scholarly journals GENETIC VARIABILITY OF INDONESIAN PAPAYA ACCESSIONS AS REVEALED BY RANDOM AMPLIFIED POLYMORPHIC DNA AND MORPHOLOGICAL CHARACTERIZATION

2019 ◽  
Vol 20 (1) ◽  
pp. 1
Author(s):  
Riry Prihatini ◽  
Tri Budiyanti ◽  
Noflindawati Noflindawati
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Accurate Method ◽  
Morphological Characters ◽  
Morphological Characterization ◽  
Fruit Shape ◽  
Morphological Data ◽  
Group Method ◽  
Pair Group

<p class="abstrakinggris">Diverse papaya (<em>Carica</em> sp.) accessions are found in many regions in Indonesia, but their genetic diversity have not yet been studied. Random Amplified Polymorphic DNA (RAPD) is a simple yet accurate method that can be used to examine the genetic diversity of papaya. The study aimed to examine the genetic diversity of Indonesian papaya accessions using RAPD markers and morphological characters. The RAPD was applied on 23 papaya accessions using 30 primers. The appearing bands were further analyzed with the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and Principal Component Analysis (PCA). The molecular results were then compared to the fruit morphological data, including fruit shape, size, flesh color, texture, and flavor. The RAPD analysis revealed that the 23 papaya accessions clustered into six main clades with Dice-Sorensen coefficient similarity ranged from 0.71 to 0.98. The first group consisted of 11 accessions, including both the hybrids and local accessions. The second group consisted of eight accessions especially six Indonesian hybrids, a Mexican Hybrid and a Hawaiian hybrid. The other four groups had a single member namely Sicincin Panjang, Lokal Sumani, Cariso, and Carica. The molecular grouping, however, did not align with the fruit character grouping. Overall, it was implied that the Indonesian papaya accessions were genetically narrow, of which some accessions were closely related to Hawaiian and Mexican accessions. These results can be used as a reference on papaya crossbreeding program in Indonesia.</p>

scholarly journals Molecular techniques in the assessment of genetic relationships between populations of Consolida (Ranunculaceae)

Caryologia ◽  
2021 ◽  
Vol 74 (2) ◽  
pp. 149-161
Author(s):  
Jing Ma ◽  
Wenyan Fan ◽  
Shujun Jiang ◽  
Xiling Yang ◽  
Wenshuai Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Morphological Characters ◽  
Mantel Test ◽  
Molecular Techniques ◽  
Group Method ◽  
Plant Resources ◽  
High Genetic Diversity

Genetic diversity studies are essential to understand the conservation and management of plant resources in any environment. The genus Consolida (DC.) Gray (Ranuculaceae) belongs to tribe Delphinieae. It comprises approximately 52 species, including the members of the genus Aconitella Spach. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Consolida genetic diversity. Therefore, we collected and analyzed 19 species from 12 provinces of regions. Overall, one hundred and twenty-seven plant specimens were collected. We showed significant differences in quantitative morphological characters in plant species. Unweighted pair group method with arithmetic mean and principal component analysis (PCA) divided Consolida species into two groups. All primers produced polymorphic amplicons though the extent of polymorphism varied with each primer. The primer OPA-06 was found to be most powerful and efficient as it generated a total of 24 bands of which 24 were polymorphic. The Mantel test showed correlation (r = 0.34, p=0.0002) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Consolida species can adapt to changing environments since high genetic diversity is linked to species adaptability. Present results highlighted the utility of RAPD markers and morphometry methods to investigate genetic diversity in Consolida species. Our aims were 1) to assess genetic diversity among Consolida species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa.

scholarly journals Description and analysis of genetic diversity among squash accessions

2009 ◽  
Vol 52 (2) ◽  
pp. 271-283 ◽  
Author(s):  
Athanasios L. Tsivelikas ◽  
Olga Koutita ◽  
Anastasia Anastasiadou ◽  
George N. Skaracis ◽  
Ekaterini Traka-Mavrona ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Clustering Algorithm ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Molecular Data ◽  
Optimal Number ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group

In this work, the part of the squash core collection, maintained in the Greek Gene Bank, was assessed using the morphological and molecular data. Sixteen incompletely classified accessions of the squash were characterized along with an evaluation of their resistance against two isolates of Fusarium oxysporum. A molecular analysis using Random Amplified Polymorphic DNA (RAPD) markers was also performed, revealing high level of polymorphism. To study the genetic diversity among the squash accessions, a clustering procedure using Unweighed Pair Group Method and Arithmetic Average (UPGMA) algorithm was also adopted. Two independent dendrograms, one for the morphophysiological and one for molecular data were obtained, classifying the accessions into two and three main clusters, respectively. Despite the different number of the clusters there were many similarities between these two dendrograms, and a third dendrogram resulting from their combination was also produced, based on Gower's distance and UPGMA clustering algorithm. In order to determine the optimal number of clusters, the upper tail approach was applied. The more reliable clustering of the accessions was accomplished using RAPD markers as well as the combination of the two different data sets, classifying the accessions into three significantly different groups. These groups corresponded to the three different cultivated species of C. maxima Duch., C. moschata Duch., and C. pepo L. The same results were also obtained using Principal Component Analysis.

