APPLICATIONS OF ISSR MARKERS IN STUDIES OF GENETIC DIVERSITY OF Pityrocarpa moniliformis

ABSTRACT Pityrocarpa moniliformis (Benth.) Luckow & R. W. Jobson (Fabaceae) is a native brazilian species with high potential for economic development programs in semiarid regions, mainly related to the production of honey, animal food and firewood. Thus, the objective of this work was to select Inter-Simple Sequence Repeat (ISSR) molecular markers for genetic diversity studies, as well as to test the efficiency of this approach in quantifying the genetic diversity of a natural P. moniliformis population. For this, 28 ISSR molecular markers were tested, evaluating the total number of loci, polymorphism rate and the Polymorphism Information Content (PIC) for the selected primers, the “Marker Index”, and the “Resolving Power”. Genetic diversity parameters (Nei genetic distance and Shannon index) were evaluated for 30 individuals located in Macaíba, Rio Grande do Norte State, Brazil. Seven primers were selected, which provided 74 loci, with 82% being polymorphic, while the PIC value was 0.344. The Nei genetic distance was 0.244, and the Shannon index was 0.374. Therefore, ISSR molecular markers (UBC 827, 840, 844, 857, 859, 860 and 873) are considered efficient in studying the genetic diversity of populations for the selection of matrices and germplasm banks, and may contribute to the conservation and genetic improvement of P. moniliformis populations.

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Genetic diversity of Panax vietnamensis var. langbianensis populations in Lam Vien plateau - Vietnam detected by inter simple sequence repeat (ISSR) markers

Vietnam Journal of Biotechnology ◽

10.15625/1811-4989/17/4/14720 ◽

2020 ◽

Vol 17 (4) ◽

pp. 651-661

Author(s):

Le Ngoc Trieu ◽

Nong Van Duy ◽

Tran Van Tien

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Simple Sequence Repeat ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Sequence Repeat ◽

New Variety ◽

Gene Differentiation ◽

The Stability ◽

Simple Sequence

Panax vietnamensis var. langbianensis is a new variety from Lam Vien plateau of Vietnam. In this study, inter simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and variability of 115 individuals belonging to two naturally distributed populations of this variety, which classified by habitat. Genetic diversity at the taxon level was high (HeT = 0.284 and PPBT = 97.2 %). The result showed lightly higher genetic diversity in population in Lac Duong region (HeLD= 0.228 and PPBLD = 81.5 %) as compared to those located in Dam Rong region (HeDR= 0.213 and PPBDR = 79.4 %). The interpopulation gene differentiation was high (GST Total = 0.221) with the genetic distance among populations was DLD-DR = 0.191. Gene flow within populations was Nm = 0.8793. In Lac Duong population, the genetic diversity of older group (HeLD O = 0.233; PPBLD O = 77.1%) was higher than of younger group (HeLD Y = 0.214; PPBLD Y = 72.4 %) and the intergroup gene differentiation was GSTDL = 0.0205 with the genetic distance between these two group was DLD O-Y = 0.0061 showed the risk of reduction in genetic diversity. In Dam Rong population, the genetic diversity of older group (HeDR O = 0.204; PPBDR O = 75.2 %) was equal to younger group (HeDR Y = 0.209; PPBDR Y = 72.7 %) and the intergroup gene differentiation was GSTDR = 0.0304 with the genetic distance between them was DDR O-Y = 0.01393 showed the stability in genetic diversity. Data for genetic diversity and variation from this study can be used to further investigate and protect this variety for conservation and development purposes and for sustainable exploiting and use of these valuable natural resources.

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Identification and Genetic Diversity Analysis of Edible and Medicinal Malva Species Using Flow Cytometry and ISSR Molecular Markers

Agronomy ◽

10.3390/agronomy10050650 ◽

2020 ◽

Vol 10 (5) ◽

pp. 650

Author(s):

Iwona Jedrzejczyk ◽

Monika Rewers

Keyword(s):

Flow Cytometry ◽

Molecular Markers ◽

Genome Size ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Size Estimation ◽

Flow Cytometric ◽

First Choice ◽

Issr Molecular Markers

The Malva genus contains species that reveal therapeutic properties and are mostly important in medicine and the functional food industry. Its breeding, cultivation, and utilization are based on proper germplasm/plant identification, which is difficult using morphological features. For this reason, we applied flow cytometry and inter simple sequence repeat polymerase chain reaction (ISSR-PCR) for fast and accurate species identification. Genome size estimation by flow cytometry was proposed as the first-choice method for quick accession screening. Out of the 12 tested accessions, it was possible to identify six genotypes based on genome size estimation, whereas all species and varieties were identified using ISSR markers. Flow cytometric analyses revealed that Malva species possessed very small (1.45–2.77 pg/2C), small (2.81–3.80 pg/2C), and intermediate (11.06 pg/2C) genomes, but the majority of accessions possessed very small genomes. Additionally, this is the first report on genome size assessment for eight of the accessions. The relationships between the investigated accessions showed the presence of two clusters representing malvoid and lavateroid group of species. Flow cytometry and ISSR molecular markers can be effectively used in the identification and genetic characterization of Malva species.

