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Molecular Characterization of Cultivated Bromeliad Accessions with Inter-Simple Sequence Repeat (ISSR) Markers  [PDF]
Fei Zhang,Yaying Ge,Weiyong Wang,Xinying Yu,Xiaolan Shen,Jianxin Liu,Xiaojing Liu,Danqing Tian,Fuquan Shen,Yongming Yu
International Journal of Molecular Sciences , 2012, DOI: 10.3390/ijms13056040
Abstract: Bromeliads are of great economic importance in flower production; however little information is available with respect to genetic characterization of cultivated bromeliads thus far. In the present study, a selection of cultivated bromeliads was characterized via inter-simple sequence repeat (ISSR) markers with an emphasis on genetic diversity and population structure. Twelve ISSR primers produced 342 bands, of which 287 (~84%) were polymorphic, with polymorphic bands per primer ranging from 17 to 34. The Jaccard’s similarity ranged from 0.08 to 0.89 and averaged ~0.30 for the investigated bromeliads. The Bayesian-based approach, together with the un-weighted paired group method with arithmetic average (UPGMA)-based clustering and the principal coordinate analysis (PCoA), distinctly grouped the bromeliads from Neoregelia, Guzmania, and Vriesea into three separately clusters, well corresponding with their botanical classifications; whereas the bromeliads of Aechmea other than the recently selected hybrids were not well assigned to a cluster. Additionally, ISSR marker was proven efficient for the identification of hybrids and bud sports of cultivated bromeliads. The findings achieved herein will further our knowledge about the genetic variability within cultivated bromeliads and therefore facilitate breeding for new varieties of cultivated bromeliads in future as well.
Genetic similarity among strawberry cultivars assessed by RAPD and ISSR markers
Morales, Rafael Gustavo Ferreira;Resende, Juliano Tadeu Vilela;Faria, Marcos Ventura;Andrade, Marcela Carvalho;Resende, Luciane Vilela;Delatorre, Carla Andrea;Silva, Paulo Roberto da;
Scientia Agricola , 2011, DOI: 10.1590/S0103-90162011000600010
Abstract: most strawberry (fragaria × ananassa duchesne) cultivars used in brazil are developed in other countries, it became clear the need to start the strawberry breeding program in the country. to start a breeding program is necessary the genetic characterization of the germplasm available. molecular markers are important tools that can be used for this purpose. the objectives of the present study were to assess the genetic similarity among 11 strawberry cultivars using rapd and issr molecular markers and to indicate the possible promising crosses. the dna of the eleven strawberry cultivars was extracted and amplified by pcr with rapd and issr primers. the dna fragments were separated in agarose gel for the rapd markers and in polyacrylamide gel for the issr markers. the genetic similarity matrix was estimated by the jaccard coefficient. based on this matrix, the cultivars were grouped using the upgma method. the dendogram generated by the rapd markers distributed the cultivars in three groups while the issr markers generated two groups. there was no direct relationship between the marker groups when the two types of markers were compared. the grouping proposed by the issr markers was more coherent with the origin and the genealogy of the cultivars than that proposed by the rapd markers, and it can be considered the most efficient method for the study of genetic divergence in strawberry. the most promising crosses, based on the genetic divergence estimated from the rapd and issr molecular data were between the tudla and ventana and the oso grande and ventana cultivars, respectively.
Characterization of genetic structure of Podophyllum hexandrum populations, an endangered medicinal herb of Northwestern Himalaya, using ISSR-PCR markers and its relatedness with podophyllotoxin content
A Alam, PK Naik, P Gulati, AK Gulati, GP Mishra
African Journal of Biotechnology , 2008,
Abstract: To obtain accurate estimates of genetic structure for purpose of conservation planning for wild Indian May apple (Podophyllum hexandrum) in the Northwestern region of Himalayas, Himachal Pradesh, genetic diversity among and within 28 populations were analyzed. Eleven microsatellite DNA markers were isolated and used to quantify genetic structure. Out of 68 ISSR loci tested, 88.23% were polymorphic. The genetic diversity was high (percentage of polymorphic bands, PBB = 83.82%; Shannon’s information index, I = 0.4413) at the population level, but low within individual study populations (PBB = 34.22%; Shannon’s information index I = 0.1879). The mean coefficient of gene differentiation (Gst) was 0.7484, indicating that 29.44% of the genetic diversity resided within the population. Analysis of molecular variance (AMOVA) indicated that 48% of the genetic diversity among the study populations was attributed to geographical location while 29% was attributed to differences in their habitats. An overall value of mean estimated number of gene flow (Nm = 0.1618) indicated that there was limited gene flow among the sampled populations. We found a clear tendency for higher Gst values and podophyllotoxin levels between the populations with increasing geographical altitude. However, the existing variation in podophyllotoxin content among the populations was proved to be coupled with geographical altitude (r = 0.922) but not with genetic variations (r = - 0.273). Hence we recommend that any further cultivation of this species requires optimization of environmental factors in order to increase the rate of production of podophyllotoxin from any collected population.