scholarly journals Evaluation of genetic diversity in geranium (Geraniaceae) using RAPD marker

Genetika ◽  
2021 ◽  
Vol 53 (1) ◽  
pp. 363-378
Author(s):  
Juan Yin ◽  
Majid Khayatnezhad ◽  
Abdul Shakoor
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Morphological Characters ◽  
Mantel Test ◽  
Group Method ◽  
Plant Resources ◽  
High Genetic Diversity ◽  
Pair Group ◽  
Genetic Structure Of Populations

Genetic diversity studies are essential to understand the conservation and management of plant resources in any environment. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Geranium genetic diversity. Therefore, we collected and analyzed thirteen species from nine provinces. Overall, one hundred and twenty-five plant specimens were collected. Our aims were 1) to assess genetic diversity among Geranium species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. Unweighted pair group method with arithmetic mean and multidimensional scaling divided Geranium species into two groups. G. sylvaticum depicted unbiased expected heterozygosity (UHe) in the range of 0.11. Shannon information was high (0.38) in G. columbinum. G. sylvaticum showed the lowest value, 0.14. The observed number of alleles (Na) ranged from 0.25 to 0.55 in G. persicum and G. tuberosum. The effective number of alleles (Ne) was in the range of 1.020-1.430 for G. tuberosum and G. collinum. Gene flow (Nm) was relatively low (0.33) in Geranium. The Mantel test showed correlation (r = 0.27, p=0.0002) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Geranium species can adapt to changing environments since high genetic diversity is linked to species adaptability. Present results highlighted the utility of RAPD markers and morphometry methods to investigate genetic diversity in Geranium species.

scholarly journals Morphological and genetic diversity of Senecio vulgaris L. (Asteraceae) in Iran

2021 ◽  
Vol 80 (2) ◽  
Author(s):  
Mostafa Ebadi ◽  
Rosa Eftekharian
Keyword(s):  
Genetic Diversity ◽  
Principal Component ◽  
Morphological Characters ◽  
Mantel Test ◽  
Morphological Data ◽  
Principal Coordinates Analysis ◽  
Cauline Leaf ◽  
Senecio Vulgaris ◽  
Molecular Features ◽  
Principal Coordinates

Senecio vulgaris L., an annual herb belonging to the Asteraceae, is widely distributed in different regions of the world. There is no information on the intraspecific variations of the morphological and molecular features of this species. In the present investigation, we studied the morphological and genetic diversity of 81 accessions of S. vulgaris collected from 10 geographical populations. Eleven inter simple sequence repeat (ISSR) primers were used for the examination of genetic variations among the populations. Analysis of molecular variance (AMOVA) and GST analyses revealed significant differences among the investigated populations. A significant correlation between genetic distance and geographical distance was revealed by the Mantel test. However, reticulation analysis indicated the occurrence of gene flow among most of the populations studied. Principal component analysis (PCA) plot showed that the number of capitula, length of the cauline leaf and plant height were the most variable morphological characters. Principal coordinates analysis (PCoA) plot revealed two groups of populations, according to molecular and morphological data. The results suggested the existence of possible intraspecific taxonomic ranks within this species.

scholarly journals Morphologic and molecular assessments of cucumber (Cucumis sativus L.) landraces

2020 ◽  
Vol 48 (2) ◽  
pp. 604-614
Author(s):  
Esra CEBECI ◽  
Volkan GOZEN ◽  
Levent KESKIN ◽  
Aytul YILDIRIM
Keyword(s):  
Genetic Diversity ◽  
Cucumis Sativus ◽  
Polymorphic Marker ◽  
Morphological Data ◽  
Group Method ◽  
Srap Marker ◽  
Discrimination Power ◽  
Cucumis Sativus L ◽  
Pair Group ◽  
Morphologic Data

