scholarly journals Genetic diversity of Pericopsis mooniana from South Kalimantan based on Random Amplified Polymorphism DNA (RAPD) Markers

2021 ◽  
Vol 914 (1) ◽  
pp. 012029
Author(s):  
V Yuskianti ◽  
P Sulistyawati
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Seed Orchard ◽  
Ex Situ ◽  
Natural Distribution ◽  
Total Genetic Diversity ◽  
Two Samples ◽  
Residential House ◽  
Relationship Of ◽  
Random Amplified Polymorphism Dna

Abstract The genetic diversity and relationship of Pericopsis mooniana collected from Pulau Laut, South Kalimantan, was analyzed using RAPD markers. Currently, the natural distribution of P. mooniana in Pulau Laut no longer exists. Instead, PT Inhutani II, as the concession holder in the area, had collected the remaining P.mooniana and planted it in the seed orchard, arboretum, or around PT Inhutani’s mess/office. Forty-two samples from four locations: mess/residential house (3), seed orchard (33), arboretum (3), and PT Inhutani II Unit Stagen (3) were analyzed using seven RAPD primers. Our study showed that the total genetic diversity of all populations was low (He = 0.191 ± 0.013). P. mooniana collected from seed orchards had the highest diversity (He = 0.289 ± 0.021), while the lowest was from mess/residential houses (He = 0.134 ± 0.025). The genetic relationship data indicated the possibility that P. mooniana from mess/residential house, arboretum, and seed orchard may come from the same origin. These results can be used to support the development of ex-situ conservation plots to avoid inbreeding depression. At the same time, the genetic diversity will be helpful in its conservation and further utilization, such as establishing the plantations to reduce the pressure of the species in nature and provide valuable timber production in Indonesia.

Evaluation of molecular diversity of ex situ conserved germplasm of palmyrah (Borassus flabellifer L.) accessions using RAPD markers

2016 ◽  
Vol 44 (2) ◽  
Author(s):  
Jiji George, K.T. Venkataramana, ◽  
P. Nainar M.K. Rajesh ◽  
Anitha Karun
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationship ◽  
Tamil Nadu ◽  
Andhra Pradesh ◽  
Rapd Markers ◽  
Molecular Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Ex Situ ◽  
Random Samples ◽  
Relationship Of

The genetic relationship of 96 palmyrah palms, consisting of 24 indigenous accessions from Tamil Nadu and Andhra Pradesh, was investigated using Random Amplified Polymorphic DNA (RAPD) markers. Hundred and eighty primers were used initially to identify the polymorphic primers in six random samples and 10 polymorphic primers were selected to amplify the 96 palms. These 10 primers produced a total of 112 reproducible bands and out of them, 41 fragments (36.6 %) showed polymorphism.  The number of bands produced with each primer varied from seven to 15 with an average of 11.2 bands per primer.  The percent polymorphism ranged from 7.7 to 71.4 with an average of 37.4 per cent when all the primers were taken collectively.  UPGMA grouped all the accessions into two major clusters at 0.85 similarity value. The highest similarity value (0.96) was observed between the accessions KLKM-8 and THY-54 and the lowest similarity value (0.782) was obtained between ANBI-17 and RCML-11. The relatively low polymorphism suggests a narrow genetic diversity of palmyrah populations from which the present accessions have been derived and maintained over the years.

Genetic diversity of mocó cotton (Gossypium hirsutum race marie-galante) from the northeast of Brazil: implications for conservation

Botany ◽  
2010 ◽  
Vol 88 (8) ◽  
pp. 765-773 ◽  
Author(s):  
Ivandilson Pessoa Pinto de Menezes ◽  
Paulo Augusto Vianna Barroso ◽  
Lúcia Vieira Hoffmann ◽  
Valeska Silva Lucena ◽  
Marc Giband
Keyword(s):  
Genetic Diversity ◽  
Gossypium Hirsutum ◽  
Geographic Origin ◽  
Rio Grande ◽  
Ex Situ ◽  
High Genetic Diversity ◽  
Breeding Programs ◽  
Extinction Process ◽  
Total Genetic Diversity ◽  
High Level