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Efficiency of different PCR-based marker systems for assessment of Iris pumila genetic diversity

Biologia ◽

10.2478/s11756-013-0192-4 ◽

2013 ◽

Vol 68 (4) ◽

Cited By ~ 8

Author(s):

Olena Bublyk ◽

Igor Andreev ◽

Ruslan Kalendar ◽

Kateryna Spiridonova ◽

Viktor Kunakh

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Gene Diversity ◽

Issr Markers ◽

Genetic Distances ◽

Resolving Power ◽

Abiotic Stress Response ◽

Genetic Population ◽

Iris Pumila ◽

Polymorphic Bands

AbstractWe investigated informativeness and effectiveness of different marker types (ISSR, IRAP, REMAP, RGAP and LP-PCR that employ primers based on the conservative sequences of abiotic stress response genes) to study genetic diversity of Iris pumila L. By the number of amplicons per primer, number of polymorphic amplicons per primer and resolving power index (Rp), ISSR-markers were the most efficient followed by LP-PCR-markers. In order of decreasing value of indicators of genetic diversity “the percentage of polymorphic bands”, and “the average Jaccardś genetic distance between plants”, marker systems may be arranged as follows: ISSR > RAPD > LP-PC > RGAP ≈ IRAP. For ISSR-markers, the percentage of polymorphic bands was 1.3–1.7 times higher than for the others, and the average genetic distance was 1.2–1.3 times higher. Different marker systems were ranked by the value of Neiś gene diversity and the Shannonś index as follows: ISSR > RAPD ≈ LP-PCR > RGAP ≈ IRAP, with the highest and the lowest values differing 1.4 times. Genetic population structure was investigated with program Structure 2.3. The data of all marker systems suggest that all genomes under study belonged to one population. The PCoA and cluster analyses based on genetic distances showed distinctions in clustering generated from different markers data and summarized data, as well as the lack of strong clusters. Mantel test revealed significant positive correlation between the matrices of genetic distances generated by the data of almost all marker systems. The strongest correlation was found between RGAP- and IRAP-markers (r = 0.452, p = 0.01) and between RGAP and ISSR (r = 0.430, p = 0.01). ISSR, RAPD and LP-PCR proved to be more effective for the study of I. pumila genetic diversity, nevertheless, joint use of different marker systems will provide a more comprehensive assessment of variation in different genomic regions.

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Evaluation of Genetic Diversity by Molecular Markers ISSR of Algodoeiro (Gossypium mustelinum) in Native Populations of Pernambuco, Brazil

Journal of Experimental Agriculture International ◽

10.9734/jeai/2019/v33i530154 ◽

2019 ◽

pp. 1-10

Author(s):

Luiz Sergio Costa Duarte Filho ◽

Edson Ferreira Da Silva ◽

Danielson Ramos Ribeiro ◽

Allison Vieira Da Silva ◽

Iêda Ferreira De Oliveira

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Genetic Variability ◽

Urban Areas ◽

Issr Markers ◽

Ex Situ ◽

Native Populations ◽

Gossypium Mustelinum ◽

New Germplasm ◽

Diversity Studies

In order to assure and evaluate the genetic diversity, wild populations of Cotton (Gossypium mustelinum) were collected and evaluated from the coastal plain north of Pernambuco, Brazil. Such populations occur in urban areas in a state of real expansion and with imminent risks of extinction. As a result of these risks and the state of real expansion, aiming at the ex situ conservation of these genetic resources, branches of 66 plants were collected in three populations of G. mustelinum that are located in restinga vegetation in the localities of Ponta de Pedras and Bara of Catuama, both in the municipality of Goiana and in the locality Sossego Beach in the municipality Island of Itamaracá. The collected genotypes were inserted in a new Germplasm Bank (BAG) at the Federal Rural University of Pernambuco, after which a sample composed of 24 genotypes contained in the BAG was collected to perform genetic diversity studies using molecular markers of ISSR type. For the molecular analysis, 24 accesses with 4 ISSR primers were analyzed, which produced a total of 36 bands, with a mean of 1,52 alleles per amplified locus. The genetic dissimilarity values, calculated according to the complement of the Jaccard index, ranged from 0.000 to 0.080. The UPGMA method grouped the accesses into three groups. The UFRPE30, UFRPE42 and UFRPE45 accessions were more dissimilar and UFRPE-48, UFRPE-50, UFRPE-52, UFRPE-55, UFRPE60, UFRPE06, UFRPE28, UFRPE29, UFRPE1, UFRPE2, UFRPE17 the least dissimilar. The ISSR markers used in this study demonstrated efficiency in the detection of molecular polymorphisms, revealing genetic variability among the 24 accessions. Considering the results obtained in this work, it is possible to infer that there is considerable genetic variability among the accessions of cotton, demonstrating the importance of the markers in the analysis of variability of species not studied, such as (G. mustelinum).