In this study, 90 locally grown cucumber (Cucumis sativus L.) landraces were collected and morphologically characterized using 20 descriptors derived from UPOV (International Union for the Protection of New Varieties of Plants). Genetic diversity and relationships of the genotypes were revealed using 20 sequence-related amplified polymorphism (SRAP) marker combinations. The discrimination power of each polymorphic marker (estimated by the polymorphism information content) ranged from 0.15 to 0.99 with an average of 0.73. Dice's similarity coefficient ranged between 0.00-1.00. The cluster analysis that was conducted using the unweighted pair group method of arithmetic averages (UPGMA) for both molecular and morphologic data showed that all of the genotypes fell into two main groups and many subdivisions. According to morphological data, fruit length, diameter and weight of the genotypes were determined between 6.5 - 32.5 cm, 25 - 52 mm and, 28 - 625 g respectively. It is clear from the results, a moderate level of genetic diversity, which has the potential for broadening the genetic base, was observed among the Turkish cucumber landraces.

scholarly journals Blueberry Cultivar Identification Using Random Amplified Polymorphic DNA and Sequence-characterized Amplified Region Markers

HortScience ◽  
2017 ◽  
Vol 52 (11) ◽  
pp. 1483-1489 ◽  
Author(s):  
Kang Hee Cho ◽  
Seo Jun Park ◽  
Su Jin Kim ◽  
Se Hee Kim ◽  
Han Chan Lee ◽  
...  
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
The United States ◽  
Morphological Characters ◽  
Polymorphic Band ◽  
Group Method ◽  
Highbush Blueberry ◽  
United States Department ◽  
Scar Markers ◽  
Sequence Characterized Amplified Region ◽  
Pair Group

Blueberry cultivars have traditionally been identified based on the evaluation of sets of morphological characters; however, distinguishing closely related cultivars remains difficult. In the present study, we developed DNA markers for the genetic fingerprinting of 45 blueberry cultivars, including 31 cultivars introduced from the United States Department of Agriculture. We obtained 210 random amplified of polymorphic DNA (RAPD) markers using 43 different primers. The number of polymorphic bands ranged from three (OPG-10 and OPQ-04) to eight (OPR-16), with an average of five. A cluster analysis performed with the unweighted pair group method using arithmetic averages produced genetic similarity values among the blueberry cultivars ranging from 0.53 to 0.85, with an average similarity of 0.68. A dendrogram clustered the 45 blueberry cultivars into two main clusters, with a similarity value of 0.65. Cluster I consisted of four rabbiteye cultivars (Pink Lemonade, Alapaha, Titan, and Vernon) and the Ashworth northern highbush cultivar. Cluster II consisted of 31 northern highbush cultivars, eight southern highbush blueberry cultivars, and Northland half-highbush blueberry cultivar. Fifty five RAPD fragments selected were sequenced to develop sequence-characterized amplified region (SCAR) markers, resulting in the successful conversion of 16 of 55 fragments into SCAR markers. An amplified polymorphic band has the same size as the RAPD fragment or smaller according to the primer combinations in the 16 SCAR markers. Among these markers, a combination of 11 SCAR markers provided sufficient polymorphisms to distinguish the blueberry cultivars investigated in this study. These newly developed markers could be a fast and reliable tool to identify blueberry cultivars.

scholarly journals Assessment of Genetic Diversity in Cultivated Tomato (Solanum Lycopersicum L.) Genotypes Using Rapd Primers

2013 ◽  
Vol 21 (1) ◽  
pp. 83-89 ◽  
Author(s):  
Saida Sharifova ◽  
Sabina Mehdiyeva ◽  
Konstantinos Theodorikas ◽  
Konstantinos Roubos
Keyword(s):  
Genetic Diversity ◽  
Rapd Analysis ◽  
Diversity Index ◽  
Random Amplified Polymorphic Dna ◽  
Arithmetic Mean ◽  
Similarity Coefficient ◽  
Group Method ◽  
Solanum Lycopersicum L ◽  
Pair Group ◽  
Upgma Cluster Analysis

Abstract Random Amplified Polymorphic DNA (RAPD) analysis was carried out on 19 Azerbaijan tomato genotypes, both cultivars and local populations. A total of 26 amplified products were revealed by 6 primers. The genetic similarity among evaluated genotypes ranged from 0.188 to 1.000. The lowest similarity was observed between cultivars ‘Azerbaijan’ and ‘Shakar’ (0.188), while the highest between ‘Elnur’ and ‘Garatag’ (1.000). The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster analysis based on Jaccard’s similarity coefficient divided genotypes into four main groups. The first group was the largest and consisted of 12 genotypes, while the fourth group was the smallest consisted of 1 genotype only. The most polymorphic primer was OPB-18 that presented a genetic diversity index of 0.823, while the least informative was primer OPG-17 with an index of 0.349. The average genetic diversity calculated from RAPD data was 0.665.