Mocó cotton ( Gossypium hirsutum  L. race marie-galante (Watt) Hutch.) is a potential source of valuable alleles for breeding programs, mainly because of its great adaptability to semi-arid conditions. With the aim of quantifying mocó cotton genetic variability, 187 plants collected in the northeast of Brazil were evaluated using 12 microsatellite markers. A total of 62 alleles were amplified, ranging from three to eight polymorphic alleles per locus. Total genetic diversity was high (0.52), and when measured on a per state basis, was of 0.37 on average. The population showed a low level of heterozygozity (HO = 0.16), reflecting a high level of endogamy (FIS = 0.67). Phylogenetic analysis using the neighbor-joining method revealed that plants sampled in different states tended to cluster according to their geographic origin, except for those collected in the states of Paraíba and Rio Grande do Norte, which grouped together. Plants from the state of Piauí formed two groups, one with an apparent allelic contribution from G. barbadense, while the second group of plants was closer to those from the states of Paraíba and Rio Grande do Norte. Despite the high genetic diversity that was observed in the remaining populations, urgent conservation efforts should be undertaken, owing to the high level of endogamy and accelerated extinction process that characterizes these populations. Such efforts should focus on the collection and ex situ maintenance of representative genetic diversity.

scholarly journals Genetic Diversity between Yacon Landraces from Different Countries Based on Random Amplified Polymorphic DNAs

2011 ◽  
Vol 41 (No. 2) ◽  
pp. 73-78 ◽  
Author(s):  
L. Milella ◽  
J. Salava ◽  
G. Martelli ◽  
I. Greco ◽  
E.F. Cusimamani ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Genetic Relationship ◽  
Genetic Similarity ◽  
Morphological Traits ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Coefficient ◽  
Crop Germplasm ◽  
Relationship Of

Random amplified polymorphic DNA (RAPD) markers are widely used for evaluating the genetic relationship of crop germplasm. Five different landraces of yacon (Smallantus sonchifolius (Poepp. and Hendl.) H. Robinson; Asteraceae) collected in various countries and showing different morphological traits were investigated using a total of 61 decamer primers. A total of 282 RAPD markers were scored and 28.7% of them were polymorphic at least within landraces. RAPD markers generated by one primer (OBP14) discriminated between all landraces. Markers were used to calculate genetic similarity coefficient and to build a dendrogram representing the genetic relationship between analysed landraces. The results suggest that RAPD markers could be used as a reliable tool to perform fingerprinting studies in Smallantus sonchifolius genome. This is the first report on the use of RAPDs to evaluate genetic distance and to distinguish between different landraces in yacon.  

scholarly journals Assessment of the genetic diversity among oily spot (Xanthomonas axonopodis pv. punicae) pathogen of pomegranate by randomly amplified polymorphic DNA analysis

2015 ◽  
Vol 7 (2) ◽  
pp. 1006-1011
Author(s):  
Wayde Jitendra Eknath ◽  
Akshay S. Dange ◽  
Trishala A. Pagar ◽  
Deepak Rameshwar Sapkal ◽  
Monika Bansal
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Punica Granatum ◽  
Economic Loss ◽  
Xanthomonas Axonopodis ◽  
Major Region ◽  
Relationship Of ◽  
Punica Granatum L

Pomegranate (Punica granatum L.) is an important fruit crop of India and other subtropical countries. Bacterial blight caused by Xanthomonas axonopodis pv. Punicae is becoming a major threat in Maharashtra as well as other states of India. It causes yield losses up to the extent of 80 – 90 %. This study aims to the collection of 7 strains (X. axonopodis) and utilized for assessment of genetic diversity by using RAPD markers. Whereas 7 strains of X. axonopodis were differentiated and distinguished into seven major region representing Malegaon, Nampur, Satana, Khakurdi, Ramnagar, Rahuri and Nashik region. However the genetic similarity within 7strains of X. axonopodis was ranged between 72.72-100 %. Similarly the genetic relationship of strains X. axonopodis was also established and showed 72.72 %, 72.72 %, 72.72 % 92.30%, 94.11% and 100 % similarity with region of Malegaon, Nampur, Satana, Khakurdi, Ramnagar, Rahuri and Nashik region. Average polymorphism in strains of X. axanopodis based on RAPD analysis was 84.095 %. The combine data analysis by using UPGMA method also revealed the two distinct groups representing seven strains of X. axonopodis and in first group M1 and second group R4 and subgroup RH6, N2, NS7, S3, K5, these genotypes were present respectively. Considering predominance and economic loss caused by X. axonopodis pv. punicae in pomegranate, it is an essential to undertake preliminary work on characterization of this pathogen at the molecular level.

