Assessment of genetic diversity and identification of core collection in sandalwood germplasm using RAPDs

Shashidhara, G. B.; Hema, M.; Koshy, Binu; Farooqi, A. A.

doi:10.1080/14620316.2003.11511659

Cited by 31 publications

(20 citation statements)

References 18 publications

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“…These results showed that the eight accessions of jelutong can be distinguished using these highly polymorphic primers. Similar results were observed in different plant species (Pither et al, 2003;Poerba, 2003;Shashidhara et al, 2003;Telles et al, 2003;Mori et al, 2004;Runo et al, 2004;Singh et al, 2005;Sarkhosh et al, 2006;Fernandez et al, 2006;Parjanto et al, 2006).…”

Section: Primer Screening and Rapd Profile Analysessupporting

confidence: 72%

“…Consistency of DNA bands produced indicated that RAPD markers can be used for distinguishing variation of D. costulata tested. Similar results was also observed in various plant for identifying individual plant, clone or cultivar (Shashidhara et al, 2003;Mori et al, 2004;Runo et al, 2004;Fernandez et al, 2006;Sarkhosh et al, 2006).…”

Section: Pcr Optimationsupporting

confidence: 70%

“…Eight accessions of D. costulata collected from those areas are used for developing a protocol of DNA extraction and isolation, optimation of DNA amplification with Polymerase Chain Reaction (PCR), and primer using RAPD marker. RAPD analyses is used because of its simple and cost effective, and the analyses has been used with other species of tropical timber trees (Rath et al, 1998;Shashidhara et al, 2003;Pither et al, 2003;Telles et al, 2003;Mori et al, 2004;Runo et al, 2004;Singh et al, 2005;Sarkhosh et al, 2006) and used for other identification purposes (Poerba, 2003;Fernandez et al, 2006;Parjanto et al, 2006,).…”

Section: Introductionmentioning

confidence: 99%

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Primer Screening for Dyera costulata (Miq) Hook.f Random Amplified Polymorphic DNA Analyses

Poerba

Widjaya

2008

Biodiversitas

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Dyera costulata (Miq.) Hook.f (Apocynaceae) is a large tree of the lowland tropical rain forest of Southeast Asia, Thailand, Malay Peninsula and Indonesia, especially in Sumatra and Kalimantan (Borneo) islands. Its economic value was in its copious latex, used as gum in the manufacture of chewing gum. Today the timber of this species is much sought after for the manufacture of pencils and picture frames. Information on genetic diversity of the species is very limited. Hence studies were initiated to screen primers for RAPD analyses of Dyera costulata for use in genetic variation studies. Seventy one Operon primers (10 mer) were used to generate a total of 864 consistent and ambiguous amplification products ranging from 200 bp to 2.0 kb. Rare and genotype specific bands were identified which could be effectively used to distinguish the genotypes. 34 highly polymorphic primers (100%) are recorded from 71 primers used. Three primers (OPA-04, OPU-06, and OPU-07) produced highest variable RAPD profiles. The dendrogram separated the 8 genotypes into 2 groups. Genetic dissimilarity ranged from 0.07 to 0.71 %.

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Section: Primer Screening and Rapd Profile Analysessupporting

confidence: 72%

Section: Pcr Optimationsupporting

confidence: 70%

Section: Introductionmentioning

confidence: 99%

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Primer Screening for Dyera costulata (Miq) Hook.f Random Amplified Polymorphic DNA Analyses

Poerba

Widjaya

2008

Biodiversitas

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“…Additionally, management costs in field banks are usually higher than those to maintain seed banks, they are highly vulnerable to environmental conditions, and field analyses are usually a lengthy and costly process, as it may be necessary waiting for several years from planting the trees to obtain their first crop. Molecular markers provide here a cost-feasible alternative that can be used on young, non-bearing trees, but nowadays the examples of the use of molecular markers to develop core collections in woody perennial species are yet restricted to few cases in apple (Laquidain et al, 2005;Volk et al, 2005), pear (Santesteban et al, 2008), table grapevine (Jiménez-Cantizano et al, 2008), cashew (Dhanaraj et al, 2002), sandalwood (Shashidhara et al, 2003) or cherimoya (Escribano et al, 2008). Two important issues in the context of using molecular markers for constructing core collections could explain this.…”

Section: Introductionmentioning

confidence: 99%

Assessment of the genetic and phenotypic diversity maintained in apple core collections constructed by using either agro-morphologic or molecular marker data

Santesteban

Jiménez

Royo

2009

Span. j. agric. res.

