Genetic structure and diversity analysis revealed by AFLP on different Echinochloa spp. from northwest Turkey

Rice is one of the most economically important cereal crops in the world. The genus Echinochloa is the most competitive and difficult to control weeds in the rice fields. Improving the knowledge on the genetic diversity and structure of Echinochloa spp. can supply crucial information for designing effective management strategies for weed control in rice breeding. In the study, 28 Echinochloa spp. genotypes were subjected to the analysis of genetic diversity using four amplified fragment length polymorphism selective primer combinations. The number of polymorphic fragments per primer combination detected ranged from 28 to 50 bands with an average of 41.5 bands. Average polymorphic information content (PIC) was 0.26 in overall primer combinations. E_ACA-M_CAG primer combination showed the highest PIC (0.52) which can be a good candidate primer combination to verify genetic diversity in Echinochloa spp. 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 two populations. The accessions were clearly assigned to a single population in which >70 % of their inferred ancestry was derived from one of the model-based populations. However, three genotypes (10.7 %) in the sample were categorized as having admixed ancestry. The study showed that genetic variation and population structure are determined among genotypes collected from different locations. High level of genetic variation in both intra and inter species was detected.     

Plasmon analysis in wheat alloplasmic lines using morphological and chloroplast microsatellite markers

Inheritance of plant traits mainly depends upon nuclear genes, cytoplasmic factors and their interactions. In the present study, 32 alloplasmic lines accompanied by a euplasmic parental line (control) were evaluated using molecular (chloroplast microsatellite) and morpho-physiological traits during 2010–2011 and 2011–2012. The results of combined analysis of variance showed the significant effect of growing seasons on most of the studied traits as well as the significant effect of cytoplasm on plant height, leaf net CO₂ assimilation rate and grain yield per plant. Results of cluster analysis divided the six plasmons based on their phenotypic effects into three groups: (1) R and S^v type, D (Aegilops typica and Ae. ventricosa) and D² type, as well as B-type plasmon (euplasmic line); (2) a single plasmon of M type and three plasmons of B type; (3) all other B-type and a single D-type plasmon (Aegilops cylindrica). Molecular analysis showed that 20 primer pairs out of 26 chloroplastic microsatellite markers (cpSSR) produced polymorphic bands in the alloplasmic lines. A total of 50 alleles were identified with an average of 2.5 alleles per locus. In this study, polymorphism information content (PIC) ranged from 0.05 (WCt17 primer) to 0.49 (WCt9 primer). Cluster analysis of molecular data revealed that the alloplasmic lines belong to two major clusters, in which differentiation of cytoplasmic types belonging to the genus Triticum and Aegilops has been evident. Likewise, analysis of molecular variance showed significant differences between two studied groups (F _ST = 0.67, P < 0.001). Overall, our findings indicated that the cpSSR markers can be valuable resources of polymorphic markers for the analysis of cytoplasm of Triticeae species, with the potential for clear differentiation in close species and genera of this tribe.     

Association analysis,genetic diversity and structure analysis of tobacco based on AFLP markers

Knowledge in the area of genetic diversity could aid in providing useful information in the selection of material for breeding such as hybridization programs and quantitative trait loci mapping. To this end, 50 Nicotiana tabacum genotypes were genotyped with 21 primer combination of amplified fragment length polymorphism (AFLP). A total of 480 unambiguous DNA fragments and 373 polymorphic bands were produced with an average of 17.76 per primer combination. Also, the results revealed high polymorphic rate varing from 52.63 to 92.59 %, demonstrating that AFLP technique utilized in this research can be a powerful and valuable tool in the breeding program of N. tabacum. Cluster analysis based on complete linkage method using Jaccard’s genetic distance, grouped the 50 tobacco genotypes into eight clusters including three relatively big clusters, one cluster including Golden gift, Burly 7022 and Burly Kreuzung, one cluster consisting of two individuals (Pereg234, R9) and three single-member clusters (Pennbel69, Coker176 and Budisher Burley E), Recent genotypes showed high genetic distance from other genotypes belonging to cluster I and II. Association analysis between seven important traits and AFLP markers were performed using four statistical models. The results revealed the model containing both the factors, population structure (Q) and general similarity in genetic background arising from shared kinship (K), reduces false positive associations between markers and phenotype. According to the results nine markers were determined that could be considered to be the most interesting candidates for further studies.     

