scholarly journals Genetic variability of Indonesian eggplant (Solanum melongena) based on ISSR markers

2019 ◽  
Vol 20 (10) ◽  
Author(s):  
U.B. HUSNUDIN ◽  
B.S. DARYONO ◽  
Purnomo Purnomo
Keyword(s):  
Genetic Variability ◽  
Solanum Melongena ◽  
Similarity Index ◽  
Molecular Data ◽  
Issr Markers ◽  
Jaccard Coefficient ◽  
Sample Collection ◽  
Multivariate Statistical ◽  
Main Cluster ◽  
Pair Group

Abstract. Husnudin UB, Daryono BS, Purnomo. 2019. Genetic variability of Indonesian Eggplant (Solanum melongena) based on ISSR markers. Biodiversitas 20: 3049-3055. Eggplant (Solanum melongena L.) is one of important vegetable in Indonesia and this country has a variety of eggplant germplasm, whereas molecular data of Indonesian eggplant is limited. This study describes an analysis of genetic variation based on ISSR markers to determine the diversity and phenetic relationship of Indonesian eggplants. 23 samples were collected from the Indonesian Center for Agricultural Biotechnology Research and Development (ICABIOGRAD) and some commercial cultivars. Data were analyzed by ISSR analysis using UBC 809, UBC 880, UBC 888, UBC 892 and UBC 895 primers. Similarity index was counted by Jaccard Coefficient formula based on molecular scoring. Cluster analysis was conducted by Unweighted Pair Group Methods using Arithmetic averages (UPGMA) method to create a dendrogram with Multivariate Statistical Program (MVSP) v.3.1 software. The results showed that ISSR markers were effective in the estimation of the genetic variability of eggplant accessions characterized by different level of polymorphism. Five ISSR primers generated 40 polymorphic bands (64.5% of the total). The dendrogram divided 23 eggplant accessions into 2 main clusters and one accession ("terong jawa"/K18) located outside from the main cluster. Results suggested that all accessions were grouped randomly into some clusters not in accordance with the locations of sample collection.

scholarly journals Genetic variability of lemon basil (Ocimum × africanum Lour.) from Indonesian archipelago based on morphological and inter-simple sequence repeats markers

2020 ◽  
Vol 21 (12) ◽  
Author(s):  
Kurnia Makmur ◽  
TATIK CHIKMAWATI ◽  
SOBIR SOBIR
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Similarity Index ◽  
Morphological Characters ◽  
Molecular Data ◽  
Issr Markers ◽  
Morphological Observation ◽  
Indonesian Archipelago ◽  
Morphological And Molecular Data ◽  
Issr Primers

Abstract. Makmur K, Chikmawati T, Sobir. 2020. Genetic variability of lemon basil (Ocimum × africanum Lour.) from Indonesia based on morphological characters and ISSR markers. Biodiversitas 21: 5948-5953. Lemon basil (Ocimum × africanum Lour.) or kemangi is a highly beneficial plant, yet still underutilized. Therefore, providing necessary information on genetic diversity of this species is essential for further utilization. The aim of this study was to elucidate genetic diversity of 33 accessions of O. × africanum collected from four Islands of Indonesia along with three accessions of Ocimum basilicum L. Morphological observation was conducted on 37 morphological characters following the International Union for the Protection of New Varieties of Plants descriptor guidelines; subsequently, 13 ISSR primers were employed in molecular analysis. Both morphological and molecular data were analyzed based on simple matching similarity index using UPGMA method. Morphologically, O. × africanum and O. basilicum were clearly separated at the similarity index of 0.52, and among two species were divided into two groups according to two either character. ISSR analysis using 13 ISSR primers produced 111 DNA bands, and 108 of them (97.29%) were polymorphic. Cluster analysis based on ISSR data could not explicitly separate O. × africanum and O. basilicum accessions. Besides, Ocimum accessions collected from the same area did not always cluster into one group.

