 bands were scored, of which 44 (55.8%) were polymorphic. The unweighted pair group method arithmetic average (UPGMA) and principle component analysis (PCoA) showed moderate genetic diversity at the species and population level. The percentages of polymorphic bands (PPB) ranged from 53.8 to 61.5 (58.01%?±?3.2) and average gene diversity (h) at the population and species level was estimated to be 0.17 and 0.23, respectively. The Shannon’s information index (SI) ranged from 0.24 to 0.29 at the population level and was 0.35 at the species level. The determined gene flow (Nm) was 1.83. The UPGMA tree indicated that the four populations were not genetically distinct obviously. In analysis of molecular variance (AMOVA), the percentage of the variance was 38.72% among populations and 61.28% within populations. The data which small population size, habitat fragmentation and moderate levels of genetic diversity demonstrate that A. argaeus possess threat of extinction if its narrow habitat is destroyed.     

Evaluation of genetic diversity amongst <Emphasis Type="Italic">Descurainia sophia</Emphasis> L. genotypes by inter-simple sequence repeat (ISSR) marker

Descurainia sophia is a valuable medicinal plant in family of Brassicaceae. To determine the range of diversity amongst D. sophia in Iran, 32 naturally distributed plants belonging to six natural populations of the Iranian plateau were investigated by inter-simple sequence repeat (ISSR) markers. The average percentage of polymorphism produced by 12 ISSR primers was 86 %. The PIC values for primers ranged from 0.22 to 0.40 and Rp values ranged between 6.5 and 19.9. The relative genetic diversity of the populations was not high (Gst =0.32). However, the value of gene flow revealed by the ISSR marker was high (Nm = 1.03). UPGMA clustering method based on Jaccard similarity coefficient grouped the genotypes into two major clusters. Graph results from Neighbor-Net Network generated after a 1000 bootstrap test using Jaccard coefficient, and STRUCTURE analysis confirmed the UPGMA clustering. The first three PCAs represented 57.31 % of the total variation. The high levels of genetic diversity were observed within populations, which is useful in breeding and conservation programs. ISSR is found to be an eligible marker to study genetic diversity of D. sophia.     

Population Genetic Study of Fagopyrum tataricum from Western Himalaya Using ISSR Markers

Inter-simple sequence repeat (ISSR) markers were used to analyze genetic diversity and relatedness of 15 germplasms of Fagopyrum tataricum. Samples representing 75 individuals were collected from a range of altitudes in the Western Himalaya. The 13 ISSR primers revealed 98.1% polymorphism among populations, whereas average polymorphism was extremely low (2.18%) within populations. The coefficient of population differentiation was 0.9750, with limited gene flow (N _m) of 0.0128. The average PIC value of the ISSR markers was high (0.812), with a marker ratio of 0.65 and marker index of 6.66. The genetic diversity of F. tataricum significantly correlated with altitude and gene diversity, Shannon’s index, and the percentage of polymorphic bands. The genetic diversity among populations showed broad genetic base and provided a developmental strategy for crop improvement.     

四川省草莓主产区灰葡萄孢菌的遗传多样性

为明确四川省草莓灰葡萄孢Botrytis cinerea群体遗传结构及其多样性水平,采用ISSR分子标记技术对分离自四川省10个县（市）的195株灰葡萄孢菌进行了遗传多态性分析。结果表明,四川省灰葡萄孢菌多态性丰富,6条ISSR引物共产生了63个多态性位点,应用Popgene32软件计算四川省不同主产区域（除德阳广汉种群外）种群的Nei’s基因多样性指数（H）和Shannon信息指数（I）均达到了H>0.2、I>0.3的水平,表明四川省的灰葡萄孢菌具有丰富的遗传多样性;灰葡萄孢菌群体的遗传多样性（Ht）均值为0.2976,种群内遗传多样性（Hs=0.2458）远远高于种群间（Dst=0.0518）的遗传多样性;遗传分化系数（Gst）均值0.1742,基因流（Nm）均值2.3696,说明该地区灰葡萄孢菌种群间遗传分化不明显,群体内基因交流频繁。通过UPGMA法和Omishare Tools热图软件均可将10个采集点分为3个类群,来自绵阳江油的菌株单独构成一个类群,来自成都崇州和德阳广汉的菌株构成一个类群,其余的菌株构成另外一个类群;利用Structure 2.3软件对195份灰葡萄孢菌进行群体结构分析,可将134份菌株划分成21个群,另外61个菌株被列为混合群体。     

Assessment of genetic diversity and differentiation of <Emphasis Type="Italic">Liposcelis bostrychophila</Emphasis> (Psocoptera: Liposcelidae) in China using inter-simple sequence repeat (ISSR) fingerprinting