SRAP-based mapping and QTL detection for inflorescence-related traits in chrysanthemum (Dendranthema morifolium)

Chrysanthemum (Dendranthema morifolium) is an economically important ornamental species and comprises a large proportion of the flower industry in south-east Asian and European countries. In this study, a segregating population of 142 F₁ progeny of the cross between the two chrysanthemum cultivars ??Yuhualuoying?? and ??Aoyunhanxiao?? was used to construct two separate genetic linkage maps via a double pseudo-testcross mapping strategy. Genotyping was performed using 500 SRAP primer combinations, of which about 50% were informative. This allowed the definition of 896 SRAP loci, of which about 23% showed some segregation distortion. The ??Yuhualuoying?? map consisted of 333 testcross markers arranged into 57 linkage groups (LGs). It covered >1,900 cM with a mean inter-marker distance of 6.9 cM. The map constructed from ??Aoyunhanxiao?? comprised 342 test cross markers arranged into 55 LGs. It spanned nearly 1,900 cM, with a mean inter-marker distance of 6.6 cM. The markers were distributed rather uniformly along both maps. A quantitative trait loci analysis was conducted to investigate the pattern of inheritance of three inflorescence traits. This led to the detection of 12 putative loci at a LOD score >2.5, of which four each specified flower diameter, ray floret layer number, and ray floret length. This study provides molecular mapping information on marker-assisted selection programs for the improvement of multiple traits of interest.     

Genetic and phenotypic variation of Turkish Okra (<Emphasis Type="Italic">Abelmoschus esculentus</Emphasis> L. Moench) accessions and their possible relationship with American,Indian and African germplasms

Okra is an important vegetable crop that provides a significant portion of vitamins and minerals for populations in several countries. Okra has been cultivated in Turkey for centuries, and was likely introduced by the Arabs from Africa in ancient times. In this study, we aimed to clarify the genetic variation within 35 Turkish okra germplasm, by comparing it against 25 different genotypes from India, Africa, and the United States, using 30 morphological characters and 19 sequence-related amplified polymorphism (SRAP) primer combinations. Fruit, leaf, and stem color were the primary characteristics to distinguish the okra accessions. Those features, among 30 individual phenotypic traits, explained 42 % of phenotypic variation in the first three axes of the principal component analysis (PCA) with leaf shape, flower size, cotyledon length, fruit-surface angularity, cotyledon width, and petal color. Phenotypic observation results showed that while 1051 Togo (10.76), Red Wonder (7.99), TR-05-1 (7.2), 1159 Togo (7.17), and Red Balady (7.15) were found to be more divergent accessions, Cajun Queen (5.06), Perkins Spineless (5.09), Jade (5.18), TR-01-1 (5.2), and DLGG (5.32) were the closest okra accessions. According to phenotypic data, Turkish okra accessions were located adjacent to the Indian, American, and African okra accessions in clusters three and four. However, marker data showed that African okra possessed a more distinct form compared to the other okra germplasms. Nineteen SRAP primer combinations produced 92 bands and 29 (31.5 %) of them were found to be polymorphic among okra accessions. 1051 Togo was found to be the most divergent accession in phenotypic observation.     