scholarly journals The Diversity And Classification Of Intraspecies Of Gembolo (Dioscorea Bulbifera L.) Based On Morphological Character

2018 ◽  
Vol 73 ◽  
pp. 04022
Author(s):  
Andri Prasetia ◽  
Purnomo ◽  
Budi Setiadi
Keyword(s):  
Morphological Character ◽  
Leaf Shape ◽  
Similarity Index ◽  
Morphological Characters ◽  
Multivariate Statistical ◽  
Pair Group ◽  
Group I ◽  
Dioscorea Bulbifera ◽  
Phenetic Relationship ◽  
Special Region

Gembolo (Dioscorea bulbifera L.) is a dioecious, annual, herbaceous, climbing plants and has heart-shaped leaves. Gembolo has aerial tubers (bulbil) and main tuber that has irregular shapes, as well as many rough roots at the base of the stem. The purpose of this research is to know the phenetic relationship of the germplasm of Gembolo in Special Region of Yogyakarta based on morphological character. The results of this study are expected to provide information on intraspecies diversity, phenetic relationship and Gembolo distribution. Gembolo plant samples were taken from D.I Yogyakarta. The sample was observed based on the difference of morphological character, so the number of accessions obtained from D.I Yogyakarta could be determined. Morphological characters would be described and characterized to determine the Operational Taxonomic Units (OTU’s). Based on morphological character data, then the grouping analysis was done by grouping analysis method and the dendrogram was formed by the method of Unweighted Pair Group Methods using Arithmetic averages (UPGMA) using Multivariate Statistical Program (MVSP) software version 3.1pc. The results showed that gembolo had morphological variation in tuber shape, stem color, leaf shape, leaf base shape and leaf tip shape. Based on the morphological characters, 2 main groups with the value of similarity index of 62,8% was formed. Group I consisted of four accessions with a similarity value of 85%. Group II consisted of eight accessions with a similarity value of 75%. A high similarity based on the morphological character on gembolo accession caused the gembolo plants in Special Region of Yogyakarta did not vary.

scholarly journals GENETIC VARIABILITY OF Rottboellia cochinchinensis POPULATIONS IN SUGARCANE FIELDS

2016 ◽  
Vol 34 (3) ◽  
pp. 475-484 ◽  
Author(s):  
A.R. SCHIAVETTO ◽  
D. PERECIN ◽  
L.R. PINTO ◽  
C.A.M. AZANIA ◽  
F.S. ZERA ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Genetic Similarity ◽  
Sao Paulo ◽  
The State ◽  
Group Method ◽  
Jaccard Coefficient ◽  
São Paulo ◽  
Pair Group ◽  
Analysis System ◽  
Rottboellia Cochinchinensis

ABSTRACT The hypothesis assumed was the existence of biotypes within populations, which has been the cause of difficulties in itchgrass control by farmers. For that, the genetic variability of three populations of Rottboellia cochinchinensis in sugarcane fields in the state of São Paulo was investigated by using the Amplified Fragment Length Polymorphism (AFLP) technique. Six primers were used to obtain molecular characterization data. AFLP gels were analyzed based on marker presence (1) and absence (0). Using NTSYs (Numerical Taxonomy and Multivariate Analysis System) software, the genetic similarity was calculated by the Jaccard coefficient and, from that, a dendrogram was built through the UPGMA (Unweighted Pair Group Method Arithmetic averages) method, besides determining the isopolymorphic marks. The average genetic similarities seen in the region was 0.742 for Igarapava, 0.793 for Mococa and 0.808 for Piracicaba. Between regions it was 0.730 (Igarapava vs Mococa), 0.735 (Mococa vs Piracicaba) and 0.694 (Igarapava vs Piracicaba). In line with the dendrogram, it is possible to detect the formation of two groups, one with 8 plants from Igarapava and Mococa and the other with 21 plants from Igarapava, Mococa and Piracicaba, as well as the presence of 1 discriminant individual from Piracicaba. It can be concluded that the genetic similarity among itchgrass populations from the state of São Paulo was high (72%), which denotes that the difficulties in chemical management are not only due to different biotypes but also due to other characteristics linked to tolerance of the species to herbicides. However, biotype existence cannot be discarded because of the polymorphic marks generating 22% average genetic variability.

