scholarly journals Molecular identification and genetic relationships among coffee species (Coffea L.) inferred from ISSR and SRAP marker analyses

2011 ◽  
Vol 63 (3) ◽  
pp. 667-679 ◽  
Author(s):  
Kumar Mishra ◽  
Sandhyarani Nishani ◽  
J Jayarama
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Genetic Relationships ◽  
Resolving Power ◽  
Diversity Analysis ◽  
Srap Marker ◽  
Genetic Diversity Analysis ◽  
Species Specific ◽  
Coffee Species ◽  
Issr Primers

The identification and genetic relationships of 23 coffee species and one coffee-related species Canthium diccocum were studied using ISSR and SRAP markers. The average polymorphism information content of SRAP primers (0.81) was lower than ISSR primers (0.86), whereas the average resolving power of the SRAP primers (9.74) is higher than the ISSR primers (8.64). The genetic similarity among the species ranged from 0.30 to 0.89 using ISSR and 0.11 to 0.90 using SRAP marker systems. Based on marker analysis, all twenty three coffee species were clustered into two major groups. Both the markers amplified species-specific fragments and are useful in genetic diversity analysis of coffee.

scholarly journals Genetic diversity analysis of yardlong bean genotypes (Vigna unguiculata subsp. sesquipedalis) based on IRAP marker

2020 ◽  
Vol 21 (3) ◽  
Author(s):  
Muhammad Habib Widyawan ◽  
Sri Wulandary ◽  
Taryono
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Vigna Unguiculata ◽  
Genetic Similarity ◽  
Polymorphic Information Content ◽  
Resolving Power ◽  
Diversity Analysis ◽  
Genetic Diversity Analysis ◽  
Irap Marker ◽  
Yardlong Bean

Abstract. Widyawan MH, Wulandary S, Taryono. 2020. Genetic diversity analysis of yardlong bean genotypes (Vigna unguiculata subsp. sesquipedalis) based on IRAP marker. Biodiversitas 21: 1101-1107. Inter-Retrotransposon Amplified Polymorphism (IRAP) marker is a PCR-based molecular marker that detects polymorphism between retrotransposon sites. This marker has been utilized and successfully assessed genetic diversity in many crop species. Yardlong bean (Vigna unguiculata subsp. sesquipedalis) was an important vegetable legume crop that grown mainly for its fresh pod that rich in nutritional benefits for humans, ultimately dietary fiber and protein. Trends of people awareness to nutritional content of food are increasing, therefore breeding for quality traits is important. Genetic diversity analysis is an important and elementary step in breeding programs in order to determine the breeding strategy. The aims of this research are to perform an optimization of IRAP marker and applied it for genetic diversity analysis in 16 yardlong bean genotypes. Seven primers were used as marker in a pair or single combination and resulted in 11 optimized markers that able to be used for genetic diversity analysis. Sixteen yardlong bean genotypes consisting of commercial cultivars and local genotypes from Indonesia were genotyped using eleven IRAP markers. Marker polymorphism and diversity parameters from each marker i.e. Percentage of Polymorphic Loci (PPL), Expected Heterozygosity (He), Polymorphic Information Content (PIC), Effective Multiplex Ratio (EMR), Marker Index (MI), Discriminating Power (D), and Resolving Power (RP) were calculated. Based on those values, several markers used in this study were considered as informative and efficient in terms of analyzing genetic diversity in yardlong bean. Jaccard's method was used to measure genetic similarity and it is revealed that there is high level of similarity between yardlong bean genotypes used in this study. Thus, it is implied that there is a narrow genetic diversity of yardlong bean genotypes used in this study. Cluster analysis was performed to construct dendrogram based on genetic similarity and classified 16 yardlong genotypes into 4 clusters. Interestingly, majority of the clusters formed were not able to classified genotypes based on their origin. The result of cluster analysis then confirmed by Principal Coordinate Analysis (PCoA) that able to explain 47.76 % of total variation. The results of this study provide a foundation for the genetic diversity analysis based on IRAP marker and genetic improvement in yardlong bean.

scholarly journals (235) Genetic Diversity Analysis of Five Passiflora Genotypes

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1002A-1002
Author(s):  
Eric Stafne ◽  
Jon Lindstrom ◽  
John Clark
Keyword(s):  
Genetic Diversity ◽  
North American ◽  
Genetic Similarity ◽  
The Other ◽  
Diversity Analysis ◽  
Breeding Programs ◽  
Genetic Diversity Analysis ◽  
Native North American ◽  
Cold Hardy ◽  
High Degree

