Random genomic scans at microsatellite loci for genetic diversity estimation in cold-adaptedLepidium latifolium

2012 ◽  
Vol 10 (3) ◽  
pp. 224-231 ◽  
Author(s):  
Atul Grover ◽  
Sanjay Mohan Gupta ◽  
Pankaj Pandey ◽  
Sadhana Singh ◽  
Zakwan Ahmed
Keyword(s):  
Genetic Diversity ◽  
Molecular Marker ◽  
Geographical Area ◽  
Arid Environment ◽  
Molecular Data ◽  
Inter Simple Sequence Repeat ◽  
Microsatellite Sequence ◽  
Novel Approach ◽  
Genome Walker ◽  
Ecological Importance

Lepidium latifoliumL. (Brassicaceae) grows successfully in a high-altitude cold arid environment. Little molecular data are available for this plant despite its immense ecological importance as a cold- and drought-adapted species. We used a novel approach to identify microsatellite regions using genome walker libraries, called as Random Scans at Microsatellite Regions (RaSMiR), and implemented them on genotypes collected from relatively different topographical conditions within a small geographical area. The success rate of finding a microsatellite sequence using this methodology was 100%, and on developing the RaSMiR technique itself as a molecular marker, 230 electrophoretic bands were obtained using 13 different RaSMiR primers in combination with a microsatellite sequence primer. On an average, 17 bands were obtained for each primer. The electrophoretic profiles generated by RaSMiR markers were distinct from those produced by inter-simple sequence repeat markers. This information has been documented as a dominant marker data, and has been used to construct a neighbour-joining tree that successfully distinguished all genotypes. RaSMiR is an attractive approach for the development of unique and informative microsatellites, or for genome scanning directly as a molecular marker that can potentially be employed for the estimation of genetic diversity or to identify polymorphic loci involved in adaptations particularly in the non-model species, for which sufficient genomic data are not available.

Genetic diversity among geographically separated populations of Nepenthes mirabilis

Biologia ◽  
2006 ◽  
Vol 61 (3) ◽  
Author(s):  
Arunrat Chaveerach ◽  
Alongkod Tanomtong ◽  
Runglawan Sudmoon ◽  
Tawatchai Tanee
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
Geographical Area ◽  
Inter Simple Sequence Repeat ◽  
Genetic Distances ◽  
High Genetic Diversity ◽  
Total Genetic Diversity ◽  
Environmental Variations ◽  
Diversity Profile ◽  
Great Genetic Diversity

AbstractThe distribution of Nepenthes mirabilis ranges from Northeast (NE) to South (S) Thailand. Eleven individuals from NE, S and Suen Jatujak market in Bangkok, Central (C) Thailand, were collected and divided into four populations according to their geographical areas. These four populations were analyzed to determine a genetic diversity profile using thirteen inter-simple sequence repeat markers. The individuals produced 75.18% polymorphic banding profiles. The Shannon’s index was used to estimate genetic diversity. Total genetic diversity (H T) and inter-population genetic diversity (H S) were 0.854 and 0.678, respectively. The degree of genetic differentiation (G ST) of the species populations is 0.206, whereas the gene flow (Nm) among all the various geographical area populations is 1.016. Both the dendrogram and the results of the Shannon’s diversity index suggest great genetic diversity. These results support the broad range of distribution sites of Nepenthes mirabilis, which would require high genetic diversity to adapt to the environmental variations that can be found between NE, C, and S Thailand. ANOVA shows that the genetic diversity in each population is not significantly different (P > 0.05). Mantel tests reveal that geographical distance is an important factor for affecting the genetic distances among populations.

scholarly journals Evaluation of Genetic Diversity Among Kongpo Monkshood (Aconitum kongboense L.) Germplasm Accessions Revealed by Inter Simple Sequence Repeat Markers