Liposcelis bostrychophila (Psocoptera: Liposcelidae) is a widely distributed pest that can cause considerable economic losses and pose human health risks. Rapid development of insecticide resistance has made L. bostrychophila increasingly difficult to control. To obtain information potentially useful for pest management, genetic diversity and differentiation of L. bostrychophila from five geographic locations in China was studied using inter-simple sequence repeat (ISSR). A total of 104 loci were found by ISSR markers and amplified using 9 selected primers. The percentage of polymorphic bands (PPB) was 91.4%. Shannon’s information index (I) and Nei’s gene diversity (He) indicated high genetic diversity at the species level. Population differentiation (Gst = 0.484) was average in these populations. Analysis of molecular variation (AMOVA) indicated that genetic variation was mainly distributed within populations. Gene flow (Nm = 0.534) was moderate. Cluster analysis showed that genotypes isolated from the same locations displayed higher genetic similarity and permitted the grouping of isolates of L. bostrychophila into three distinct clusters. The correlation between genetic distance and geographic distance was not significant.     

Phenotype and genetic diversity in potato onion cultivars from three provinces of northeast China

Phenotypic characters and ISSR markers in forty nine potato onion cultivars (Allium cepa L. var. aggregatum G. Don) were investigated. Twenty three phenotypic characters, including sprouting time, plant height, spherical index, and yield, were investigated. Cluster analysis separated forty nine cultivars into five groups (D = 0.52). 143 polymorphic amplified bands, with an average of 8.41 polymorphic bands per primer, were obtained from seventeen ISSR primers. The number of polymorphic bands detected with each primer ranged from 6 to 12, with an average of 8.82. The percentage of polymorphisms was 93.5%. Genetic similarity varied from 0.4969 to 0.8616, the average value of the effective number of alleles, Nei's genetic diversity and Shannon's information index was 1.4716, 0.3072 and 0.4590, respectively. Forty nine varieties were classified into six groups according to the ISSR (D = 0.72). These results showed that two methods combined were accuracy for characterization of the genetic diversity and identification of potato onion cultivars.     

黄淮麦区小麦品种(系)的ISSR位点遗传多样性分析

选用11个ISSR引物,对黄淮麦区96个小麦推广品种（系）进行遗传多样性分析。共检测到96个多态性位点,每个引物多态性位点数平均为8．7个,变幅为3～23个;ISSR引物的多态性信息含量PIC变幅为0．601～0．941,平均0．791,表明ISSR具有较强的品种间区分能力,是研究小麦种质资源遗传多样性的有效分子标记技术之一。96个品种（系）间,Nei’s遗传相似系数变化范围为0．53～0．91,平均为0．60,品种间遗传相似性变幅较大,表明黄淮麦区不同小麦品种（系）间存在着不同程度的遗传多样性差异。根据品种间遗传相似系数聚类,96份材料被聚成8大类群,共14个亚类,类群与系谱和原产地无关。     

A comparative analysis of genetic diversity in blackgram genotypes using RAPD and ISSR markers

Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were used to study the DNA polymorphism in elite blackgram genotypes. A total of 25 random and 16 ISSR primers were used. Amplification of genomic DNA of the 18 genotypes, using RAPD analysis, yielded 104 fragments that could be scored, of which 44 were polymorphic, with an average of 1.8 polymorphic fragments per primer. Number of amplified fragments with random primers ranged from two (OPA-13) to nine (OPK-4) and varied in size from 200 bp to 2,500 bp. Percentage polymorphism ranged from 16.6% (OPK-7) to a maximum of 66.6% (OPE-5, OPH-2, and OPK-8), with an average of 42.7%. The 16 ISSR primers used in the study produced 101 bands across 18 genotypes, of which 55 were polymorphic. The number of amplified bands varied from two (ISSR 858) to ten (ISSR 810), with a size range of 200–2,200 bp. The average numbers of bands per primer and polymorphic bands per primer were 6.3 and 3.4, respectively. Percentage polymorphism ranged from 25% (ISSR 885) to 100% (ISSR 858), with an average percentage polymorphism of 57.5% across all the genotypes. The 3-anchored primers based on poly(GA) and poly(AG) motifs produced high average polymorphisms of 54.98% and 58.32%, respectively. ISSR markers were more efficient than the RAPD assay, as they detected 57.4% polymorphic DNA markers in Vigna mungo as compared to 42.7% for RAPD markers. The Mantel test between the two Jaccards similarity matrices gave r =0.32, showing low correlation between RAPD- and ISSR-based similarities. Clustering of genotypes within groups was not similar when RAPD and ISSR derived dendrogram were compared, whereas the pattern of clustering of the genotypes remained more or less the same in ISSR and combined data of RAPD and ISSR.     

Comparison of ISSR,IRAP and REMAP markers for assessing genetic diversity in different species of <Emphasis Type="Italic">Brassica</Emphasis> sp.

