scholarly journals Genomic diversity of Sri Lankan New Improved Rice Varieties revealed by AFLP markers

2016 ◽  
Vol 4 (1) ◽  
pp. 32-38
Author(s):  
Gowri Rajkumar ◽  
Jagathpriya Weerasena ◽  
Rangika Silva ◽  
Kumudu Fernando
Keyword(s):  
Genetic Relationships ◽  
Genomic Diversity ◽  
Aflp Markers ◽  
Ex Situ ◽  
Group Method ◽  
Sri Lankan ◽  
Rice Varieties ◽  
Cophenetic Correlation ◽  
Upgma Dendrogram ◽  
Clustering Pattern

Genetic relationships among 28 new improved rice varieties were established using Amplified Fragment Length Polymorphism (AFLP) markers. Cultivars were analyzed with 10 EcoR1 and MseI primer combinations. A total of 517 fluorescent AFLP markers were generated and analyzed. Of these 480 fragments were polymorphic (92.84%) and 37 (7.16%) fragments were monomorphic. The Jaccard’s similarity indices (J) based on the AFLP profiles of the 28 varieties were computed and Unweighted Pair Group Method with Arithmetic mean (UPGMA) based dendrogram was constructed. The dendrogram separated varieties into three major clusters. Outliers used in the study were uniquely separated from the rest confirming the reliability of data and analysis. The Cophenetic correlation with 0.862 strongly supported the clustering pattern of UPGMA dendrogram. Principal Coordinate analysis and the unrooted tree also confirmed the clustering pattern of the UPGMA dendrogram. Rice varieties in the same cluster showed similar characteristic features (Eg. Grain colour, life span etc). Therefore this genetic diversity data at molecular level will provide detailed estimates of the genetic variation among Sri Lankan new improved rice varieties and also useful in ex situ and in situ genetic conservation, utilization and exchange of genetic material. Int J Appl Sci Biotechnol, Vol 4(1): 32-38

Assessment of genetic diversity among Sri Lankan rice varieties by AFLP markers

2011 ◽  
Vol 9 (2) ◽  
pp. 224-228 ◽  
Author(s):  
Gowri Rajkumar ◽  
Jagathpriya Weerasena ◽  
Kumudu Fernando ◽  
Athula Liyanage
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Sri Lanka ◽  
Germplasm Collection ◽  
Molecular Techniques ◽  
Group Method ◽  
Aflp Analysis ◽  
Sri Lankan ◽  
Rice Varieties ◽  
Cophenetic Correlation

Sri Lanka has a valuable repository of germplasm collection due to the availability of a large number of different traditional and improved rice varieties. Molecular techniques can increase the effectiveness of traditional technologies in assessing genetic diversity. Amplified fragment length polymorphism (AFLP) was used to evaluate the genetic diversity among rice varieties available in the germplasm collection of Plant Genetic Resources Centre, Sri Lanka. AFLP analysis of rice varieties using ten different primer combinations yielded a total of 772 polymorphic bands (98.4%). Genetic similarities were estimated using Jaccard's (J) similarity coefficient. Unweighted pair group method with arithmetic mean (UPGMA)-based dendrogram was constructed. Genetic similarities varied from 0.073 to 0.565. Cluster analysis by genetic similarity divided the accessions into four main groups. The Cophenetic correlation with r = 0.781 indicated high confidence of AFLP data to group the varieties in UPGMA clusters. Principal component analysis further confirmed the patterns obtained by the cluster analysis. The results revealed very high genetic diversity at molecular level among the Sri Lankan rice varieties used in this study.

scholarly journals Assessment of Genetic Relationships among Philodendron Cultivars Using AFLP Markers

2004 ◽  
Vol 129 (5) ◽  
pp. 690-697 ◽  
Author(s):  
Pachanoor S. Devanand ◽  
Jianjun Chen ◽  
Richard J. Henny ◽  
Chih-Cheng T. Chao
Keyword(s):  
Genetic Similarity ◽  
Near Infrared ◽  
Genetic Relationships ◽  
Aflp Markers ◽  
Group Method ◽  
Limited Information ◽  
Similarity Coefficients ◽  
Arithmetic Average ◽  
Ornamental Foliage Plants ◽  
Pair Group