HortScience ◽  
2015 ◽  
Vol 50 (7) ◽  
pp. 940-943 ◽  
Author(s):  
Fanjuan Meng ◽  
Ruoding Wang ◽  
Mu Peng ◽  
Chao Wang ◽  
Zhongkui Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Gene Diversity ◽  
Molecular Data ◽  
Inter Simple Sequence Repeat ◽  
Tibet Plateau ◽  
Polymorphism Analysis ◽  
Sequence Repeat ◽  
The Mean ◽  
Simple Sequence

Inter simple sequence repeat (ISSR) were used to evaluate the genetic diversity of Kongpo Monkshood (Aconitum kongboense L.) in Motuo, Tibet Plateau. From 70 accessions of three populations, 10 out of 100 informative ISSR primers were chosen for polymorphism analysis. Percentage of polymorphic bands was 50% to 66.67% with a mean of 58.42%. The effective number of alleles (Ne) was between 1.545 (population 3) and 1.586 (population 2), and the mean value was 1.564; the Nei’s gene diversity (h) ranged from 0.315 to 0.327 with the average value of 0.320; the value of Shannon’s information index (I) ranged from 0.459 to 0.478, with the mean of 0.469. Based on molecular data, cluster analysis classified the 70 cultivars into three groups. Most accessions were related to the geographical origin and their genetic backgrounds. Bayesian structure and PCoA analysis were consistent with the dendrogram result. Based on the analysis, it will provide a reference for Kongpo Monkshood breeding purposes and contribute to identification, rational exploitation, and conservation of germplasms.

Genetic diversity revealed by ISSR molecular marker in different species of Ocimum

Planta Medica ◽  
2010 ◽  
Vol 76 (12) ◽  
Author(s):  
K Shinde ◽  
V Shinde ◽  
J Kurane ◽  
A Harsulkar ◽  
K Mahadik
Keyword(s):  
Genetic Diversity ◽  
Molecular Marker

Genetic diversity of Symplocos paniculata of Hunan province revealed by inter-simple sequence repeat (ISSR)

2019 ◽  
Vol 51 (5) ◽  
Author(s):  
Huifang Cao ◽  
Qiang Lin ◽  
Peiwang Li ◽  
Jingzhen Chen ◽  
Changzhu Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Hunan Province ◽  
Sequence Repeat ◽  
Simple Sequence

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.

ISSR Marker Based Genetic Diversity in Morinda Spp. For Its Enhanced Collection, Conservation and Utilization

2021 ◽  
Author(s):  
Lalit Arya ◽  
Ramya Kossery Narayanan ◽  
Anjali Kak ◽  
Chitra Devi Pandey ◽  
Manjusha Verma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Morinda Citrifolia ◽  
Species Differentiation ◽  
Information Index ◽  
Upgma Cluster Analysis ◽  
Simple Sequence

Abstract Morinda (Rubiaceae) is considerably recognized for its multiple uses viz. food, medicine, dyes, firewood, tools, oil, bio-sorbent etc. The molecular characterization of such an important plant would be very useful for its multifarious enhanced utilization. In the present study, 31 Morinda genotypes belonging to two different species Morinda citrifolia and Morinda tomentosa collected from different regions of India were investigated using Inter Simple Sequence Repeat (ISSR) markers. Fifteen ISSR primers generated 176 bands with an average of 11.7 bands per primer, of which (90.34%) were polymorphic. The percentage of polymorphic bands, mean Nei’s gene diversity, mean Shannon’s information index in Morinda tomentosa and Morinda citrifolia was [(69.89%, 30.68%); (0.21 ± 0.19, 0.12 ± 0.20); (0.32 ± 0.27 0.17 ± 0.28)] respectively, revealing higher polymorphism and genetic diversity in Morinda tomentosa compared to Morinda citrifolia. Structure, and UPGMA cluster analysis placed the genotypes into well-defined separate clusters belonging to two species Morinda tomentosa and Morinda citrifolia revealing the utility of ISSR markers in species differentiation. Distinct ecotypes within a particular species could also be inferred emphasizing the collection and conservation of Morinda genotypes from different regions, in order to capture the overall diversity of respective species. Further higher diversity of M. tomentosa must be advanced for its utilization in nutraceutical, nutritional and other nonfood purposes.

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