scholarly journals Morphological and molecular studies of three species of Boerhavia L. from Ile-Ife, Nigeria

2020 ◽  
Vol 22 (2) ◽  
pp. 225-236
Author(s):  
S.O. Azeez ◽  
J.O. Matthew ◽  
E.A. Olaoluwa ◽  
G.B. Adegboyega ◽  
I.O. Akinyoola
Keyword(s):  
Cluster Analysis ◽  
Phylogenetic Relationship ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Pollen Grains ◽  
Morphological Characters ◽  
Morphological Data ◽  
Group Method ◽  
Wide Range ◽  
High Level

A wide range of plasticity and polymorphism have been documented in the genus Boerhavia. More so, the possible presence of natural hybrids  among the species of the genus has made species identification more difficult. This study employed morphological characters, pollen parameters as well as Random Amplified Polymorphic DNA (RAPD) to identify and elucidate the phylogenetic relationship that exists among the three species of Boerhavia distributed in Ile-Ife, Nigeria. Qualitative and quantitative morphological characters were observed and measured respectively. The acetolysis of the pollen grains was carried out according to Erdtman method. Fresh and young leaves of the Boerhavia species studied were  collected for genomic DNA extraction using modified Dellarpota procedure. The quality and concentration of DNA was assessed by gel electrophoresis on 2% agarose with known concentrations of undigested lambda DNA. Subsequently, the DNA quantification was done according to standard measurement. The Principal Components Analysis of the morphological traits and the pollen grain studies indicated that the three Boerhavia species studied have a very high level of relationship. However, the Single Linkage Cluster Analysis of the morphological data and the unweighted pair group method with arithmetic mean (UPGMA) cluster analysis of RAPD data revealed that B. erecta is distantly related to B. coccinea and B. diffusa. Despite the fact that the three Boerhavia species studied possess high level of similarity, they can still be distinguished from each other. In conclusion, B. coccinea and B. diffusa are more closely related to each other than B. erecta. Key words: RAPD marker, Pollen grains, Phylogenetic relationship, Polymorphism

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 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 Determination of genetic variations among different Trichoderma isolates using RAPD marker in Bangladesh

1970 ◽  
Vol 9 (1) ◽  
pp. 9-20 ◽  
Author(s):  
MSI Sagar ◽  
MB Meah ◽  
MM Rahman ◽  
AK Ghose
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Genetic Variations ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
High Level ◽  
Cluster 2

Some Trichoderma isolates were collected from different locations of Bangladesh for evaluating their bioefficiency by determining their genetic variations. PCR-based Random Amplified Polymorphic DNA (RAPD) Marker employing 3 decamer primers produced 29 scorable bands of which all (100%) were polymorphic. The co-efficient of gene differentiation (Gst) was 1.0000 reflecting the existence of high level of genetic diversity among the isolates. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei’s (1972) genetic distance produced 2 main clusters (16 isolates in cluster 1 and 19 isolates in cluster 2). The result indicating their genetic diversity has opened new possibility of using the most efficient and more isolates of Trichoderma in the preparation of effective biopesticide. Keywords: Genetic diversity; Trichoderma; RAPD DOI: http://dx.doi.org/10.3329/jbau.v9i1.8738 JBAU 2011; 9(1): 9-20

scholarly journals Overview of the Genetic Diversity of African Macrotermes (Termitidae: Macrotermitinae) and Implications for Taxonomy, Ecology and Food Science

Insects ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 518
Author(s):  
Bronwyn Egan ◽  
Zwannda Nethavhani ◽  
Barbara van Asch
Keyword(s):  
Negative Impact ◽  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Food Science ◽  
Cryptic Diversity ◽  
African Species ◽  
Genetic Groups ◽  
Wide Range ◽  
Coi Sequences ◽  
High Level

Macrotermes termites play important ecological roles and are consumed by many communities as a delicacy and dietary complement throughout Africa. However, lack of reliable morphological characters has hampered studies of Macrotermes diversity in a wide range of scientific fields including ecology, phylogenetics and food science. In order to place our preliminary assessment of the diversity of Macrotermes in South Africa in context, we analysed a comprehensive dataset of COI sequences for African species including new and publicly available data. Phylogenetic reconstruction and estimates of genetic divergence showed a high level of incongruity between species names and genetic groups, as well as several instances of cryptic diversity. We identified three main clades and 17 genetic groups in the dataset. We propose that this structure be used as a background for future surveys of Macrotermes diversity in Africa, thus mitigating the negative impact of the present taxonomic uncertainties in the genus. The new specimens collected in Limpopo fell into four distinct genetic groups, suggesting that the region harbours remarkable Macrotermes diversity relative to other African regions surveyed in previous studies. This work shows that African Macrotermes have been understudied across the continent, and that the genus contains cryptic diversity undetectable by classic taxonomy. Furthermore, these results may inform future taxonomic revisions in Macrotermes, thus contributing to advances in termitology.

scholarly journals The Genetic Variability of Sicilian Lemon Germplasm Revealed by Molecular Marker Fingerprints