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Various types of data have been used for sampling plant core collections, including morphological, agronomic and ecogeographical traits, and molecular and biochemical markers. However, little is known about the ability of woody perennial core collections to retain the diversity and structure of the whole collection for characters that were not considered in the selection, especially when molecular markers are used. In this study, three core subsets were established for the apple germplasm bank curated at the Public University of Navarre (UPNa, Spain): based upon the diversity found with 10 SSR markers, another based upon the diversity assessed with 12 isozyme loci; and a third based upon morpho-agronomic diversity evaluated by 23 morpho-agronomic traits. Comparisons between these three subsets and to the whole collection were assessed to determine the impact of the data used in the selection on phenotypic and genetic diversity and on their population structure. The three subsets had a similar diversity and they did not differ from the original collection, according to Nei and Shannon-Weaver indices. The allelic/class frequencies were also always maintained in the three subsets. Overall, the kind of data used to constitute a core collection had little influence on the phenotypic and genetic diversity retained, so in the case of apple collections the use of molecular markers is preferable for this task because they allow a rapid and reliable characterization.Additional key words: characterization, germplasm, isozyme, Malus × domestica, microsatellite, pomology, stepwise clustering. Resumen Evaluación de la diversidad genética y fenotípica retenida en colecciones nucleares de manzano formadas a partir de caracterizaciones agro-morfológicas o molecularesLas colecciones nucleares de plantas pueden formarse a partir de la información obtenida en caracterizaciones morfológicas, agronómicas o eco-geográficas, así como a partir de caracterizaciones bioquímicas o moleculares. Un aspecto poco estudiado de la formación y validación de colecciones nucleares es la capacidad de éstas para conservar la estructura y diversidad de la colección global en aquellos caracteres que no han sido empleados para formar la colección nuclear. En el presente estudio se determinaron tres colecciones nucleares para el Banco de Germoplasma de Manzano de la Universidad Pública de Navarra: para el primero se emplearon los datos de caracterización de 10 marcadores SSR, la segunda fue formada a partir de la caracterización hecha con 12 loci de isoenzimas, y la tercera se construyó a partir de la información proporcionada por 23 caracteres morfo-agronómicos. Se comparó la estructura y diversidad genotípica y fenotípica de las tres colecciones, entre sí y respecto de la colección original, para determinar el impacto que sobre dicha estructura y diversidad tenía el tipo de dato con que se formó la colección nuclear. Las tres colecciones conservaron una diversidad similar y no difirieron de la original en sus índices de Nei y Shannon-Weaver, y ...

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“…From the PCA of the 38 accessions, it was evident that some of the accessions were found overlapping each other depicting redundancy which should be eliminated. Since there are diferent strategies for developing a core collection using morphological or marker data, however molecular markers are more stable and eicient in estimating the genetic relatedness among the individuals [65,66].…”

Section: Discussionmentioning

confidence: 99%

Evaluation of Genetic Diversity in Chlorophytum borivilianum (Santp. and Fernan.) Using Molecular Markers: An Endangered Medicinal Plant

Samantaray¹,

Ngangkham²

2017

Active Ingredients From Aromatic and Medicinal Plants

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Chlorophytum borivilianum is a traditional medicinal plant distributed throughout the tropics and subtropics. In the present investigation, RAPD and ISSR analyses were used to assess the genetic diversity among 21 accessions collected from diferent geographical regions of India using 20 RAPD primers and 6 ISSR primers. RAPD and ISSR primers revealed 92.26% and 82.76% polymorphism, respectively. Similarity in coeicient values ranged from 0.321 to 0.707 for RAPD and 0.363 to 0.846 for ISSR markers. The dendrogram developed by RAPD and ISSR marker-based analysis grouped the 21 accessions into diferent clusters. Mantel test employed for detection of goodness of it established the cophenetic correlation value for both the primer systems and it was observed to be signiicant. Clustering of accessions within groups was also similar based on RAPD-and ISSR-derived dendrograms. In our study, both marker systems were similar except for the percentage polymorphism which was found to be greater using RAPD, thus indicating the greater efectiveness of RAPD primers for estimating genetic variation of C. borivilianum.

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Assessment of genetic diversity and identification of core collection in sandalwood germplasm using RAPDs

Cited by 31 publications

References 18 publications

Primer Screening for Dyera costulata (Miq) Hook.f Random Amplified Polymorphic DNA Analyses

Primer Screening for Dyera costulata (Miq) Hook.f Random Amplified Polymorphic DNA Analyses

Assessment of the genetic and phenotypic diversity maintained in apple core collections constructed by using either agro-morphologic or molecular marker data

Evaluation of Genetic Diversity in Chlorophytum borivilianum (Santp. and Fernan.) Using Molecular Markers: An Endangered Medicinal Plant

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