scholarly journals Variations and Phenetic Analysis of Peanut Cultivars (Arachis hypogaea L.) Based on Morphological Characteristics

2019 ◽  
Vol 4 (1) ◽  
pp. 24
Author(s):  
Purnomo Purnomo ◽  
Nurul Khotimah
Keyword(s):  
Arachis Hypogaea ◽  
Similarity Index ◽  
Morphological Characteristics ◽  
Principal Component ◽  
Morphological Characters ◽  
Morphological Properties ◽  
Multivariate Statistical ◽  
Pair Group ◽  
Arachis Hypogaea L ◽  
Peanut Cultivars

Peanut (Arachis hypogaea L.) is a food commodity that is widely cultivated in Indonesia. At present there has been no analysis of the relationship between peanut cultivars with phenetic methods based on the morphological properties of the plants. Four cultivars of Arachis hypogaea L. Tuban, Talam 1, Talam 2, and Talam 3 used in this research. Morphological characters data was analyzed by description to construct identification key. Similarity index was counted by Simple Matching Coefficient (SSm) formula based on morphological scoring. Cluster analysis was conducted by UPGMA (Unweighted Pair Group Methods using Arithmetic Averages) method to construct dendrogram. PCA (Principal Component Analysis) were performed to defined role of each morphological character in grouping of accessions with MVSP (Multivariate Statistical Program) v. 3.1 software.  The dendrogram showed that four cultivars of Arachis hypogaea L. divided into two main clusters, 4 sub-clusters. The similarity index of clusters is 0.85%.

scholarly journals SIMILARITY RELATIONSHIPS AMONG GREEK MIDDLE MIOCENE TO EARLY - MIDDLE PLEISTOCENE MAMMAL ASSEMBLAGES

2018 ◽  
Vol 40 (1) ◽  
pp. 134 ◽  
Author(s):  
D. S. Kostopoulos ◽  
G. D. Koufos
Keyword(s):  
Small Mammal ◽  
Similarity Index ◽  
Middle Pleistocene ◽  
Group Method ◽  
Large Mammal ◽  
Main Cluster ◽  
Pair Group ◽  
Small Mammal Community ◽  
Mammal Assemblages ◽  
Similarity Relationships

The Greek fossil record of small and large mammal Local Faunal Assemblages is studied and compared by means of cluster analysis techniques using Jaccard similarity index and unweighted pair-group method. The analysis allow recognizing a good arrangement of the Greek LFAs according to time and a main cluster gap, corresponding to an important faunal renewal that, however, is not synchronous in the large and small mammal community. Minor groupings of large mammal faunas seem also to fit with main climatic trends, whereas the small mammal assemblage appears to undergo longer periods oftaxonomic stability

scholarly journals Developmental, morphological and molecular variation of commercial Ganoderma spp. accessions from southern Vietnam

2019 ◽  
Vol 20 (12) ◽  
Author(s):  
Viet The Ho ◽  
Thi Ngoc Ha Vo ◽  
Ngoc Giau Le
Keyword(s):  
Measurement Data ◽  
Molecular Data ◽  
Morphological Characterization ◽  
Issr Markers ◽  
Molecular Variation ◽  
Genetic Composition ◽  
Sample Collection ◽  
Morphological Variations ◽  
Southern Vietnam ◽  
Molecular Assisted Selection