UTILIZATION OF DNA MARKERS BASED ON MICROSATELLITE POLYMORPHISM FOR IDENTIFICATION OF POTATO VARIETIES CULTIVATED IN THE CZECH REPUBLIC  [PDF]
Alena Nováková,Kate?ina ?imá?ková,Jan BáRTA,Vladislav ?urn
Journal of Central European Agriculture , 2011,
Abstract: In the year 2007, there were one hundred and seventy-eight potato varieties enlisted in the Czech list of registered potato varieties. The classical morphometric approach to characterization is not effective for such a number of varieties especially for identification at the level of tubers. The needfulness of variety identification at the level of tubers is important mainly for trade aspect. The Czech law no.110/1997 Sb. about the food-stuff and tobacco products and the consequential ordinance (MZe . 332 / 1997 Sb.) require guarantee of variety declaration in commercial relation for table potato. In this study we analyzed twenty potato varieties (Solanum tuberosum L.) cultivated in the Czech Republic. Every variety was represented by four independent replicates. This set of samples was analyzed by methods of PCR-SSR (Simple Sequence Repeats) and PCR-ISSR (Inter Simple Sequence Repeats). We discovered that both of tested methods afford sufficient polymorphism for variety identification, but the method of PCR-ISSR is not utilizable, because we observed the variability within variety. For outright identification of the whole set of potato varieties cultivated in the Czech Republic we recommend to use SSR, AFLP and retrotransposene-based markers as well as morphological markers.
Assessment of diversity using RAPD and ISSR markers in Sorghum varieties across Gujarat, India
Sudeshna Chakraborty*, Indrapratap Thakare, Rallapalli Ravikiran, Vivek Nikam, Ruchi Trivedi, Sasidharan N and G.C. Jadeja
Electronic Journal of Plant Breeding , 2011,
Abstract: Molecular characterization of twelve varieties of Sorghum bicolor L. was carried out with 11 RAPD and three ISSR primers. Outof the different anchored primer combinations, ISSR primers with TC and GA motifs produced clear and maximum scorablebands, thus revealing a better coverage of the genome. Genetic diversity parameters [viz., average and effective number ofalleles, polymorphic information content (PIC)] were calculated for both RAPD and ISSR markers. UPGMA clustering based onJaccard’s coefficient was calculated. RAPD markers were more efficient than ISSR markers with regards to detection ofpolymorphism, number of bands scored and PIC values. Genetic variations detected among the geographically differentpopulations of Sorghum bicolor L. could be of much use for the introgression of new characters from wild counterparts to thecultivars, isolation of stable segregating markers and selection of improved varieties and conservation of germplasm resources.
