Genetic diversity in natural populations of Gmelina arborea: implications for breeding and conservation
24
Citation
31
Reference
10
Related Paper
Citation Trend
Keywords:
Fixation index
Gmelina
Dendrogram
UPGMA
Morphological and molecular characterization of forty rice (Oryza sativa L.) accessions using 14 agro-botanical traits recommended by IRRI and 10 RAPD primers, respectively, was done in a field experiment in an augmented randomized complete block design. The aim of the work was to study variations and to select lines that can be used as potential parents in a future breeding programme. A principal components plot and, a dendrogram generated by cluster analysis using the unweighted pair group method with arithmetic mean (UPGMA) based on distance measures assessed for mean values of the morphological variables were used to group the accessions. Genetic relatedness among accessions based on RAPD molecular marker data (57 RAPD bands) was also presented in the bands form of a dendrogram generated by cluster analysis using (UPGMA). The relative effectiveness of the RAPD markers compared to botanical descriptors in assessing diversity among the accessions was investigated. A dendrogram was created by the UPGMA for morphological data and the 40 accessions classified into six morphological groups, whereas PCA re-ordered the accessions into four broad groups that had within cluster similarities and inter-cluster differences in morphological variation. Reaction products (bands) of the RAPD analysis were highly polymorphic, more discriminatory and informative as they were able to differentiate more pairs of accessions than the botanical descriptors. IITA rice accessions TOX 3052-46-3-3-2-1 and TOX 3027-44-1-E4-2-2 and Brazilian accessions (CL SELECCION 3B and 450) performed better in terms of yield, total tillers and number of filled tillers than accessions used as checks and could be selected for a future breeding programme.
UPGMA
Dendrogram
Cite
Citations (2)
Daluga (Cyrtosperma merkusii (Hassk.) Schott) is one of the edible cormus belonging to Araceae which has not been cultivated in Indonesia. Morphological evaluation and characterization are needed to determine characters of Daluga for genetic variability to improve edible Daluga variants, so this research aims to determine the diversity and the phenetic relationship of Daluga based on morphological traits. Thirty-six accessions were collected from Siau, Sangihe and Talaud (Salibabu and Karakelang) Islands and there were eleven variants of Daluga. Cluster analysis was conducted by UPGMA (Unweighted Pair Group Methods using Arithmetic Average) methods to construct a dendrogram using MultiVariate Statistical Program (MSVP) version 3.1 software. The dendrogram showed that 11 variants of Daluga in fourteen sampling sites divided into two main clusters, cluster A consisted of eight variants whereas cluster B consisted of three variants which each cluster are divided into two sub-clusters. The result of the phenetic analysis showed that the variant 1 and 4 are two variants that are a very close relationship with the percent similarity is 73.6%. This new information is important for the future of the plant varietal improvement program and for the conservation of Daluga.
UPGMA
Dendrogram
Cite
Citations (2)
Two separate experiments were carried out between local and exotic apple among the locally available varieties. Ten varieties of local apple (Malus spp.) were selected from South west Nigeria. The choice of the samples was based on observed morphological differences such as size of fruits, fruits color, flower color, leaf shape and plant height while the choice of imported exotic type was based solely on the color of the fruit. Total genomic DNA was isolated from local and exotic apples separately and assessed with RAPD markers. Nine primers generated a total of forty-six polymorphic bands, which were used to generate a UPGMA dendrogram. The dendrogram consists of a single cluster from 0 – 65% similarity coefficient. At 71%, two clusters were discerned with sample 6 and 7 having separated from the clusters. However, two samples 3 and 4 tied at 87% showing the possibility of very close relationships. Two local apples (green and red color) and one exotic apple (green color) were analyzed with 132 bands from 16 polymorphic primers. The dendrogram generated showed a closer relationships between green exotic and green local varieties of apple.
Key words: Apple, RAPD, UPGMA, polymorphic.
UPGMA
Dendrogram
Malus
Similarity (geometry)
Genetic relationship
Cite
Citations (10)
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
Dendrogram
UPGMA
Jaccard index
Similarity (geometry)
Cite
Citations (1)
Fifteen species belonging to 3 genera (Onobrychis, Hedysarum and Sartoria), collected from different geographical regions of Turkey were studied for the polypeptide patterns of their seed storage proteins. The variability of seed storage proteins was analysed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). As many as 72 bands were scored and a dendrogram was constructed using UPGMA (unweighted pair group method with arithmetic mean). The dendrogram of the electrophoretic protein profiles of seeds showed 2 main clusters. While the first cluster with further subclusters included Onobrychis species, the second cluster included Sartoria and Hedysarum species present in 2 separate subclusters. The results showed that Sartoria and Hedysarum are closer to each other than they are to Onobrychis. It is also suggested that Sartoria hedysaroides should be included in the genus Hedysarum. Additionally, it is concluded that seed storage protein profiles could be useful markers in studies of genetic diversity, genetic relationships, and classification of adapted cultivars.
