scholarly journals Assessment of genetic diversity of Musa species accessions with variable genomes using ISSR and SCoT markers

2021 ◽  
Author(s):  
David Okeh Igwe ◽  
Onyinye Constance Ihearahu ◽  
Anne Adhiambo Osano ◽  
George Acquaah ◽  
George Nkem Ude
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Allelic Richness ◽  
Crop Improvement ◽  
Inter Simple Sequence Repeat ◽  
Start Codon ◽  
Information Index ◽  
Cluster Resolution ◽  
Musa Species ◽  
Simple Sequence

AbstractAssessing the effectiveness of different molecular markers is essential for identification of appropriate ones for crop improvement and conservation, hence, inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) markers were used for this study. Sixty-six accessions with different genomes obtained from International Transit Center, Belgium, were used for DNA extraction, amplification with ISSR and SCoT markers and agarose gel electrophoresis. The reproducible bands were scored for analyses. We identified high allelic richness of 299 (ISSR) and 326 (SCoT). Polymorphic information contents (ISSR: 0.9225; SCoT: 0.9421) were high but SCoT exhibited higher level of informativeness. The two markers demonstrated high percentage polymorphic loci (ISSR: 91.21–100%; SCoT: 96.97–100%). Other genetic indicators including effective number of alleles, Nei’s genetic diversity, and Shannon information index were higher in SCoT and further elucidated the usefulness of the markers. Intraspecific genetic diversity, interspecific genetic diversity, coefficient of gene differentiation and level of gene flow revealed extensive gene flow and larger variability within the accessions. Both ISSR and SCoT grouped the accessions via dendrogram, biplot and structure analyses. Though the two marker systems varied in their informativeness, they demonstrated high effectiveness in resolving genetic diversity (GD) of the different accessions, with higher efficiency in SCoT markers. Due to higher GD indices exhibited by SCoT, AS is the most genetically endowed one. Our study showed that SCoT markers are more informative than ISSR for GD exploration, assessment and cluster resolution of Musa species, thereby revealing the potential of SCoT markers for improved breeding and conservation.

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.

Genetic diversity of oil-tea camellia germplasms revealed by ISSR analysis

2015 ◽  
Vol 08 (05) ◽  
pp. 1550070 ◽  
Author(s):  
Lan-Ying Zhou ◽  
Xiang-Nan Wang ◽  
Li-Ping Wang ◽  
Yong-Zhong Chen ◽  
Xiao-Cheng Jiang
Keyword(s):  
Genetic Diversity ◽  
Reaction System ◽  
Inter Simple Sequence Repeat ◽  
Genetic Distances ◽  
Similarity Coefficient ◽  
Hunan Province ◽  
Information Index ◽  
Group I ◽  
Issr Pcr ◽  
Simple Sequence

Genetic diversity of 51 oil-tea camellia germplasms was analyzed using the optimized inter-simple sequence repeat (ISSR)–PCR reaction system with 22 primers screened from a set of 100 ISSR primers. The results showed that 493 discernible loci with distinct electrophoretic bands were obtained, of which, 478 loci (96.78%) were polymorphic. This indicated that oil-tea germplasms possess abundant genetic diversities. By clustering analysis performed using softwares of NTSYS 2.10 and Winboot, 51 oil-tea germplasms were divided into two groups: Group I had 48 lines of Camellia oleifera Abel, while Group II had three C. oleifera Abel related species and their similarity coefficient was 0.62. Group I was further divided into Group I-1 and Group I-2, and their similarity coefficient (Gs) was 0.634. All members of Group I-1 originated from Hunan Province, while Group I-2 included the rest of Hunan lines and those originated from other regions of China. Analyzed by software POPGENE 1.32, the Shannon's information index (I*) of genetic polymorphism was 0.3852, the genetic diversity among different region populations (Ht) was 0.2537, the genetic diversity within populations (Hs) was 0.15545, the differentiation coefficient of genetic diversity among populations (Gst) was 0.3967, and the gene flow among populations (Nm*) was 0.8262. The Nei's genetic distances between the Hunan population and the populations originated from other regions of China implied that geographic isolation strongly influenced genetic differentiation among populations. Meanwhile, seedling rootstock grafting and high grafting for tree crown produced genetic variations among clonal offsprings.