Study of genetic variation in sesame (<Emphasis Type="Italic">Sesamum indicum</Emphasis> L.) using agro-morphological traits and <Emphasis Type="Italic">ISSR</Emphasis> markers

This research was conducted to study the genetic variation among eighteen genotypes of sesame (Sesamum indicum L.) collected from various agro-climatic regions of Iran along with six exotic genotypes from the Asian countries using both agro-morphological and ISSR marker traits. The results showed significant differences among genotypes for all agro-morphological traits and a relatively high genetic coefficient of variation observed for number of fruiting branches per plant, capsules per plant, plant height and seed yield per plant. Cluster analysis based on these traits grouped the genotypes into five separate clusters. Larger interthan intra cluster distances implies the presence of higher genetic variability between the genotypes of different groups. Genotypes of two clusters with a good amount of genetic divergence and desirable agronomic traits were detected as promising genotypes for hybridization programs. The 13 ISSR primers chosen for molecular analysis revealed 170 bands, of which 130 (76.47%) were polymorphic. The generated dendrogram based on ISSR profiles divided the genotypes into seven groups. A principal coordinate analysis confirmed the results of clustering. The agro-morphological traits and ISSR markers reflected different aspects of genetic variation among the genotypes as revealed by a non significant cophenetic correlation in the Mantel test. Therefore the complementary application of both types of information is recommended to maximize the efficiency of sesame breeding programs. The discordance among diversity patterns and geographical distribution of genotypes found in this investigation implies that the parental lines for hybridization should be selected based on genetic diversity rather than the geographical distribution.     

Study of genetic variation in sesame (Sesamum indicum L.) using agro-morphological traits and ISSR markers

This research was conducted to study the genetic variation among eighteen genotypes of sesame (Sesamum indicum L.) collected from various agro-climatic regions of Iran along with six exotic genotypes from the Asian countries using both agro-morphological and ISSR marker traits. The results showed significant differences among genotypes for all agro-morphological traits and a relatively high genetic coefficient of variation observed for number of fruiting branches per plant, capsules per plant, plant height and seed yield per plant. Cluster analysis based on these traits grouped the genotypes into five separate clusters. Larger inter- than intra cluster distances implies the presence of higher genetic variability between the genotypes of different groups. Genotypes of two clusters with a good amount of genetic divergence and desirable agronomic traits were detected as promising genotypes for hybridization programs. The 13 ISSR primers chosen for molecular analysis revealed 170 bands, of which 130 (76.47%) were polymorphic. The generated dendrogram based on ISSR profiles divided the genotypes into seven groups. A principal coordinate analysis confirmed the results of clustering. The agro-morphological traits and ISSR markers reflected different aspects of genetic variation among the genotypes as revealed by a non significant cophenetic correlation in the Mantel test. Therefore the complementary application of both types of information is recommended to maximize the efficiency of sesame breeding programs. The discordance among diversity patterns and geographical distribution of genotypes found in this investigation implies that the parental lines for hybridization should be selected based on genetic diversity rather than the geographical distribution.     

Preservation of Solanum pimpinellifolium genomic fragments in recombinant genotypes improved the fruit quality of tomato

Five recombinant inbred lines obtained from the F₂ generation of an interspecific cross between cultivar, Caimanta (Cai, Solanum lycopersicum) and wild accession, LA722 (P, S. pimpinellifolium) were crossed to obtain the second cycle hybrids (SCH). Eleven fruit quality traits were assessed in evaluating phenotypic variability among genotypes P, Cai, F₁ (Cai × P), five RILs, and 10 SCH. One of the five recombinant inbred lines and three SCH had higher values than P, as the best genotype for shelf life. Sequence-related amplified polymorphism was used as the molecular method for detecting polymorphism among these 18 genotypes. The percentage of polymorphism in RILs and SCH was 61% and 66% respectively. Moreover, some bands detected in P were present in SCH. Several multivariate analyses were performed to find agreement between the phenotypic variability observed for fruit quality traits and the polymorphism obtained from sequence-related amplified polymorphism markers. A general Procrustes analysis estimated that there was a consensus proportion of 75% between phenotypic and molecular data. There was considerable preservation of some bands from the wild genotype, which could increase the variability in fruit quality traits in populations where the genetic diversity is limited.     