Molecular markers provide facilities in order to study genetic diversity and relationship among genotypes. In this study, genetic diversity among 35 genotype of Brassica sp. (belonging B. napus, B. juncea, B. rapa, B. nigra) were determined using 13 ISSR, 3 IRAP markers and 18 REMAP (primer combinations of ISSR and retrotransposon primer). The percentage of polymorphism for ISSR, IRAP and REMAP was 96.38, 94 and 96%, respectively. By comparison between markers, ISSRs indicated the highest expected heterozygosity (He) and Shannon’s information index (I) with value of 0.34 and 0.51, respectively, while REMAP marker had by far the highest number of polymorphic bands (340) and marker index (7.1) among all fragments scored over all markers. In pattern of clustering based on Bayesian methods, K = 8 was resulted for combined data clustering that was more organized clustering for genotypes compared to others. This research suggests the combined data of ISSR, IRAP and REMAP markers are most reliable than each solely marker whilst have been clustered genotypes in their taxonomic classification of Brassica without any mixture. Principle coordinate analysis (PCoA) separated 35 genotypes in four groups which all of genotypes were clustered correctly based on their taxonomic classification. The findings of this study provide the valuable insight into the Brassica species relationships in terms of similarity among genotypes which can be helpful in breeding programs, and also demonstrate that retrotransposon markers are legible for genetic diversity and next genetic analysis in Brassica genus.     

Inter simple sequence repeat (ISSR) analysis of genetic diversity in tef [Eragrostis tef (Zucc.) Trotter

The DNA polymorphism among 92 selected tef genotypes belonging to eight origin groups was assessed using eight inter simple sequence repeat (ISSR) primers. The objectives were to examine the possibility of using ISSR markers for unravelling genetic diversity in tef, and to assess the extent and pattern of genetic diversity in the test germplasm with respect to origin groups. The eight primers were able to separate or distinguish all of the 92 tef genotypes based on a total of 110 polymorphic bands among the test lines. The Jaccard similarity coefficient among the test genotypes ranged from 0.26 to 0.86, and at about 60 % similarity level the clustering of this matrix using the unweighted pair-group method based on arithmetic average (UPGMA) resulted in the formation of six major clusters of 2 to 37 lines with further eight lines remaining ungrouped. The standardized Nei genetic distance among the eight groups of origin ranged between 0.03 and 0.32. The UPGMA clustering using the standardized genetic distance matrix resulted in the identification of three clusters of the eight groups of origin with bootstrap values ranging from 56 to 97. The overall mean Shannon Weaver diversity index of the test lines was 0.73, indicating better resolution of genetic diversity in tef with ISSR markers than with phenotypic (morphological) traits used in previous studies. This can be attributed mainly to the larger number of loci generated for evaluation with ISSR analysis as compared to the few number of phenotypic traits amenable for assessment and which are further greatly affected by environment and genotype x environment interaction. Analysis of variance of mean Shannon Weaver diversity indices revealed substantial (P < or = 0.05) variation in the level of diversity among the eight groups of origin. In conclusion, our results indicate that ISSR can be useful as DNA-based molecular markers for studying genetic diversity and phylogenetic relationships, DNA fingerprinting for the identification of varieties or cultivars, and also for genome mapping in tef.     

Development of Dof (DNA binding with one finger) transcription factor gene-specific primers through data mining as a functional marker and their use for genetic diversity study in barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.) germplasm

The genetic diversity among Hordeum vulgare L. species were assessed based on PCR amplification pattern derived from 75 set of Dof domain and Dof genes specific primers. Multiple bands showing variability in terms of both number and sizes of bands ranging from 0.1 to 3.0 kbp were observed. Out of a total of 2449 bands, 2328 polymorphic and 121 monomorphic bands were obtained and the percentage of polymorphism ranged from 70.27 to 100%. A very high degree of polymorphism was observed with all the primers except HvDof3, HvDof4, HvDof10, HvDof16, HvDof18, HvDof18, HvDof24, Dof4, Dof11, Dof13, Dof15, Dof16, Dof19, Dof20, Dof21, Dof22, Dof23, Dof28, dof38, sbDof23 and sbDof24 primers. Unweighted pair group method based on arithmetic average (UPGMA) analysis was performed on Jaccard’s similarity coefficient matrix. According to results, the genetic resources and diversity in barley germplasm of H. vulgare were rich. The number of polymorphic fragments per primer detected ranged from 11 to 56 bands with an average of 32.65 bands. Average polymorphic information content (PIC) was 0.81 in overall Dof domain and gene specific primers. HvDof 39 showed the highest PIC (0.99) which can be a good candidate primer to verify genetic diversity in H. vulgare. The unweighted pair-group method of the arithmetic average and principal coordinate analysis showed a clear distinction among the genotypes and the genotypes divided into three clusters in the dendrogram results. A model-based structure analysis revealed the presence of three groups. The study showed that genetic variation and population structure are determined among the species of H. vulgare collected from different geographical origins.     