scholarly journals STUDY OF GENETIC DIVERSITY AND ANALYSIS OF THE DEGREE OF SIMILARITY IN SOME APPLE AND PLUM VARIETIES USING RAPD MARKERS

2021 ◽  
Vol 37 (37) ◽  
pp. 19-26
Author(s):  
Adina Iancu ◽  
◽  
Mihai Chivu ◽  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Rapd Markers ◽  
The Other ◽  
Ex Situ ◽  
Allelic Polymorphism ◽  
High Genetic Diversity ◽  
Ex Situ Collection ◽  
Plum Varieties ◽  
Degree Of Similarity

Molecular evaluation of germplasm is an important step in breeding programs, and the application of molecular biological techniques has led to important results in terms of both within- and between-species variability of traits. The RAPD technique has been successfully used to reveal allelic polymorphism as well as to measure genetic similarity. In this study, the genetic diversity of 25 genotypes and cultivars for apple species and 26 genotypes and cultivars for plum species was assessed with six RAPD markers. All these cultivars belong to the ex situ collection of apple and the ex situ collection of plum at the Research Institute for Fruit Growing Pitesti. The average number of amplified bands was 19.2 for apple and 17.66 for plum. Statistical analysis of intraspecific allelic polymorphism was expressed using the PIC (Polymorphic Information Content) index, which takes into account the allelic frequency. Two statistical indices were used to quantify genetic diversity: the Shannon index and the Simpson index. The degree of similarity between varieties was analyzed using the NTSYSpc version 2.1. Following RAPD analyses, the allele sizes of the analyzed varieties were within the range quoted in the literature, the genetic profiles of the studied varieties suggesting a medium to high genetic diversity, except for markers OPBC-04 and OPBB-05 for plum species, which expressed a high genetic diversity. Genetic distances calculated based on polymorphism of migrated bands in agarose gel confirmed the known genealogies of the apple and plum varieties studied. Thus, the smallest genetic distance for apple species was found between 'Jonagold' and 'Golden Delicious', 'Pionier' and 'Rustic', 'Jonathan' and 'Idared', 'Wagener Premiat' and 'Granny Smith', 'Remar' and 'Aura', 'Romus 3' and 'Rome Beauty', and the largest between Malus floribunda and the other genotypes studied. In plum, the smallest genetic distance was found between 'Dani' and 'Tita', 'Roman' and 'Tuleu gras', 'Dara' and 'Haganta', 'Romanța' and 'Stanley', 'Anna Spath' and 'Renclod Violet', and the largest between 'Lama', 'Black Diamond' and the other genotypes studied.

scholarly journals Assessment of Genetic Diversity in Five Nicaraguan Populations of Cedrela odorata L. (Meliaceae) using RAPD Markers

Encuentro ◽  
2016 ◽  
pp. 28-39
Author(s):  
Arlen Tijerino ◽  
Lourdes Callejas ◽  
David A. Cerda-Granados
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Rapd Markers ◽  
Diversity Index ◽  
Random Amplified Polymorphic Dna ◽  
Natural Populations ◽  
Cedrela Odorata ◽  
Total Genetic Diversity ◽  
Geographical Distances ◽  
The Mean

The goal of this study was to assess the genetic diversity of Nicaraguan populations of Cedrela odorata using Random Amplified Polymorphic DNA (RAPD) markers. Thus, genomic DNA was isolated from leaf samples collected from ninety-two trees belonging to five Nicaraguan natural populations of C. odorata. The mean number of alleles per locus, effective number of alleles per locus, percentage of polymorphic loci, genetic diversity (He ) of Nei and diversity index (Ho ) of Shannon were estimated for each population assuming that the populations were in HardyWeinberg equilibrium. Total genetic diversity was partitioned in intrapopulational and interpopulational diversity using Nei’s genetic differentiation (GST) and through an Analysis of Molecular Variance (AMOVA). The ΦST matrix was used to construct a dendrogram by the neighbor-joining method. According to values of both He and Ho , Esquipulas (Deparment of Matagalpa) presented the lowest diversity level; while La Trinidad (Department of Estelí) showed the highest diversity level. Genetic differentiation was calculated obtaining a GST value of 13.36%. AMOVA also showed a similar differentiation value ΦST =13.81%). Neighbour-joining dendrogram clustered the five populations in two groups, where the group formed by La Trinidad and El Refugio (Department of Granada) presented the biggest differentiation. Correlation between genetic and geographical distances was not found.