秦岭秀雅杜鹃7个野生群体形态性状的变异分析

对秦岭山区的7个秀雅杜鹃野生群体的表型变异情况进行分析。结果表明:秀雅杜鹃表型性状在种群间和种群内都存在一定程度的变异,但变异不大。各性状总的平均变异系数在0(雄蕊数目)~0.28(花梗长)之间,种群间总的平均变异系数在0.08(周至)~0.14(南郑),花色性状种群间变异大,种群内变异较小。秀雅杜鹃表型性状与地理生态因子的相关分析表明,各个性状的变异和地理生态因子并无显著的相关性,说明表型受环境影响的程度相对较小。利用群体间欧氏距离进行的UPGMA聚类分析结果表明,秀雅杜鹃野生群体可以划分为3类。     

Analysis of genetic diversity and population structure in <Emphasis Type="Italic">Capsicum</Emphasis> landraces from North Eastern India using TE-AFLP markers

North eastern (NE) India harbours a precious germplasm repository of Capsicum in the form of various landraces. The present study was undertaken to characterise the extent of genetic variation present in different Capsicum landraces from north eastern India. A set of 171 Capsicum accessions were characterised using three-endonuclease amplified fragment length polymorphism (AFLP) markers. Out of 416 bands obtained from six primer combinations, 254 (61 %) were polymorphic. The pairwise genetic dissimilarity among accessions ranged from 0.03 to 0.97. Cluster analysis based on neighbour joining showed two major clusters. Cluster I contained most of the bhut jolokia accessions whereas cluster II contained all of the Capsicum annuum genotypes. Similar grouping was observed with population STRUCTURE analysis as well as principle coordinate analysis. Analysis of molecular variance (AMOVA) revealed 45 and 54 % variation among and within populations, respectively. This information on population structure analysis and molecular characterisation will be helpful for effective utilisation of this germplasm in Capsicum improvement programs.     

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 variation in the reduction of attractive floral traits of an annual tarweed in response to drought and apical damage

Aims Foliar herbivory and water stress may affect floral traits attractive to pollinators. Plant genotypes may differ in their responses to the interplay between these factors, and evolution of phenotypic plasticity could be expected, particularly in heterogeneous environments. We aimed at evaluating the effects of simulated herbivory and experimental drought on floral traits attractive to pollinators in genetic families of the annual tarweed Madia sativa, which inhabits heterogeneous environments in terms of water availability, herbivore abundance and pollinator abundance.Methods In a greenhouse experiment with 15 inbred lines from a M. sativa population located in central Chile (Mediterranean-type climate), we measured the effects of apical bud damage and reduced water availability on: number of ray florets per flower head, length of ray florets, flower head diameter, number of open flower heads per plant, flowering plant height and flowering time.Important findings Apical damage and water shortage reduced phenotypic expression of floral traits attractive to pollinators via additive and non-additive effects. Plants in low water showed decreased height and had fewer and shorter ray florets, and fewer and smaller flower heads. Damaged plants showed delayed flowering, were less tall, and showed shorter ray florets and smaller flower heads. The number of ray florets was reduced by damage only in the low water treatment. Plant height, flowering time and number of flower heads showed among-family variation. These traits also showed genetic variation for plasticity to water availability. Ray floret length, flower head size and time to flowering showed genetic variation for plastic responses to apical damage. Plasticity in flowering time may allow M. sativa to adjust to the increased aridity foreseen for its habitat. Because genetic variation for plastic responses was detected, conditions are given for evolutionary responses to selective forces acting on plastic traits. We suggest that the evolution of adaptive floral plasticity in M. sativa in this ecological scenario (heterogeneous environments) would result from selective forces that include not only pollinators but also resource availability and herbivore damage.     

Development and Characterization of SSR Markers to Study Genetic Diversity and Population Structure of Horsegram Germplasm (<Emphasis Type="Italic">Macrotyloma uniflorum</Emphasis>)