Philodendrons (Philodendron Schott) are among the most popular tropical ornamental foliage plants used for interior decoration. However, limited information is available on the genetic relationships among popular Philodendron species and cultivars. This study analyzed genetic similarity of 43 cultivars across 15 species using amplified fragment length polymorphism (AFLP) markers with near infrared fluorescence labeled primers. Forty-eight EcoR I + 2/Mse I + 3 primer set combinations were screened, from which six primer sets were selected and used in this investigation. Each selected primer set generated 96 to 130 scorable fragments. A total of 664 AFLP fragments were detected, of which 424 (64%) were polymorphic. All cultivars were clearly differentiated by their AFLP fingerprints, and the relationships were analyzed using the unweighted pair-group method of arithmetic average cluster analysis (UPGMA) and principal coordinated analysis (PCA). The 43 cultivars were divided into five clusters. Cluster I comprises eight cultivars with arborescent growth style. Cluster II has only one cultivar, `Goeldii'. There are 16 cultivars in cluster III, and most of them are self-heading interspecific hybrids originated from R.H. McColley's breeding program in Apopka, Fla. Cluster IV contains 13 cultivars that exhibit semi-vining growth style. Cluster V has five cultivars that are true vining in morphology, and they have lowest genetic similarity with philodendrons in other clusters. Cultivated philodendrons are generally genetically diverse except the self-heading hybrids in cluster III that were mainly developed using self-heading and semi-vining species as parents. Seven hybrid cultivars have Jaccard's similarity coefficients of 0.88 or higher, suggesting that future hybrid development needs to select parents with diverse genetic backgrounds.

Genetic diversity in bambara groundnut (Vigna subterranea (L.) Verdc) landraces revealed by AFLP markers

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1175-1180 ◽  
Author(s):  
F J Massawe ◽  
M Dickinson ◽  
J A Roberts ◽  
S N Azam-Ali
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Geographic Origin ◽  
Bambara Groundnut ◽  
Aflp Markers ◽  
Group Method ◽  
Aflp Analysis ◽  
Vigna Subterranea ◽  
Marker Assisted Breeding ◽  
Pair Group

Bambara groundnut (Vigna subterranea (L.) Verdc), an African indigenous legume, is popular in most parts of Africa. The present study was undertaken to establish genetic relationships among 16 cultivated bambara groundnut landraces using fluorescence-based amplified fragment length polymorphism (AFLP) markers. Seven selective primer combinations generated 504 amplification products, ranging from 50 to 400 bp. Several landrace-specific products were identified that could be effectively used to produce landrace-specific markers for identification purposes. On average, each primer combination generated 72 amplified products that were detectable by an ABI Prism 310 DNA sequencer. The polymorphisms obtained ranged from 68.0 to 98.0%, with an average of 84.0%. The primer pairs M-ACA + P-GCC and M-ACA + P-GGA produced more polymorphic fragments than any other primer pairs and were better at differentiating landraces. The dendrogram generated by the UPGMA (unweighted pair-group method with arithmetic averaging) grouped 16 landraces into 3 clusters, mainly according to their place of collection or geographic origin. DipC1995 and Malawi5 were the most genetically related landraces. AFLP analysis provided sufficient polymorphism to determine the amount of genetic diversity and to establish genetic relationships in bambara groundnut landraces. The results will help in the formulation of marker-assisted breeding in bambara groundnut.Key words: under-utilized, African legume, molecular markers.

Prospects for celeriac (Apium graveolensvar.rapaceum) improvement by using genetic resources ofApium, as determined by AFLP markers and morphological characterization

2004 ◽  
Vol 2 (3) ◽  
pp. 189-198 ◽  
Author(s):  
Jasmina Muminović ◽  
Albrecht E. Melchinger ◽  
Thomas Lübberstedt
Keyword(s):  
Genetic Resources ◽  
Morphological Traits ◽  
Genetic Relationships ◽  
Morphological Characterization ◽  
Aflp Markers ◽  
Group Method ◽  
Pair Group ◽  
New Genes ◽  
Amova Analysis ◽  
Elite Germplasm