Genetic similarity between coriander genotypes using ISSR markers
Melo, Roberto de A;Resende, Luciane V;Menezes, Dimas;Beck, Ana Paula A;Costa, José Carlos da;Coutinho, Alisson E;Nascimento, Ana Ver?nica S do;
Horticultura Brasileira , 2011, DOI: 10.1590/S0102-05362011000400014
Abstract: with the development of new cultivars, a precise genetic characterization is essential for improvement programs or for cultivar registration and protection. molecular markers have been complementing the traditional morphological and agronomic characterization techniques because they are virtually unlimited, cover the whole genome and are not environmentally influenced. genetic characterization constitutes the basis for studies involving estimates of genetic similarity. therefore, the objective of the present study was to evaluate the genetic similarity between ten coriander genotypes (nine cultivars and one line) using issr markers. the cultivars used were: americano, asteca, palmeira, português, santo, supéria, tabocas, tapacurá, verd?o and the experimental line htv-9299. the genetic similarity between the cultivars was estimated using 227 banded regions of issr molecular markers. the ubc 897 oligonucleotide generated the highest number of fragments (16), resulting in a higher polymorphism. the results indicate that the twenty-nine oligonucleotides chosen were satisfactory for detecting polymorphism. based on the grouping analysis determined from the similarity data, there were two groups and two sub-groups. the calculated similarity for the genotypes varied from 52 to 75%. the lowest similarity was observed between português and verd?o, at 52%. the highest similarity was found between português and palmeira, at 75%. the issr is efficient for identifying dna polymorphism in coriander.
Analysis of genetic variability by ISSR markers in Calibrachoa caesia
Pérez de la Torre,Mariana; García,Martín; Heinz,Ruth; Escandón,Alejandro;
Electronic Journal of Biotechnology , 2012,
Abstract: background: calibrachoa cerv. (ex la llave & lexarza) is a genus of the solanaceae family (la llave and lexarza, 1825). this genus has a high ornamental and economic value due to its intrinsic variability and multiplicity of flower colours. in argentina there are eight native species, and one of them is calibrachoa caesia. the genetic diversity among 35 accessions of c. caesia, from five departments in the province of misiones, was analyzed using issr markers. results: thirteen issr primers yielded a reproducible banding pattern, with 701 amplified loci and 98% of polymorphism. the issr primers 5’ct, 5’ca, 5’ga, 5’gaca, 3’cac, 3’tg and 3’tc generated 100% polymorphic patterns. the rp values ranged from 23.20 to 10.29 for 5’gaca and 3’ag primers, respectively, while the average values for mi and pic were 0.367 and 0.231, respectively. the more informative primers were 5’gaca and 5’ga, and the less informative was 3’ac. simple matching coefficient of similarity varied from 0.8875 to 0.6659, indicating high levels of genetic similarity among the genotypes studied. the upgma cluster analysis indicated three distinct clusters; one comprised genotypes of the five departments, while the second included individuals from guaraní and oberá regions and the third cluster included the san pedro individuals. the overall grouping pattern is in agreement with principal coordinate analysis (pcoa). conclusions: the bayesian cluster analysis revealed structuring of the c. caesia population and two clusters were identified, which correspond to upgma major clades. the amova test for all populations showed highest genetic variation within populations (90%), meanwhile the fst coefficient was 0.098, indicating a medium differentiation between populations. these results showed a great intrapopulation genetic diversity but no significant difference was detected among populations. in this work the use of thirteen issr markers, allowed the characterization of every individual examined. therefo
Efficiency of RAPD and ISSR markers in assessing genetic variation in Arthrocnemum macrostachyum (Chenopodiaceae)
Saleh, Basel;
Brazilian Archives of Biology and Technology , 2011, DOI: 10.1590/S1516-89132011000500002
Abstract: the goal of this study was to investigate the molecular characterization of a. macrostachyum genotypes grown in the western coast of syria using rapd and issr techniques. pcr amplifications with 20 rapd primers gave an average of 9.25 selected markers/ primer, with a maximum of 17 (opg05) and a minimum of four (opa02). percentage of polymorphic bands ranged from 40 to 100% according to rapd primers tested. among the 185 selected bands, 160 (84.96%) were polymorphic. the amplification with seven issr primers generated 88 bands, and 80 (90.91%) were polymorphic. (ca)8rg and (ag)8gtg issr primers tested in this study yielded highly informative patterns. rapd and issr fragment sizes ranged from 0.2-3 kb. based on this study, the use of rapd and issr fingerprints could be a powerful tool to assess the genetic diversity in a. macrostachyum. both the techniques gave similar results regarding the degree of relatedness among the genotypes tested, with genotype 2 being suggested to represent a distinct subspecies from that of genotypes 1 and 3.