Abstract. Ho VT, Vo TNH, Le NG. 2019. Developmental, morphological and molecular variation of commercial Ganoderma spp. accessions from southern Vietnam. Biodiversitas 20: 3684-3689. In Vietnam, the market value of Ganoderma spp. increases markedly recently due to the high demand as an effective medicine. However, the breeding programs for this mushroom are still less effective due to the poor knowledge of genetic composition. This study was conducted to investigate the diversity of some commercial Ganoderma spp. accessions from southern Vietnam using both traditional techniques using developmental and morphological characterization, and molecular method using ISSR markers. A total of nine Ganoderma spp. samples were collected from production areas and research institutes in southern provinces of Vietnam and targeted for developmental and molecular characterization. Developmental and morphological variations among accessions were evaluation. In addition, 20 ISSR markers were also utilized for further understanding genetic composition of these mushrooms. The obtained measurement data show a large variation among the studied Ganoderma spp. accessions in term of mycelia growth, diameter, shape, and dried weight of fruiting bodies. Molecular data from 20 ISSR markers also supported genetic variation of the examined samples. Based on the results of this study, the samples of Ganoderma spp. accessions from southern Vietnam can be divided into two main groups which are not correlated to geographical locations of sample collection sites. The results are potential for classification and provide new insights for molecular assisted selection of Ganoderma spp.

scholarly journals Studies on genetic variability of Capsicum frutescens var. Cakra Hijau induced by ethyl methane sulphonate (EMS) using SSR marker

2020 ◽  
pp. 125-131
Author(s):  
Nur Rahmattullah ◽  
Ramya Khrisnamurty ◽  
Kalaiselvi Senthil ◽  
Estri Laras Arumingtyas
Keyword(s):  
Genetic Variability ◽  
Morphological Traits ◽  
Ssr Marker ◽  
Polymorphic Information Content ◽  
Similarity Index ◽  
Capsicum Frutescens ◽  
Arithmetic Means ◽  
Phenotypic Characters ◽  
Pair Group ◽  
Methane Sulphonate

Genetic variability of wild type and EMS induced mutant cayenne peppers (Capsicum frutescens) var. Cakra Hijau is studied morphological traits and simple sequence repeat (SSR) markers. Phenotypic characters were investigated using standard pepper descriptors. The polymorphic SSR marker Ca19, Ca26, Ca52, Ca56, and Ca96were analyzed using unweighted pair group methods with arithmetic means (UPGMA) with Jaccard’s similarity index. The Polymorphic information content (PIC) value ranging from 0-0.228 with the highest index on Ca96. The Morphological traits showed of clusters (6 clades) with a lower cut-off value (0.2568) than SSR-based dendrogram did (4 clades; 0,5108). Therefore, genetic variability induced by EMS mutant were differentiated using morphological and SSR genotyping.

Assessment of genetic variability amongst cultivated populations of Khasi mandarin (Citrus reticulata Blanco) detected by ISSR

2021 ◽  
pp. 1-11
Author(s):  
Karishma Kashyap ◽  
Rasika M. Bhagwat ◽  
Sofia Banu
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Inter Simple Sequence Repeat ◽  
Northeast India ◽  
Issr Markers ◽  
Citrus Reticulata ◽  
Brahmaputra Valley ◽  
Indian Food ◽  
Cultivated Populations ◽  
High Level

Abstract Khasi mandarin (Citrus reticulata Blanco) is a commercial mandarin variety grown in northeast India and one of the 175 Indian food items included in the global first food atlas. The cultivated plantations of Khasi mandarin grown prominently in the lower Brahmaputra valley of Assam, northeast India, have been genetically eroded. The lack in the efforts for conservation of genetic variability in this mandarin variety prompted diversity analysis of Khasi mandarin germplasm across the region. Thus, the study aimed to investigate genetic diversity and partitioning of the genetic variations within and among 92 populations of Khasi mandarin collected from 10 cultivated sites in Kamrup and Kamrup (M) districts of Assam, India, using Inter-Simple Sequence Repeat (ISSR) markers. The amplification of genomic DNA with 17 ISSR primers yielded 216 scorable DNA amplicons of which 177 (81.94%) were polymorphic. The average polymorphism information content was 0.39 per primer. The total genetic diversity (HT = 0.28 ± 0.03) was close to the diversity within the population (HS = 0.20 ± 0.01). A high mean coefficient of gene differentiation (GST = 0.29) reflected a high level of gene flow (Nm = 1.22), indicating high genetic differentiation among the populations. Analysis of Molecular Variance (AMOVA) showed 78% of intra-population differentiation, 21% among the population and 1% among the districts. The obtained results indicate the existence of a high level of genetic diversity in the cultivated Khasi mandarin populations, indicating the need for preservation of each existing population to revive the dying out orchards in northeast India.