Passiflora is an important ornamental genus, mainly within tropical zones. However, two cold-hardy, North American Passiflora species exist. Previous work has been done to incorporate these species into breeding programs with some success. The intent of this study was to evaluate the extent of genetic diversity among five different Passiflora genotypes, including the two native North American species, P. incarnata L. and P. lutea L. Results indicate low genetic similarity among all genotypes with none at 50% or greater. P. incarnata and the ornamental cultivar `Lady Margaret' displayed the highest relationship at 49%. P. incarnata averaged 35.5% similarity with the other genotypes and P. lutea was 29.5%. Average overall similarity among all genotypes was 31.1%. These and other results show that the Passiflora genus has a high degree of genetic variation and breeding efforts could expand interest within North America.

Genetic diversity analysis in underutilized medicinal climber Mucuna pruriens (L.) DC. germplasm revealed by inter simple sequence repeats markers

2018 ◽  
Author(s):  
A. Chinapolaiah ◽  
K. Hima Bindu ◽  
G.N. Khadke ◽  
G.N. Manjesh ◽  
N. Hariprasad Rao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Issr Markers ◽  
Mucuna Pruriens ◽  
Diversity Analysis ◽  
Velvet Bean ◽  
Genetic Diversity Analysis ◽  
Inter Simple Sequence Repeats ◽  
Diversity Assessment ◽  
Simple Sequence

Velvet bean is an important medicinal legume, its seeds are prominent source of L-Dopa. The present investigation on genetic diversity assessment of 58 germplasm of velvet bean by using 11 ISSR markers. Out of 63 amplified products 59 were showed polymorphism and 4 were monomorphic with an average of 5.7 bands amplified per primer. According to band statistics and efficiency parameters showed the primers UBC 827, UBC 834 and UBC 836 were more efficient. The highest genetic similarity values (0.90) were observed between IIHR MP 102 and IIHR MP 74-3. In dendrogram germplasm grouped into two major clusters at 63 per cent similarity. Among the germplasm, IIHR Selection 4, IIHR Selection 10, IIHR MP 9, IC 33243 and IIHR MP 7 were found to be distinctly divergent, can be used in the further breeding programme.

scholarly journals Development of SSR markers and their application to genetic diversity analysis of Curcuma alismatifolia varieties

2020 ◽  
Vol 99 (1) ◽  
pp. 124-131
Author(s):  
Lihui Mao ◽  
Jianxin Liu ◽  
Huaqiao Ding ◽  
Qingcheng Zou ◽  
Danqing Tian
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Polyacrylamide Gel Electrophoresis ◽  
Diversity Analysis ◽  
Cut Flowers ◽  
Sequencing Technology ◽  
Genetic Diversity Analysis ◽  
Single Cell Sequencing ◽  
The Past ◽  
Maximum Proportion

Background: Curcuma alismatifolia is an ornamental cultivar with several varieties introduced into China from Thailand within the past fifteen years. Curcuma alismatifolia is widely used as cut flowers and potted flowers and is also used in flower beds. Questions and/or Hypotheses: However, limited genetic and genomic information is available for this species, which has impeded studies on the enhancement of its ornamental value and stress resistance. Studied species Curcuma alismatifolia Study site and dates: Zhejiang, 2018   Methods: single-cell sequencing technology of PCR and polyacrylamide gel electrophoresis   Results: (A/T)n accounted for 43.6 % of the SSRs, the maximum proportion, and mononucleotide and trinucleotide repeats were the two most abundant repeat types. A total of 3,637 primer pairs flanking SSR sequences were successfully designed, and 70 sets of primers were randomly selected for validation in 10 varieties. Forty-one (59 %) of the 70 primer pairs successfully amplified alleles, of which 35 were identified as polymorphic markers and used to assess the level of genetic diversity and genetic relationships among the 10 varieties. The genetic diversity analysis showed that the number of alleles (Na) at each locus ranged from 2 to 8, with an average of 3.97, and that PIC had a mean of 0.524 and ranged from 0.095 to 0.795. Conclusions: The genetic distance between 10 varieties varied from 0.30 to 0.96, and the dendrogram clustered all varieties into three groups.

scholarly journals Isozyme Variation in Lychee (Litchi chinensis Sonn.)