Genetic relationships among elite celeriac varieties and celeriac accessions conserved in genebanks are generally unknown. The objective of this study was to use amplified fragment length polymorphism (AFLP) markers and morphological characterization to identify material that could be of use in celeriac breeding. Genetic relationships were estimated in 34 elite celeriac varieties bred in Europe and 28 celeriac accessions conserved at the German genebank. Two varieties of celery, two varieties of leaf celery and three genebank accessions of wildApiumspecies were additionally analysed. FifteenEcoRI/MseI-based AFLP primer combinations were used. Polymorphic AFLP fragments were scored for calculation of Jaccard's coefficient of genetic similarity (GS). Morphological distances (MD) were determined based on 11 morphological traits. Average GS estimate in elite germplasm (GS=0.90) was higher than in exotic germplasm (GS=0.80). An AMOVA (analysis of molecular variance) revealed that a high proportion of variation was due to variation within elite celeriac varieties and genebank accessions. Although GS and MD matrices were poorly correlated (r=0.22), UPGMA (unweighted pair group method using arithmetic averages) cluster analyses revealed clear genetic groupings of celeriac germplasm, which was supported by morphological traits. Elite, moderately bred and exotic varieties formed distinct clusters, indicating that only a part of the available genetic diversity in celeriac germplasm has been exploited in breeding. DistinctApiumspecies might be useful for the introgression of new genes into cultivated celeriac material. Broadening of celeriac collections in genebanks and detection of new genetic resources are vital for improvements in celeriac breeding.

Genetic variation and relationship among and within Withania species as revealed by AFLP markers

Genome ◽  
2000 ◽  
Vol 43 (6) ◽  
pp. 975-980 ◽  
Author(s):  
M S Negi ◽  
A Singh ◽  
M Lakshmikumaran
Keyword(s):  
Genetic Variation ◽  
Medicinal Plant ◽  
Genetic Relationships ◽  
Similarity Coefficient ◽  
Aflp Markers ◽  
Group Method ◽  
Intermediate Type ◽  
Aflp Data ◽  
Pair Group ◽  
High Level

Withania somnifera is an important medicinal plant, and its anticancerous properties have been attributed to various classes of withanolide compounds. The objective of the present study was to investigate the inter- and intraspecific genetic variation present in 35 individuals of W. somnifera and 5 individuals of W. coagulans using AFLP (amplified fragment length polymorphism) marker technique. The information about genetic variation determined from AFLP data for 40 individuals was employed to estimate similarity matrix value based on Jaccard's coefficient. The similarity values were further used to construct a phenetic dendrogram revealing the genetic relationships. The dendrogram generated by UPGMA (unweighted pair group method of arithmetic averages) distinguished W. somnifera from W. coagulans and formed two major clusters. These two main clusters shared a similarity coefficient of 0.3, correlating with the high level of polymorphism detected. The dendrogram further separated W. somnifera into three subclasses corresponding to Kashmiri and Nagori groups and an intermediate type. The AFLP profile of Kashmiri individuals was distinct from that of the Nagori group of plants. The intermediate genotype was distinct as it shared bands with both the Kashmiri and Nagori individuals, even though it was identified as a Kashmiri morphotype. Furthermore, the intermediate type shared a similarity coefficient of 0.8 with the Kashmiri individuals. The present work revealed low levels of variation within a population though high levels of polymorphism were detected between Nagori and Kashmiri populations. The ability of AFLP markers for efficient and rapid detection of genetic variations at the species as well as intraspecific level qualifies it as an efficient tool for estimating genetic similarity in plant species and effective management of genetic resources.Key words: Withania, AFLP, genetic variation, phenetic relationships, medicinal plant.

scholarly journals Analysis of Genetic Relationships of Calathea Species and Cultivars by AFLP Markers

HortScience ◽  
2004 ◽  
Vol 39 (4) ◽  
pp. 888A-888
Author(s):  
Jianjun Chen* ◽  
Richard Henny ◽  
C. Thomas Chao ◽  
Pachanoor Devanand
Keyword(s):  
Genetic Relationships ◽  
Aflp Markers ◽  
Group Method ◽  
Similarity Coefficients ◽  
Low Light ◽  
Ornamental Foliage Plants ◽  
Pair Group ◽  
Light Levels ◽  
The Family ◽  
Tropical America