UPGMA
Dendrogram
Cite
Citations (24)
Seed storage proteins of 18 lentil accessions of the following Lens taxa: L. culinaris, L. orientalis, L. odemensis, L. nigricans, L. ervoides, L. lamottei, L. tomentosus and L. lenticula, were analyzed by sodium dodecyl sulfate polyacrilamide gel electrophoresis (SDS-PAGE). All visible polypeptide bands were scored for presence or absence and data were used for dendrogram construction by UPGMA method. Three clusters were formed at the dendrogram: the first one integrated accessions of L. orientalis and L. odemensis; the second cluster joined L. culinaris and L. tomentosus accessions, and related to them L. lamottei species, the third cluster included L. nigricans and L. ervoides accessions. Species affiliation of accessions L. orientalis k-2861, L. nigricans k-2859 and L. nigricans k-2860 was confirmed. Taxonomic position of L. lenticula k-2858 accession was not determined exactly.
UPGMA
Dendrogram
Sodium dodecyl sulfate
Cite
Citations (3)
For this purpose, 18 cucumber lines were evaluated for their genetic diversity using six morphological characterizations (plant morphology, plant length, length of leaf blade, fruit length, fruit diameter and fruit stem length) and eight AFLP markers. These AFLP primer combinations amplified well and also showed polymorphism. Thus, 1975 AFLP fragments were obtained and 1468 fragments were polymorphic (75.34%). Dendrograms were drawn using UPGMA (Unweighted Pair Group Method) arithmetical averages and according to the UPGMA dendrogram, the cucumber accessions clustered into two main groups. The genetic distances of the dendrogram varied between 0.92 and 0.96. Cluster analysis based on morphological data discriminated all lines into three major clusters in UPGMA dendrogram. The similarity coefficient ranged between 0.888 and 0.982 indicating that the cucumber lines used in the study have a low level of genetic variation. Results obtained from the phylogenetic dendrogram by 8 pairs of AFLP primers were consistent with those from the UPGMA clustering analysis, which were in according with the morphological taxonomy on cucumber.
UPGMA
Dendrogram
Cucumis
Genetic distance
Cite
Citations (2)
UPGMA
Dendrogram
Numerical taxonomy
Similarity (geometry)
Hierarchical clustering
Cite
Citations (0)
Bermudagrass [Cynodon dactylon (L.) Pers.], an important turfgrass used in public parks, home lawns, golf courses and sports fields, is widely distributed in China. In the present study, sequence-related amplified polymorphism (SRAP) markers were used to assess genetic diversity and population structure among 157 indigenous bermudagrass genotypes from 20 provinces in China. The application of 26 SRAP primer pairs produced 340 bands, of which 328 (96.58%) were polymorphic. The polymorphic information content (PIC) ranged from 0.36 to 0.49 with a mean of 0.44. Genetic distance coefficients among accessions ranged from 0.04 to 0.61, with an average of 0.32. The results of STRUCTURE analysis suggested that 157 bermudagrass accessions can be grouped into three subpopulations. Moreover, according to clustering based on the unweighted pair-group method of arithmetic averages (UPGMA), accessions were divided into three major clusters. The UPGMA dendrogram revealed that accessions from identical or adjacent areas were generally, but not entirely, clustered into the same cluster. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among accessions. Principal coordinate analysis (PCoA) with SRAP markers revealed a similar grouping of accessions to the UPGMA dendrogram and STRUCTUE analysis. Analysis of molecular variance (AMOVA) indicated that 18% of total molecular variance was attributed to diversity among subpopulations, while 82% of variance was associated with differences within subpopulations. Our study represents the most comprehensive investigation of the genetic diversity and population structure of bermudagrass in China to date, and provides valuable information for the germplasm collection, genetic improvement, and systematic utilization of bermudagrass.
UPGMA
Dendrogram
Cynodon dactylon
Germ plasm
Genetic distance
Cite
Citations (56)
UPGMA
Dendrogram
Molecular marker
Phytochemical
Similarity (geometry)
Cite
Citations (13)