Development of genomic resources in any crop is the pre-requisite for the construction of linkage map and implementation of molecular breeding strategies to develop superior cultivars. Large number of molecular markers are required to enrich the scanty information available in horsegram (Macrotyloma uniflorum).We employed the next-generation Illumina sequencing platform to develop a large number of microsatellite markers in this species. Of the total 23,305 potential SSRs motifs, 5755 primers were designed. Of these, 1425, 1310, 856, 1276, and 888 were of di-, tri-, tetra-, penta-, and hexa-nucleotide repeats respectively. Thirty polymorphic SSR primers and 24 morphological traits were used in 360 horsegram accessions to detect the genetic diversity and population structure. Thirty primers amplified 170 polymorphic alleles with an average of 5.6 alleles per primer having size 80 to 380 bp. The polymorphism information content (PIC) ranged from 0.15 to 0.76 with an average of 0.50, suggesting that SSR markers used in the study were polymorphic and suitable for characterization of horsegram germplasm. Dendrogram-based on Jaccard’s similarity coefficient and neighbor-joining tree grouped the horsegram accessions into two major clusters. Similarly, STRUCTURE analysis assigned genotypes into two gene pools namely Himalayan origin and Southern India. Diversity analysis based on 24 agro-morphological traits also suggested the presence of high level of diversity among the accessions.     

Sequence related amplified polymorphism (SRAP) analysis for genetic diversity and micronutrient content among gene pools in mungbean [Vigna radiata (L.) Wilczek]

Vigna radiata (L.) Wilczek, commonly called mungbean is an important pulse crop. Commercial cultivars contain low levels of iron and zinc and it is important to assess genetic variability in the available germplasm for improving micronutrient content in commercial cultivars. The present study was undertaken to study molecular diversity using Sequence-related amplified polymorphism (SRAP) among 21 Vigna radiata genotypes. Twenty nine SRAP primer combinations produced a total of 121 amplified bands which were polymorphic with an average of 4.65 bands per primer. The size of amplified bands ranged from 70 bp to 3,000 bp and 6 out of 29 SRAP primers were most useful in fingerprinting Vigna radiata genotypes under study. The similarity coefficients between different genotypes ranged from 0.45 to 0.96 with an average similarity value of 0.71. At an arbitrary cut-off at 60 % similarity level on a dendrogram, the Vigna radiata accessions were categorized into two major clusters. ML1108 and 2KM115 were found to be genetically similar. SMH99-1A and ML776 showed high iron and zinc content while Satya was poor in iron as well as zinc content. Mapping population involving ML776 and Satya could be used for tagging gene(s) for micronutrient content. The results indicated that SRAP markers were efficient for identification of Vigna radiata genotypes and assessment of the genetic relationships among them.     

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.     

Evaluation of genetic diversity in jackfruit (Artocarpus heterophyllus Lam.) based on amplified fragment length polymorphism markers

Artocarpus heterophyllus Lam., commonly called jackfruit, is a medium-sized evergreen tree that bears high yields of the largest known edible fruit. Yet, it has been little explored commercially due to wide variation in fruit quality. The genetic diversity and genetic relatedness of 50 jackfruit accessions were studied using amplified fragment length polymorphism markers. Of 16 primer pairs evaluated, eight were selected for screening of genotypes based on the number and quality of polymorphic fragments produced. These primer combinations produced 5976 bands, 1267 (22%) of which were polymorphic. Among the jackfruit accessions, the similarity coefficient ranged from 0.137 to 0.978; the accessions also shared a large number of monomorphic fragments (78%). Cluster analysis and principal component analysis grouped all jackfruit genotypes into three major clusters. Cluster I included the genotypes grown in a jackfruit region of Karnataka, called Tamaka, with very dry conditions; cluster II contained the genotypes collected from locations having medium to heavy rainfall in Karnataka; cluster III grouped the genotypes in distant locations with different environmental conditions. Strong coincidence of these amplified fragment length polymorphism-based groupings with geographical localities as well as morphological characters was observed. We found moderate genetic diversity in these jackfruit accessions. This information should be useful for tree breeding programs, as part of our effort to popularize jackfruit as a commercial crop.     