Genetic diversity of Dioscorea japonica germplasm in Taiwan revealed by inter-simple sequence repeat DNA markers

2015 ◽  
Vol 14 (3) ◽  
pp. 211-218
Author(s):  
Tsai-Li Kung ◽  
Kuan-Hung Lin ◽  
Shun-Fu Lin
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Dna Markers ◽  
Simple Sequence Repeat ◽  
Germplasm Collection ◽  
Inter Simple Sequence Repeat ◽  
Northern Region ◽  
Sequence Repeat ◽  
Dioscorea Japonica ◽  
Simple Sequence

There are three native varieties of edible yams (Dioscorea japonica Thunb.) in Taiwan, but germplasm has been collected from only a few. To assess the genetic diversity of 99 accessions collected from four geographically diverse regions, inter-simple sequence repeat (ISSR) DNA markers were analysed, and 90.2% of the polymorphic markers in these accessions were found. Genetic similarity among accessions ranged from 30.8 to 74.4%, averaging 48.4%. Cluster analyses revealed four main clusters plus one outlier (Dioscorea alata L.). The varieties oldhamii and pseudojaponica were separated into different clusters and var. japonica was grouped with both varieties. Since var. japonica was found to be genetically similar to var. oldhamii and var. pseudojaponica, we suggest that var. japonica is a hybrid or intermediate variety between the two varieties. Molecular analysis of variance results indicated that variation within counties (95.94%) was predominantly greater than variation among counties (3.63%) and among regions (0.43%). Overall, gene flow (Nm= 0.970) estimated from genetic differentiation (Gst= 0.340) suggests that gene flow among regions is relatively high. The highest genetic diversity (H= 0.191) and Shannon's index (I= 0.312), and a high gene flow (Nm= 3.926) of germplasm in the northern region suggest that this region is a possible centre of dispersal and domestication of yams in Taiwan. This study provided valuable information for germplasm collection and genetic improvement.

Evaluation of molecular diversity analysis and relation with environmental factors in accessions of Cumin (Cuminum cyminum L.) in Iran, revealed by inter-simple sequence repeat (ISSR) markers and start codon targeted (SCoT) markers

2020 ◽  
Author(s):  
Mohammad Samer Mohammadizadeh ◽  
Farzaneh Bahadori ◽  
Leila Hakimi ◽  
Abbas Dehshiri
Keyword(s):  
Genetic Diversity ◽  
Environmental Factors ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Start Codon ◽  
Geographical Distance ◽  
Sequence Repeat ◽  
Cuminum Cyminum ◽  
Simple Sequence

Abstract Cuminum cyminum (as an aromatic herb) is the sources of cumin, which has been commonly used in traditional medicine for the treatment of various diseases especially in tropical Asia. Thus, the current experiment was performed to accesses molecular genetic diversity among 22 collected accessions of cumin from different area of Iran, based on inter simple sequence repeat (ISSR) markers and start codon targeted (SCoT) markers. Analysis of molecular variance revealed that a significant genetic difference between the studied accessions reach to 43%. Mantel test between genetic diversity and geographical distance indicated that an increase in geographical distance of collected accessions did not influence on genetic differentiation. Results about all agro-morphological traits showed a significant difference between the ecotypes except the number of branches. Canonical correspondence analysis ballot of genetic features and environmental factors included 5 geographic and climatic factors for seed origin’s habitat, which have been show that the mentioned parameters had no strong effect on the plant genotypes. However, difference in elevation and latitude of accession origins had effect on genetic clustering in two major groups. The consensus tree of both molecular and morphological data relieved that the accessions Chah-Dashi, Damghan, Ferdows and Nehbandan formed discreet clusters based on genetic and agro-morphological features. In conclusion, the results confirmed that both ISSR and SCoT markers were reliable and useful tools for analyzing the genetic diversity of cumin in Iran.

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
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