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 796A-796
Author(s):  
F. Zee ◽  
K.M. Aradhya ◽  
R.M. Manshardt
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Gene Diversity ◽  
Diversity Analysis ◽  
Isozyme Variation ◽  
Litchi Chinensis ◽  
Genetic Diversity Analysis ◽  
Germplasm Collections ◽  
Enzyme Systems ◽  
Clonal Identity

A genetic diversity analysis involving 49 Iychee (Litchi chinensis Sonn.) accessions using eight enzyme systems encoding 12 loci (Idh-1, Idh-2, Mdh-2, Per-1, Pgi-2, Pgm-1, Pgm-2, Skdh, Tpi-1, Tpi-2, Ugpp-1, and Ugpp-2) revealed moderate to high levels of genetic variability. Cluster analysis of the isozyme data from 40 genetically different accessions of the total 49 identified three groups at the 50% level of genetic similarity, the largest of which contained 32 of the 40 accessions distributed in three sub-groups. The groups including the three subgroups differed in frequency and composition of alleles at different loci. Polymorphism was observed in 77% of the loci, with an overall mean of 2.2 alleles per locus and an observed heterozygosity of 0.387. The unbiased genetic identities (I) between groups ranged from 0.809 to 0.937. Summing over all 11 polymorphic loci, 16% of gene diversity was due to differentiation between groups and 84% within groups. Comparison of isozyme fingerprints revealed that some accessions with identical names, particularly of `No mai tsz', `Kwai mi', and `Hak ip', possessed different isozyme genotypes, while other accessions with different names displayed identical isozyme genotypes. Isozyme fingerprinting will be useful in revealing and resolving questions of clonal identity, which are common in Iychee germplasm collections.

Genetic relationships of Chinese prickly ash as revealed by ISSR markers

Biologia ◽  
2015 ◽  
Vol 70 (1) ◽  
Author(s):  
Shijing Feng ◽  
Tuxi Yang ◽  
Xiao Li ◽  
Lv Chen ◽  
Zhenshan Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationship ◽  
Genetic Divergence ◽  
Genetic Similarity ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Similarity Coefficient ◽  
Chinese Prickly Ash ◽  
New Cultivars ◽  
Issr Primers

AbstractChinese prickly ash, belonging to the genus Zanthoxylum L., has been one of the most important commerciallyexploited plants for its alimentary, industrial and medicinal applications. However, the breeding and promotion of Chinese prickly ash have been severely restricted due to its confusing classification. Therefore, we assessed genetic diversity and phylogenetic relationship among 45 Chinese prickly ash samples collected from 6 main cultivated regions using 11 ISSR primers. These eleven selected primers generated a total of 102 scorable bands ranging from 150 to 2000 bp, corresponding to an average of approximately 9.3 bands per primer. The percentage of polymorphic loci for all samples ranged from 75% to 100%, with an average of 84.3%. The genetic similarity coefficient across all samples varied from 0.460 to 0.919. Remarkably, UPGMA analysis showed that 45 samples were divided into six clusters with a genetic similarity of 0.7. The closest genetic relationship was observed between Dahongpao collected from Qin’an and Tianshui, and the greatest genetic divergence was found between Dahongpao collected from Hengshui and Jiuyeqing collected from Jiangjin. It could serve as a basis for identifying Chinese prickly ash cultivars, breeding new cultivars and protecting the Chinese prickly ash resources in main regions.

Analysis of Genetic Diversity and Population Structure Using SSR Markers in Tobacco

2013 ◽  
Vol 850-851 ◽  
pp. 1243-1246
Author(s):  
Yan Shi Xia ◽  
Pei Guo Guo ◽  
Rong Hua Li ◽  
Yong Hua Lü ◽  
Miao Wen Qiu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Clustering Analysis ◽  
Genetic Similarity ◽  
Diversity Analysis ◽  
Germplasm Management ◽  
Genetic Diversity Analysis ◽  
Group A ◽  
Group B

Genetic diversity analysis and population structure can estimate genetic variation of diverse materials, and can be used in germplasm management and varietal protection. In this study, the genetic diversity and population structure for tobacco germplasm (78 cultivated tobacco accessions in China) were analyzed by using 28 SSR markers. A total of 127 alleles were detected with an average of 4.5 per locus in 78 accessions, while PIC values ranged from 0.19 to 0.89 with an average of 0.63 per marker. Based on genetic similarity, most of sun-cured and flue-cured tobacco accessions were clustered into group A and group B, respectively. A model-based structure analysis for these accessions detected two subpopulations, which were generally coincident with the clustering analysis and showed the genetic similarities were relative high for these accessions. These results revealed narrow genetic diversity for the tobacco germplasm in China.