The use of RAPD markers to distinguish among juniper and cedar cultivars

2000 ◽  
Vol 78 (5) ◽  
pp. 655-659 ◽  
Author(s):  
Tom Hsiang ◽  
Junbin Huang
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Unknown Origin ◽  
Genetic Distances ◽  
Group Method ◽  
Pair Group ◽  
Juniperus Chinensis ◽  
Juniperus Scopulorum ◽  
Close Relatives

Two species of Chamaecyparis and six cultivars each of Juniperus chinensis L. and Juniperus scopulorum Sarg. (Cupressaceae) were subjected to random amplified polymorphic DNA (RAPD) analysis using seven primers. Unweighted pair group method with averages (UPGMA) and principal component analyses of genetic distances between cultivars showed that 42 polymorphic RAPD bands could distinguish among all cultivars and properly group them by species and genera. Where the origin of a specific juniper cultivar is uncertain, analysis of genetic distance can pinpoint close relatives. For example, we were unable to trace the origin of J. chinensis 'Alps', and we initially thought it was a mislabeled J. chinensis 'Blue Alps'. However, we found 'Alps' to be closer to J. chinensis 'Fairview' and 'Mountbatten' than to 'Blue Alps'. Similarly, 'Wichita Blue' has an unknown origin, but it had the highest genetic similarity with 'Medora'.Key words: juniper, cedar, RAPD, cultivars, phylogenetics.

scholarly journals Evaluation of Genetic Diversity among Persian Fig Cultivars by Morphological Traits and RAPD Markers

HortScience ◽  
2018 ◽  
Vol 53 (5) ◽  
pp. 613-619 ◽  
Author(s):  
Ghazal Baziar ◽  
Moslem Jafari ◽  
Mansoureh Sadat Sharifi Noori ◽  
Samira Samarfard
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Hierarchical Cluster ◽  
Fruit Trees ◽  
Group Method ◽  
Fars Province ◽  
Pair Group

Ficus carica L. is one of the most ancient fruit trees cultivated in Persia (Iran). The conservation and characterization of fig genetic resources is essential for sustainable fig production and food security. Given these considerations, this study characterizes the genetic variability of 21 edible F. carica cultivars in the Fars Province using random amplified polymorphic DNA (RAPD) markers. The collected cultivars were also characterized for their morphological features. A total of 16 RAPD primers produced 229 reproducible bands, of which, 170 loci (74.43%) were polymorphic with an average polymorphic information content (PIC) value of 0.899. Genetic analysis using an unweighted pair-group method with arithmetic averaging (UPGMA) revealed genetic structure and relationships among the local germplasms. The dendrogram resulting from UPGMA hierarchical cluster analysis separated the fig cultivars into five groups. These results demonstrate that analysis of molecular variance allows for the partitioning of genetic variation between fig groups and illustrates greater variation within fig groups and subgroups. RAPD-based classification often corresponded with the morphological similarities and differences of the collected fig cultivars. This study suggests that RAPD markers are suitable for analysis of diversity and cultivars’ fingerprinting. Accordingly, understanding of the genetic diversity and population structure of F. carica in Iran may provide insight into the conservation and management of this species.

scholarly journals Agro-morphological characterization based genetic diversity of Indonesian local rice germplasm

2021 ◽  
Vol 948 (1) ◽  
pp. 012004
Author(s):  
I W Mulsanti ◽  
A Risliawati ◽  
N Yunani
Keyword(s):  
Genetic Diversity ◽  
Principal Component Analysis ◽  
Quantitative Data ◽  
Morphological Traits ◽  
Principal Component ◽  
Morphological Characters ◽  
Morphological Characterization ◽  
Tiller Number ◽  
Rice Germplasm ◽  
Productive Tiller

Abstract The present study was carried out to characterize 103 Indonesian local rice germplasm on the basis of 20 agro-morphological traits. The local rice germplasm originated from Riau and Jambi province in Sumatera island. Principal Component Analysis (PCA) was used to analyzed 11 quantitative data. PCA explained the genetic diversity of the rice germplasm accession. Most of the morphological characters showed variation in different accession. PC1 and PC2 explained about 32.5% and 22.1% of the variability, respectively. PCI and PC2 mostly related with traits such as productive tiller number (PTN), vegetative tiller number (VTN), plant height (PH), and culm length (CL). PCA-Biplot showed accession from Jambi and Riau manage to be separated, even though the PCA percent is only 54.6%. Accession originated from Riau marked by number of tillers (PTN, VTN), and grain weight (GW) traits. Based on cluster analysis, rice germplasm grouped in to 4 main clusters. Most of the accession from Jambi and Riau grouped in the same cluster, which is cluster I. Whereas eight local accessions from Riau grouped in the same cluster separately (cluster II). Two accession which are Padi Jarum (Acc 2711) and Ketan Hitam (Acc 9300) are individually, separated from others.

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