461 PB 292 MAPPING RAPD MARKER DIVERSITY IN PHASEOLUS VULGARIS

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 497c-497
Author(s):  
Paul Skroth ◽  
Jim Nienhuis ◽  
Geunhwa Jung ◽  
Dermont Coyne
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Rapd Marker ◽  
Plant Genetic Resources ◽  
Ex Situ ◽  
Good Tool ◽  
Germplasm Collections ◽  
Efficient Construction ◽  
Two Populations

Knowledge of genetic relationships and genetic diversity among accessions is essential for the efficient construction, maintainance and utilization of large ex-situ germplasm collections. Furthermore, streamlining of large collections into care collections necessitates validation of germplasm sampling techniques. DNA molecular markers provide potentially unbiased estimators of genome diversity end may facilitate organization, maintainance, and sampling of plant genetic resources. Our data suggests that RAPD markers will be o good tool for testing tore collection concepts and organizing genetic diversity in common bean. However, the genomic distribution of markers is unknown. Currently we are using recombinant inbred (RI) populations to place RAPD markers in the context of the bean genetic map. We hove evaluated the the distribution of RAPD markers in three RI populations: Bat93 × Jalo EEP558, PC50 × Xan159, and BAC6 × HT7719. Cultivated P.vulgaris has two primary renters of diversity Mesoamerican and Andean, the RI populations used for mapping RAPD markers ore Meso × Andean, Andean × Andean, and Meso × Meso crosses respectively. In the Bat93 × Jalo EEP558 population 383 markers have been mapped for a map length of 735 cM. However, approximately 150 of these markers ore members of 9 dusters which span only 90 cM. This inter gone pool mop is being integrated with linkage mops constructed in the other two populations to compare within and between gene pool marker distributions and to evaluate clustering of markers on the different mops. Implications for the application of RAPD markers will be discussed.

Genetic diversity of three Israeli wild relatives of wheat from the Sitopsis section of Aegilops

2018 ◽  
Vol 65 (3-4) ◽  
pp. 161-174
Author(s):  
Hanan Sela ◽  
Smadar Ezrati ◽  
Pablo D. Olivera
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Geographic Distance ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Wild Relatives ◽  
Structured Populations ◽  
Ex Situ ◽  
Total Genetic Diversity ◽  
Wheat Wild Relatives

Israel is rich in wheat wild relatives. Some of the species have a restricted geographic distribution, grow in small populations, and are subjected to habitat fragmentation. To better conserve and exploit these species there is a need to characterize the genetic structure of ex situ collections. The population structure and genetic diversity of three wheat wild relatives from the genus Aegilops were studied. Collections of the species Ae. longissima (23 accessions), Ae. sharonensis (105 accessions) and Ae. speltoides (157 accessions) from the Institute for Cereal Crops Improvement (ICCI), Tel-Aviv University were genotyped using genotyping by sequencing (GBS) technique. Principal Component Analysis (PCA) revealed different and similar diversity patterns among the species. All species had differences between northern and southern populations, however, in Ae. sharonensis there was a more significant component differentiating western and eastern populations. Some of the southeast accessions of Ae. sharonensis clustered together with the northern - coastal Ae. longissima accessions away from the rest of the Ae. longissima and Ae. sharonensis accessions. Ae. sharonensis collection has shown much more population differentiation than Ae. speltoides collection while in Ae. speltoides the total genetic diversity within populations diversity was higher. Ae. sharonensis population structure was more correlated with geographic distance while Ae. speltoides population structure has shown less structured populations and less correlation with geographic distance. Ae. sharonensis population structure was also correlated with soil type and humidity while in Ae. speltoides northern collection no correlation with the environment was found. The evolutionary and conservation perspectives of these finding are discussed.

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