Calathea, the largest genus in the family Marantaceae, is composed of 100 species native to tropical America in moist or swampy forest habitats. Because of their brilliant patterns of leaf color and different textures plus ability to tolerate low light levels, calatheas have been widely produced as ornamental foliage plants for interiorscaping. Thus far, genetic relationships among its species and cultivars have not been documented. This study analyzed the relationships of 34 cultivars across 14 species using amplified fragment length polymorphism (AFLP) markers. Six EcoR I + 2/Mse I + 3 primer set combinations were used in this investigation. Each selected primer set generated 105 to 136 scorable fragments. A total of 733 AFLP fragments were detected of which 497 were polymorphic (68%). A dendrogram was constructed using the unweighted pair-group method of arithmetic averages (UP-GMA) technique and a principal coordinated analysis (PCOA) was used to analyze the relationships. The 34 cultivars were divided into four clusters. Cluster I had 19 cultivars derived from C. roseo-picta and C. loesnerii with Jaccard's similarity coefficients from 0.74 to 0.97, of which six are somaclonal variants or sports and two cultivars are genetic identical. Only C. kennedeae `Helen' is positioned in cluster II. Cluster III had 10 cultivars across seven species; Jaccard's similarity coefficients among them varied from 0.41 to 0.63. Four species were situated in cluster IV with Jaccard's similarity between 0.27 to 0.41. Results from this study indicate that broadening of genetic diversity is needed for cultivars in cluster I as they are the most commonly grown calatheas but genetically are very close.

scholarly journals Genetic Relationships of Spathiphyllum Cultivars Analyzed by AFLP Markers

HortScience ◽  
2006 ◽  
Vol 41 (4) ◽  
pp. 968A-968 ◽  
Author(s):  
Jianjun Chen ◽  
Richard J. Henny ◽  
Pachanoor S. Devanand ◽  
Chih-Cheng T. Chao
Keyword(s):  
Near Infrared ◽  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Aflp Markers ◽  
Group Method ◽  
Similarity Coefficients ◽  
Breeding Lines ◽  
Arithmetic Average ◽  
Commercial Cultivars ◽  
Peace Lily

Peace lily (Spathiphyllum Schott) is one of the most popular tropical ornamental foliage plants and is used worldwide for interiorscaping. However, little information is available on the genetic relationships of cultivars. Using amplified fragment length polymorphism (AFLP) markers with near-infrared fluorescence-labeled primers, this study analyzed genetic relatedness of 63 commercial cultivars and breeding lines. Forty-eight EcoRI + 2/MseI + 3 primer set combinations were initially screened, from which six primer sets were selected and used in this investigation. All cultivars were clearly differentiated by their AFLP fingerprints, and the relationships were analyzed using the unweighted pair-group method of arithmetic average cluster analysis (UPGMA). The 63 cultivars were divided into four clusters. All commercial cultivars or breeding lines resulted from crosses of some of the cultivars, a total of 45, were positioned in cluster I with Jaccard's similarity coefficients between 0.61 and 0.88. There was only one cultivar in cluster II. Cluster III contained 16 cultivars; they are either species or breeding lines generated from interspecific hybridization. Cluster IV had one unknown species. This study provides genetic evidence as to why cultivars from cluster I and III are not readily crossable because the Jaccard's similarity coefficient between the two clusters was only 0.35. Results also indicate that commercial cultivars are genetically close. Strategies for increasing genetic diversity of cultivated peace lily should be sought for future breeding efforts.

Genetic variation and differentiation of populations within the Quercus affinis – Quercus laurina (Fagaceae) complex analyzed with RAPD markers

2005 ◽  
Vol 83 (2) ◽  
pp. 155-162 ◽  
Author(s):  
Antonio González-Rodríguez ◽  
Dulce M Arias ◽  
Ken Oyama
Keyword(s):  
Population Genetics ◽  
Genetic Variation ◽  
Hybrid Zone ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Morphological Differentiation ◽  
Mantel Test ◽  
Distribution Area ◽  
Group Method ◽  
Upgma Dendrogram

The population genetics of two hybridizing Mexican red oaks, Quercus affinis Schweid. and Quercus laurina Humb. & Bonpl., was investigated with 54 randomly amplified polymorphic DNA (RAPD) markers scored in 415 individuals from 16 populations representing the distribution area of the two species and a probable secondary hybrid zone. Genetic relationships among populations, depicted in a unweighted pair group method with arithmetic averaging (UPGMA) dendrogram, were largely incongruent with the morphological classification of populations as Q. affinis-like or Q. laurina-like that was obtained in previous studies. In contrast, the two main population clusters in the UPGMA dendrogram corresponded to the location of populations in two distinct geographical areas: southwestern and northeastern. A Mantel test confirmed a significant association between geographic and genetic distances among populations. Analyses of molecular variance (AMOVA) indicated that most genetic variation is contained within populations (84%), while 10.5% (P < 0.0001) is among populations, and 5.1% (P = 0.007) is between the two morphological groups. Differentiation between the southwestern and northeastern geographical groups (as recognized by the UPGMA), was 7.8% (P < 0.0001). The incongruence between genetic and phenotypic patterns suggests that introgression of neutral markers has been considerable between the two species in the hybrid zone, while morphological differentiation has remained comparatively stable.Key words: hybridization, population genetics, Quercus, RAPD markers.