2008 ◽  
Vol 133 (2) ◽  
pp. 242-248 ◽  
Author(s):  
Mirko Siragusa ◽  
Fabio De Pasquale ◽  
Loredana Abbate ◽  
Letizia Martorana ◽  
Nicasio Tusa
Keyword(s):  
Dna Markers ◽  
Random Amplified Polymorphic Dna ◽  
Citrus Limon ◽  
Genetic Isolation ◽  
Breeding Programs ◽  
Bud Mutation ◽  
Italian Regions ◽  
Wide Range ◽  
High Level ◽  
Polymorphic Nature

There is a high level of diversity among lemons [Citrus limon (L.) Burm. f. (2n = 2x = 18)] in Sicily, where each growing area has a wide range of landraces mostly derived from bud mutation. Because this variability represents an important resource for future breeding programs and genetic improvement, the relationships among the principal 36 accessions of Sicilian lemon, belonging to three different cultivars (Femminello, Monachello, and Lunario), were examined by intersimple sequence repeat and random amplified polymorphic DNA markers. Three ‘Femminello’ accessions from nearby Italian regions were also examined to study the genetic flow from the continent. The disputed case of the accession ‘Eureka Messina lemon’ was also examined, using ‘Frost Eureka’ as a control. Our results confirmed the extreme polymorphic nature of the three principal Sicilian cultivars and the presence of a wide range of different genotypes. Twenty-two Sicilian genotypes were recognized as unique accessions, reflecting the richness of the lemon germplasm present in Sicily. Each growing area showed the presence of several genetically different landraces, probably preserved by genetic isolation, whereas the continental accessions appeared extremely similar to the island genotypes, showing an exchange of germplasm from the island to the continent.

scholarly journals Systematic Evaluation of Landrace Tea Populations in Northern Sichuan, China, Based on Morphology, DNA Markers, and Biochemistry Analyses

HortScience ◽  
2018 ◽  
Vol 53 (8) ◽  
pp. 1095-1101
Author(s):  
Li-Qiang Tan ◽  
Xin-Yu Wang ◽  
Hui Li ◽  
Guan-Qun Liu ◽  
Yao Zou ◽  
...  
Keyword(s):  
Dna Markers ◽  
Gene Diversity ◽  
Germplasm Conservation ◽  
Dry Weight ◽  
Morphological Characters ◽  
Systematic Evaluation ◽  
Total Amino Acid ◽  
Wide Range ◽  
High Level ◽  
Selection Of

Landrace tea populations are important recourses for germplasm conservation and selection of elite tea clone cultivars. To understand their genetic diversity and use them effectively for breeding, two traditional landrace tea populations, Beichuan Taizicha (BCTZ) and Nanjiang Dayecha (NJDY), localized to northern Sichuan, were evaluated for morphological characters, simple sequence repeat (SSR)–based DNA markers and the contents of biochemical components. A wide range of morphological variation and a moderately high level of DNA polymorphism were observed from both BCTZ and NJDY. NJDY had on average, bigger leaves, larger flowers, higher total catechins (TCs), and greater gene diversity (GD) than BCTZ. Interestingly, samples from BCTZ had a wide range in the ratio of galloylated catechins to nongalloylated catechins (G/NG) (1.83–8.12, cv = 48.8%), whereas samples from NJDY were more variable in total amino acid (TAA) content (25.3–50.8 mg·g−1 dry weight) than those from BCTZ. We concluded that the two Camellia sinensis landrace populations are of great interest for both individual selection breeding and scientific studies.

Development of DNA fingerprinting keys for the identification of radish cultivars

2004 ◽  
Vol 44 (1) ◽  
pp. 95 ◽  
Author(s):  
A. Pradhan ◽  
G. Yan ◽  
J. A. Plummer
Keyword(s):  
Dna Fingerprinting ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Morphological Characteristics ◽  
Group Method ◽  
Base Pairs ◽  
Difference Matrix ◽  
Pair Group ◽  
Young Leaves ◽  
Polymerase Chain

Identification of cultivars is extremely important both for cultivation and breeding of crop plants. Cultivar identification based on morphological characteristics can be difficult and complicated. Polymerase chain reaction technologies, such as random amplified polymorphic DNA (RAPD) analysis, can readily and quickly identify cultivars using seeds and young leaves. Sixty individuals representing 7 radish cultivars were examined for RAPD marker polymorphism. Based on the polymorphism generated, 5 primers were selected, out of the 14��examined, to fingerprint the cultivars. The 5 primers produced a total of 52 fragments, 6 monomorphic and 46�polymorphic fragments, ranging in size from 206 to 2258 base pairs. A total and mean character difference matrix was calculated based on the RAPD data and a dendrogram was constructed using the unweighted pair-group method with arithmetic averages (UPGMA). Three DNA fingerprinting keys were developed for the 7 cultivars and 5 markers derived from 3 primers was the minimum required to distinguish cultivars. Results demonstrated that RAPD markers could be effectively used for the identification of radish cultivars.

scholarly journals Variability among selective guava (Psidium guajava L.) varieties revealed by morphology and RAPD marker