Genetic Diversity of Pistachio Tree using Inter-Simple Sequence Repeat Markers ISSR Supported by Morphological and Chemical Markers  [PDF]
K. Fares,F. Guasmi,L. Touil,T. Triki
Biotechnology , 2009,
Abstract: The identification and the characterization of some Pistachio cultivars trees in South of Tunisia revealed a remarkable diversity between different cultivars, thanks to molecular markers (ISSR) supported by morphological markers (length sheets, leaf area, length of fruit, forms of final leaflet, their length and by chemical markers (content of vitamins). For the whole of the studied cultivars, the length of fruits is between 16.3 and 20.4 cm, the length of the final leaflet is 5.88 to 8.42 cm its form oscillates from elliptic to round, the average leaf area varies between 17.13 to 34.05 cm2 in all varieties. The analysis of chemical variability allows to distinguish in different cultivars studied a variability on the level of the composition of vitamin B1, B2, B6 and VC. The content of vitamin B1 is going from 0 to 1 mg g-1 in the varieties Kermizi, Meknessy 1, Mumtez, Mateur 2 and Mateur 3 and 0.019 mg g-1 in Lybie rouge then the range of B2 is going from 0.001 mg g-1 at the variety Mateur 3, with 0.07 mg g-1 in Lybie rouge, the content of vitamin B6 is very variable from 0. 0016 mg g-1 at Mateur 3, with 0.01643 mg g-1 in Red Aleppo and the VC is going from 0.013 mg g-1 in Meknessy 1 to 0.09 mg g-1 in Lybie blanc. The PCR amplification of Pistachio varieties revealed a high percentage of the polymorphic fragments (26 fragments are polymorphs), the varieties Mumtez, El Guettar and Mateur 1 are characterized by a high percentage of the polymorphic locus (38.46%) whereas the varieties Lybie blanc, Kermizi, Lovy, Meknessy 1, Lybie rouge, Brise vent, Mateur 2, Mateur 3, Mateur 4, Meknessy 2, Kerman, Red Aleppo have an average polymorphism (between 26.92 and 34.61%). The variety Meknessy I (rate = 3.84%) and Lybie blanc (rate = 15.38%) have a low polymorphism. Several varieties have a coefficient of similarity (ds) close to 1 they are considered genetically very similar. Among these varieties Brise vent and Mateur 3 whose a coefficient of similarity equal to 0.667 (dg = 0.333), Lovy and Mumtez whose coefficient is equal to 0.632(dg = 0.368), Lybie rouge and El Guettar whose coefficient is equal to 0.632 (dg = 0.368), Kermezi and Kerman whose coefficient of similarity is equal to 0.750 (dg = 0.250), Meknessy 2 and Red Aleppo whose coefficient of similarity is about 0.857 (dg = 0.143). Certain varieties are considered genetically very distant between them, the genetic distance which separate them is large (dg = 1) it`s the case of the variety Mateur 4 with Meknessy1 (dg = 1) and Meknessy 1 with Mumtez and Mateur 3. Other varieties can be considered distant lik
Genetic diversity as assessed by ISSR markers in Blackgram (Vigna mungo (L.) Hepper)
Kanimozhi M,Jayamani P,Nadarajan N
Electronic Journal of Plant Breeding , 2009,
Abstract: An investigation was carried out on a collection of 23 blackgram genotypes involving 16 releasedvarieties, six pre release cultures and one wild species Vigna mungo var. silvestris to study the genetic diversityusing twelve ISSR primers. The number of alleles produced by different ISSR primers ranged from eight to 17with an average of 11.5 per primer and the level of polymorphism was found to be 82.05 percent. Similaritymeasures and clustering analyses were made using ISSR data. The resulting dendrogram distributed the 23blackgram genotypes into five main clusters. The highest genetic similarity coefficient was measured betweengenotypes CBG 671 and CBG 632. The results of PCoA were comparable to that of grouping based on UPGMAand 23 genotypes were grouped into four groups. Genotype Vigna mungo var. silvestris was placed separatelyfrom rest of the genotypes in both the analyses. Grouping of varieties using ISSR markers did not show anyrelevance to their pedigree. All the pre release cultures in one group revealed that only a portion of geneticvariation has been exploited. The results revealed that, genetic diversity is low among the varieties releasedfrom the respective institute and hence genotypes were grouped according to the research institutes from whichthey released. It suggests that the research institutes have to enlarge the genetic base for variety development.
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