scholarly journals Chemical Fingerprinting of Cryptic Species and Genetic Lineages of Aneura pinguis (L.) Dumort. (Marchantiophyta, Metzgeriidae)

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 1180
Author(s):  
Rafał Wawrzyniak ◽  
Wiesław Wasiak ◽  
Beata Jasiewicz ◽  
Alina Bączkiewicz ◽  
Katarzyna Buczkowska
Keyword(s):  
Cluster Analysis ◽  
Cryptic Species ◽  
Plant Material ◽  
Chemical Constituents ◽  
Principal Component ◽  
Molecular Data ◽  
Rapid Identification ◽  
Multivariate Statistical ◽  
Genetic Lineages ◽  
Marker Compounds

Aneura pinguis (L.) Dumort. is a representative of the simple thalloid liverworts, one of the three main types of liverwort gametophytes. According to classical taxonomy, A. pinguis represents one morphologically variable species; however, genetic data reveal that this species is a complex consisting of 10 cryptic species (named by letters from A to J), of which four are further subdivided into two or three evolutionary lineages. The objective of this work was to develop an efficient method for the characterisation of plant material using marker compounds. The volatile chemical constituents of cryptic species within the liverwort A. pinguis were analysed by GC-MS. The compounds were isolated from plant material using the HS-SPME technique. Of the 66 compounds examined, 40 were identified. Of these 40 compounds, nine were selected for use as marker compounds of individual cryptic species of A. pinguis. A guide was then developed that clarified how these markers could be used for the rapid identification of the genetic lineages of A. pinguis. Multivariate statistical analyses (principal component and cluster analysis) revealed that the chemical compounds in A. pinguis made it possible to distinguish individual cryptic species (including genetic lineages), with the exception of cryptic species G and H. The classification of samples based on the volatile compounds by cluster analysis reflected phylogenetic relationships between cryptic species and genetic lineages of A. pinguis revealed based on molecular data.

scholarly journals Genetic variation among South Brazilian accessions of Lippia alba Mill. (Verbenaceae) detected by ISSR and RAPD markers

2009 ◽  
Vol 69 (2) ◽  
pp. 375-380 ◽  
Author(s):  
MF. Manica-Cattani ◽  
J. Zacaria ◽  
G. Pauletti ◽  
L. Atti-Serafini ◽  
S. Echeverrigaray
Keyword(s):  
Genetic Variability ◽  
Rapd Markers ◽  
Molecular Data ◽  
Chemical Characteristics ◽  
Hierarchical Analysis ◽  
Rio Grande Do Sul ◽  
Medicinal Species ◽  
Lippia Alba ◽  
Very High ◽  
Issr Primers

Twenty-seven accessions of Lippia alba Mill. collected in Rio Grande do Sul state, Brazil, were analysed by ISSR and RAPD markers to evaluate their genetic variability and relationships. Six ISSR primers and four RAPD primers generated 120 amplified fragments, most of which were polymorphics. The overall genetic variability among accessions was very high when compared with other plant species. The hierarchical analysis of molecular data (UPGMA) showed low relationship between accessions, and no grouping between accessions of the same chemotype. Canonical functions allowed identifying some variables related with the chemical characteristics of the essential oils. Both ISSR and RAPD markers were efficient to address the genetic diversity of L. alba, and may contribute to the conservation and breeding of this increasingly important aromatic and medicinal species.

Sign in / Sign up

Export Citation Format

Share Document