scholarly journals Genetic Characterization of Hazelnut (Corylus avellana L.) Cultivars from Turkey Using Molecular Markers

HortScience ◽  
2009 ◽  
Vol 44 (6) ◽  
pp. 1557-1561 ◽  
Author(s):  
Salih Kafkas ◽  
Yıldız Doğan ◽  
Ali Sabır ◽  
Ali Turan ◽  
Hasbi Seker
Keyword(s):  
Molecular Markers ◽  
Genetic Relationships ◽  
Three Dimensional ◽  
Similarity Index ◽  
Polymorphic Marker ◽  
Corylus Avellana ◽  
Group Method ◽  
Arithmetic Average ◽  
Upgma Dendrogram ◽  
Pair Group

Genetic relationships among 18 Turkish hazelnut (Corylus avellana L.) cultivars were investigated using randomly amplified polymorphic DNA (RAPD), intersimple sequence repeat (ISSR), and amplified fragment length polymorphism (AFLP) markers. Twenty-five RAPD primers, 25 ISSR primers, and eight AFLP primer pairs generated a total of 434 polymorphic marker loci. The three marker systems were able to differentiate the cultivars. Genetic similarity index values ranged from a high of 0.96 for ‘Kan’ and ‘UzunMusa’ to a low of 0.73 for ‘Yassi Badem’ and ‘Kalinkara’. The genetic relationships were presented as an unweighted pair group method with arithmetic average (UPGMA) dendrogram and a three-dimensional principal coordinate analysis (PCoA) plot. The UPGMA dendrogram showed two main clusters, while PCoA analysis showed three groups. Cultivar-specific markers were produced by all marker systems for 10 cultivars. This study demonstrates the usefulness of molecular markers for identification of hazelnut cultivars.

scholarly journals Genetic Diversity of Major Greek Olive Cultivars Using Molecular (AFLPs and RAPDs) Markers and Morphological Traits

2005 ◽  
Vol 130 (2) ◽  
pp. 211-217 ◽  
Author(s):  
Marianna Hagidimitriou ◽  
Andreas Katsiotis ◽  
George Menexes ◽  
Constantinos Pontikis ◽  
Michael Loukas
Keyword(s):  
Morphological Traits ◽  
Genetic Relationships ◽  
Fruit Size ◽  
Correlation Coefficients ◽  
Group Method ◽  
Reference Database ◽  
Aflp Data ◽  
Cophenetic Correlation ◽  
Pair Group ◽  
Olive Cultivars

The aim of the present study was to develop a reliable reference database to discriminate between the major Greek olive (Olea europaea L.) cultivars and reveal their genetic relationships, since Greece is considered a secondary center of diversity. In order to establish genetic relationships among the 26 Greek and eight international cultivars, four amplified fragment length polymorphism (AFLP) primer pairs, 12 randomly amplified polymorphic DNA (RAPD) primers, along with measurements from 10 morphological traits, were used. A total of 576 AFLP and 113 RAPD markers were produced. Genetic similarities, estimated using the Jaccard algorithim, ranged from 0.45 to 0.83 for the AFLP data and 0.27 to 0.87 for the RAPD data. The cophenetic correlation coefficients between the genetic similarities and the unweighted pair group method of arithmetic averages (UPGMA) phenograms were 0.77 for the AFLPs, 0.81 for the RAPDs, and 0.69 for the morphological traits. However, limited clustering similarities among the phenograms derived from the three methods were observed. This was also reflected by the low correlation between the three genetic similarity matrices produced (AFLP and RAPD, r = 0.39; AFLP and morphological traits, r = 0.11; RAPD and morphological traits, r = 0.02). According to the molecular results, olive cultivars are clustered according to fruit size but not according to geographical origin. Three of the cultivars tested, `Vasilicada,' `Throumbolia', and `Lianolia Kerkiras', were found to branch distantly to the others, according to the AFLP results, and can be considered as ancient Greek cultivars.

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