scholarly journals Genetic Diversity Analysis of <i>Cotoneaster schantungensis</i> Klotz. Using SRAP Marker

2015 ◽  
Vol 06 (18) ◽  
pp. 2860-2866 ◽  
Author(s):  
Yan Ma ◽  
Suqing Qu ◽  
Xiurong Xu ◽  
Tingting Liang ◽  
Dekui Zang
Keyword(s):  
Genetic Diversity ◽  
Diversity Analysis ◽  
Srap Marker ◽  
Genetic Diversity Analysis

scholarly journals Genetic diversity analysis of Piper betle from eight accessions of Indonesia based on SRAP markers

2021 ◽  
Vol 22 (8) ◽  
Author(s):  
Sharah Nabilla ◽  
Ukhradiya Magharaniq Safira ◽  
Puspa Julistia Puspita ◽  
Dyah Subositi ◽  
Anshary Maruzy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
Folk Medicine ◽  
Dna Amplification ◽  
Scientific Data ◽  
Piper Betle ◽  
Diversity Analysis ◽  
Srap Marker ◽  
Genetic Diversity Analysis ◽  
Srap Markers

Abstract. Nabilla S, Safira UM, Puspita PJ, Subositi D, Maruzy A, Artika IM. 2021. Genetic diversity analysis of Piper betle from eight accessions of Indonesia based on SRAP markers. Biodiversitas 22: 3401-3408. Leaves of betel vine (Piper betle Linn.) have been used as a traditional medicine in various regions in Indonesia. However, the genetic diversity of this plant has not been well recorded. Considering its diverse usage in traditional and folk medicine, it is essential to analyze and document the genetic diversity of Piper betle L. with the aim to collect the scientific data of betel vine genetics in Indonesia. This study aims at analyzing the population structure and genetic diversity of betel vine from the Singkil, Gayo Serbajadi, Baduy, Bandung, Hutan, Kalisusu, Kaledupa, and Mekongga accession groups of Indonesia using the sequence-related-amplified polymorphism (SRAP) marker technique. Genomic DNA was isolated from each accession and then used as a template for DNA amplification using PCR. As many as 16 SRAP primer combinations were screened for the genetic diversity analysis. Optimization of primer combinations resulted in 7 selected combinations based on their ability to generate clear amplification patterns and polymorphic bands. These were then employed for genetic diversity analysis. The genetic distance dendrogram showed the lowest similarity coefficient was 0.62 and that the betel vine grouping pattern was not based on genotype. The Singkil population had the highest genetic diversity and the Hutan population had the lowest. The mean value of Nei's genetic diversity index was 0.0985, while Shannon's information index was 0.01459 and the percentage of polymorphic loci was 25.81. This study concluded that the level of betel vine diversity is low.

scholarly journals The Use of ISSR and RAPD Markers for Genetic Diversity among South Tunisian Barley

ISRN Agronomy ◽  
2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Ferdaous Guasmi ◽  
Walid Elfalleh ◽  
Hédia Hannachi ◽  
Khadija Fères ◽  
Leila Touil ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Resolving Power ◽  
Poor Correlation ◽  
Rapd And Issr ◽  
South Tunisia ◽  
Issr Primers

Random amplified polymorphic DNA (RAPD) and intersimple sequence repeat (ISSR) were assayed to determine the genetic diversity of 80 barley specimens from South Tunisia. The ISSR primers showed variation in the percentage of polymorphism, band informativeness (Ib), and resolving power (Rp). The percentage of polymorphism is 66.67%, the average Ib ranged from 0.24 to 0.39, while Rp ranged from 0.74 to 1.16. In RAPD analysis, three primers yielded a total of 17 scorable bands, which are all polymorphic. The three polymorphic primers exhibited variation with regard to average band informativeness (AvIb) and resolving power (Rp). RAPD and ISSR marker systems were found to be useful for the genetic diversity among the barley specimens. The two dendrograms obtained through these markers show different clustering of 80 barely specimens, but we noted that some clusters were similar in some cases. A poor correlation () was found between both sets of genetic similarity data, suggesting that both sets of markers revealed unrelated estimates of genetic relationships. Therefore, the ISSR and RAPD molecular markers show two genetic grouping of studied barely specimens.

Sign in / Sign up

Export Citation Format

Share Document