Genetic diversity and gene flow estimation in Prosopis cineraria (L.) Druce: A key stone tree species of Indian Thar Desert

Selected amplicon data obtained through our earlier study using ISSR and DAMD markers were utilized for determination of diversity within and among the populations of Prosopis cineraria (L.) accessions collected from different districts of Rajasthan (India). A total of 83 bands were generated from eight ISSR and five DAMD primers of which 79 were found to be polymorphic (95.18%). Nei’s gene diversity (h) ranged between 0.185 and 0.301 with overall diversity of 0.316 while Shannon’s information index (I) values recorded between 0.253 and 0.438 with an average value of 0.243. The gene flow value (1.713) and the diversity among populations (0.226) demonstrated higher genetic variation within the population. It is concluded that P. cineraria is accompanied by high genetic diversity within the population and elevated gene flow showing indications of adaptation to callous and fragile dry conditions of arid environment.     

Deciphering allelic variability and population structure in buckwheat: An analogy between the efficiency of ISSR and SSR markers

Food and nutritional security continue to be the issues of concern in developing countries like ours. Exploring the reservoir of high potential unexplored genetic resources could address the world’s food and nutritional insecurity. The availability of diverse data and the population structure of any crop germplasm is a valuable genetic resource for discovering genes that can help achieve food and nutritional stability. We used seven ISSR and seven SSR markers to investigate diversity among 63 buckwheat genotypes, including landraces from India''s northwestern Himalayas. Various parameters such as percent polymorphism, PIC, resolving power, and marker index was used to evaluate the inequitable efficacy of these markers. We foundthat both marker systems are effective in detecting polymorphism in buckwheat germplasm. Seven ISSRs produced 55 polymorphic bands, while seven SSRs produced 32bands. When compared to ISSRs, SSRs had a greater average PIC value (0.43) than that of (0.36). ISSRs, on the other hand, had a resolving power of (4.38) compared to (1.42) for SSRs. The hierarchical cluster analysis dendrogram divided genotypes into three major clusters. We found that both marker systems were equally accurate in grouping buckwheat genotypes according to their geographical origins. Using 7 ISSR and 7 SSR markers, the model-based STRUCTURE analysis established a population with two sub-populations that correspond to species-based groupings. Within the population, there was a high level of genetic diversity. These results have consequences for both buckwheat breeding and conservation efforts.Keyword: Buckwheat, SSR, ISSR, Genetic diversity, Population structure     

Genetic diversity analysis and population structure in apricot (Prunus armeniaca L.) grown under north-western himalayas using ISSR markers

Investigation of genetic variability and population relationship of 50 accessions of the apricot (Prunus armeniaca L.) was carried out using ISSR markers. The results revealed that the number of alleles per locus varied from 4 to 8 with a mean value of 6.75, and the mean effective number of alleles (Ne) per locus was 1.54. Similarly, the polymorphic information content (PIC) values ranged from 0.464 to 0.424, with a mean value of 0.424. The mean heterozygosity, marker index, resolving power, and effective multiplex ratio (EMR) ranged from 0.001 to 0.002, 0.01–0.06, 1.76–3.84, and 1–4.12. The dendrogram clustered genotypes into two main clades based on their origins. The population structure revealed two sub-populations with some admixtures. The average expected heterozygosity and population differentiation within two sub-populations was 0.1428 and 0.216, respectively. The results outcome reveals that the four ISSR markers comprehensively separated the indigenous germplasm from the exotic germplasm. The genetic divergence within indigenous genotypes and exotic genotypes could allow for future insights into apricot breeding programs.     

Analysis of genetic diversity among garden- and field-pea genotypes of higher Indian Himalayas

Genetic diversity among 31 genotypes of field and garden pea including primitive cultivated forms and widely cultivated varieties of India was studied using 40 random decamer and 9 ISSR primers. A total of 274 amplicons were detected using both types of markers, which amplified 192 RAPD and 82 ISSR amplicons. Average number of bands amplified per primer was higher in case of ISSR (9.1) as compared to RAPDs (4.8). ISSR primers also exhibited higher average polymorphism (89.0%) and resolving power (4.50) than RAPDs (72.4%, 1.87, respectively). Genetic similarity estimates based on the pooled data of both types of markers using Jaccard??s coefficient ranged from 0.58 to 0.85 delineating considerable diversity among the pea genotypes studied. The 31 genotypes clustered in two major groups based on pooled data. Popular cultivars of garden and field pea of the region exhibited high similarities among themselves. However, primitive cultivated forms collected from the higher Indian Himalayas were diverse from the current varieties and hold potential in pea breeding programmes.