Genetic diversity in a collection of Cucumis sativus L. assessed by RAPD and ISSR markers

The genetic diversity among 39 cucumber collections from Karnataka, India was assessed using 23 RAPD and 18 ISSR primers. A total of 309 bands were scored of which 147 (47.57 %) were polymorphic. The average number of bands per primer was 7.82 and an average number of polymorphic bands of 3.58 per primer. The primers UBC855 revealed the highest PIC (polymorphism information content) value of 0.49 followed by the primers UBC846, OPE13, OPC01 and OPR12 (0.48). The Jaccard’s similarity coefficients ranged from 0.36 to 0.84 and the first two principal components explained 53.33 % of the total variance. The UPGMA phenogram and the PCA (Principle component analysis) indicated that the populations formed five major clusters. CSC 83 (774 g per fruit) and CSC 71 (yellow skin) are considered to be the most important collections to be stressed for further breeding purpose. The available genetic resources of cucumber in Karnataka were characterized.     

Impact of protein diversification on morphometric behavior of Andrographis paniculata Nees

Proteins are important biochemical parameters in genetic diversity and controlling morphological characteristics in plants. In this study, the proteomic and morphometric data of an important medicinal herb “Aci Pa?a” (Andrographis paniculata) were combined together to illustrate their impacts on genetic variation of the plant’s population and to realize the connection between protein patterns and phenotypic behavior of the species. We used three protein extraction buffers including Tris, potassium phosphate, and sodium citrate. The Tris buffer was significantly different (p ≤ 0.01) than other two in terms of the quality and quantity of protein bands by producing 15 types of proteins ranged from 13 to 105 kDa of which two of them were polymorphic. Consequently, a total of 12 accessions of A. paniculata were subjected to morpho-proteomic analyses. The unweighted pair group method with arithmetic average cluster analysis of the accessions based on the protein data and morphological characteristics generated three and four clusters, respectively, at a Euclidean distance of 2.53 for the morphological traits. Moreover, seed proteins analysis revealed that the two polymorphic protein bands sized 20.5 (protein “b”) and 30 kDa (protein “a”) effectively diversified the morphological characteristics and phylogenetic relationships among the 12 accessions of A. paniculata. Interestingly, the protein “b” acted as an activator agent for the number of branches, leaves and total dry weight, while the protein “a” performed a suppressive role for the same traits. Additionally, the two high-weighted faint bands “c” (75 kDa) and “d” (100 kDa) with a very low expression in accession 11228 proved their suppressive role along with the “a” band, while these bands were strongly expressed in the rest of the accessions. These findings suggest that these four proteins should be sequenced and perfectly established for further proteomic analyses. Ultimately, the mentioned proteins can be developed for any prospective breeding program or gene identification.     

Comparative Evaluation of RAPD, ISSR and Anchored-SSR Markers in the Assessment of Genetic Diversity and Fingerprinting of Oilseed Brassica Genotypes

Forty-two genotypes representing oilseed Brassica species were analyzed for the level of genetic diversity and molecular identity using Random Amplified Polymorphic DNA (RAPD), Inter-Simple Sequence Repeat (ISSR) and 5'-Anchored Simple Sequence Repeat (ASSR) markers. DNA profiles revealed high degree of interspecific polymorphism, while the level was considerably low within a species, particularly in B. juncea. The UPGMA clusters clearly delineated genotypes of the respective Brassica species. Comparison of cophenetic matrices indicated a high degree of correspondence between dendrograms generated by different marker systems. A minimum of 10 random primers (approximately 105 bands) were required for the RAPD profiles to generate the expected cluster. Comparatively less number of primers was required to do the same in case of ISSR (4 primers) and ASSR (3 primers). The principal component analysis revealed similar genetic relationship among the genotypes as in cluster analysis. Although none of the DNA profiles could individually identify all the B. juncea genotypes, a combined DNA profile consisting 125 markers from the informative primers of all the three DNA marker systems could do the same. A positive correlation was found among the marker utility parameters (calculated for individual primers of different marker systems) such as marker index (MI), resolving power (Rp) and discrimination coefficient (D) with the number of genotypes identified by each primer with a few exceptions. Single plant analysis for a set of five B. juncea varieties revealed absence of intra-varietal heterogeneity in case of ASSR profiles, thereby suggesting its utility in varietal identification and differentiation.