2018 ◽  
Vol 7 (2) ◽  
pp. 89-98 ◽  
Author(s):  
Farzana Alam ◽  
Kazi Didarul Islam ◽  
SM Mahbubur Rahman
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Scientific Information ◽  
Psidium Guajava ◽  
Morphological Characterization ◽  
Evolutionary Changes ◽  
Wide Range ◽  
The Difference ◽  
Range Of Variation

The research was conducted for the assessment of genetic diversity using both morphological and random amplified polymorphic DNA (RAPD) analysis of twelve guava (Psidium guajava L.) varieties growing in Bangladesh. Morphological characterization of guava varieties showed a wide range of variation. The highest variability was observed between Poly and Jelly varieties.Polymerase chain reaction with 5 arbitrary 10-mer and 3 arbitrary 12- mer RAPD primers produced a total of 50 bands of which 75.23 percent were polymorphic. The highest percentage of polymorphic loci (100%) was observed for primer A and the lowest (50%) for A03 primer. The UPGMA dendrogram revealed the segregation pattern and the difference of evolutionary changes. Guava varieties were separated into two main groups, one of them was made up of Chineese, Jelly, Kazi, Apple, L-49, Local-2 and Local-3. The other one was made up of Local-1, Poly, Kashi, Thai and Bombay. The highest genetic distance between Apple and Kazi peyara indicate that these varieties might be interesting in breeding programme for improving trait of interest. This scientific information could be used for further improvement of guava. Jahangirnagar University J. Biol. Sci. 7(2): 89-98, 2018 (December)

scholarly journals A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth–Death Process

2019 ◽  
Vol 69 (2) ◽  
pp. 325-344 ◽  
Author(s):  
Arong Luo ◽  
David A Duchêne ◽  
Chi Zhang ◽  
Chao-Dong Zhu ◽  
Simon Y W Ho
Keyword(s):  
Morphological Characters ◽  
Nucleotide Sequences ◽  
Tree Topology ◽  
Molecular Dating ◽  
Morphological Data ◽  
Death Process ◽  
Joint Analysis ◽  
Nucleotide Sequence Data ◽  
Wide Range ◽  
Birth Death

Abstract Bayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is tip-dating, which explicitly includes fossil data in the analysis. This can be done, for example, through the joint analysis of molecular data from present-day taxa and morphological data from both extant and fossil taxa. In the context of tip-dating, an important development has been the fossilized birth–death process, which allows non-contemporaneous tips and sampled ancestors while providing a model of lineage diversification for the prior on the tree topology and internal node times. However, tip-dating with fossils faces a number of considerable challenges, especially, those associated with fossil sampling and evolutionary models for morphological characters. We conducted a simulation study to evaluate the performance of tip-dating using the fossilized birth–death model. We simulated fossil occurrences and the evolution of nucleotide sequences and morphological characters under a wide range of conditions. Our analyses of these data show that the number and the maximum age of fossil occurrences have a greater influence than the degree of among-lineage rate variation or the number of morphological characters on estimates of node times and the tree topology. Tip-dating with the fossilized birth–death model generally performs well in recovering the relationships among extant taxa but has difficulties in correctly placing fossil taxa in the tree and identifying the number of sampled ancestors. The method yields accurate estimates of the ages of the root and crown group, although the precision of these estimates varies with the probability of fossil occurrence. The exclusion of morphological characters results in a slight overestimation of node times, whereas the exclusion of nucleotide sequences has a negative impact on inference of the tree topology. Our results provide an overview of the performance of tip-dating using the fossilized birth–death model, which will inform further development of the method and its application to key questions in evolutionary biology.

Morphologic variation in the USDA/ARS rhubarb germplasm collection

2009 ◽  
Vol 8 (1) ◽  
pp. 35-41 ◽  
Author(s):  
Alberto Pantoja ◽  
Joseph C. Kuhl
Keyword(s):  
Germplasm Collection ◽  
Morphological Characters ◽  
Morphological Data ◽  
Skin Colour ◽  
Base Thickness ◽  
Flesh Colour ◽  
Combining Data ◽  
Wide Range ◽  
Morphologic Variation ◽  
The Mean

Rhubarb includes approximately 60 species in the genusRheum. It has been utilized for thousands of years for medicinal purposes, but only recently identified for its culinary use. In the mid 1700s, edible petioles were discovered on seedlings from rhubarb species. Hundreds of cultivars have since been identified for a wide range of uses from tarts to wine. Unfortunately, propagation by seed and irregular naming has resulted in a plethora of similarly named cultivars and multitude of phenotypes. Fifteen morphological characters were evaluated to differentiate rhubarb cultivars in the USDA, ARSRheumcollection in Palmer, Alaska. Two years of morphological data, focusing on horticultural characteristics indicated variation between the years. To improve cultivar resolution, the results suggest using 1 year's data instead of combining data from different years. The mean °Brix observed was 3.8, with a range from 2.2 to 6.1. Flesh colour and basal skin colour were poorly correlated (R2 = 0.462); overall skin colour was more red at the base than in the middle of the petiole. Rhubarb character categories, in particular petiole number and petiole base thickness, need to be modified to better anticipate the range of expected values, and thereby contribute improved reproducibility and reliability to separate cultivars based on morphological characters.

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