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ISSR based analysis of genetic diversity in some endangered species of Allium subg. Melanocrommyum

Genetika ◽

10.2298/gensr1801059r ◽

2018 ◽

Vol 50 (1) ◽

pp. 59-68

Author(s):

Jalal Rezaei ◽

Zare Mehrjerdi ◽

Hassan Mastali

Keyword(s):

Genetic Diversity ◽

Endangered Species ◽

Genetic Distance ◽

Gene Diversity ◽

Program Planning ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Polymorphic Band ◽

Upgma Cluster Analysis ◽

Two Populations

Melanocrommyum, a subgenus of the Allium genus, is found in different regions of Iran and is in danger of extinction due to excessive exploitation. This study aimed to determine the genetic diversity in 170 individuals representing 17 wild populations belonging to six endangered species of Allium subg. Melanocrommyum using inter simple sequence repeat (ISSR) markers. The 10 selected ISSR primers produced 178 polymorphic fragments (100%). Polymorphic band number varied from 12 (primer 8) to 22 (primer 2). The average observed number of alleles, effective number of alleles, Shannon?s indices and Nei?s gene diversity were 1.48, 1.2, 0.2 and 0.1, respectively. According to Nei?s genetic distance, the lowest genetic distance (0.048) was observed among both two populations of A. elburzense (Emamzadeh Ebrahim and Kamelat), and two populations of A. subakaka (Jame Shoran and Ghalelan) while the highest distance (0.097) was observed among a population of A. kurdistanicum (Taze Abad Oryeh) with both A. pseudobodeanum (Shen Jari), and A. derderianum (Dareh Oson) populations. In UPGMA cluster analysis, the populations were grouped into four main clusters at a cutoff value of 0.07. The analysis of molecular variance showed that the maximum value of genetic variation was found within the populations (68%), where as a low genetic differentiation was observed among the populations (32%). Our results revealed that ISSR molecular markers are useful to display the diversity in Allium genus and can be used to improve the classification accuracy. This study provided valuable information for the conservation of these species and breeding program planning.

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Genetic divergence in basil cultivars and hybrids

Horticultura Brasileira ◽

10.1590/s0102-053620190208 ◽

2019 ◽

Vol 37 (2) ◽

pp. 180-187

Author(s):

Rodrigo P Alves ◽

Ana Veruska C Silva ◽

Camila S Almeida-Pereira ◽

Tatiana S Costa ◽

Sheila V Alvares-Carvalho ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Genetic Variability ◽

Polymorphic Information Content ◽

Dna Amplification ◽

Issr Markers ◽

Economic Importance ◽

Dissimilarity Index ◽

The World ◽

Issr Molecular Markers

ABSTRACT Basil is an aromatic herb that stands out for its economic importance. It is consumed in natura and used to obtain essential oil. The cultivation of this species in several regions of the world has allowed variations by natural crosses and euploidy, leading to the wide genetic variability found nowadays. Considering the importance of this species, we aimed to analyze the genetic diversity of 27 basil genotypes using ISSR molecular markers. Fourteen primers were employed for DNA amplification, resulting in 86% polymorphism. Based on the Jaccard’s dissimilarity index, the highest index (0.80) was observed between the individuals BAS001 and BAS012, while the lowest index (0.18) was detected between the genotypes BAS014 and BAS015. The genetic similarity among individuals was calculated, forming four distinct clusters. Most individuals (40.7%) were allocated in cluster I. The polymorphic information content (PIC) (0.89) indicated considerable levels of genetic diversity among genotypes. In this sense, the ISSR markers were efficient in the detection of polymorphisms between the accessions, suggesting the genetic variability of the collection. This result demonstrates the importance of the use of molecular markers and the advantages that this information provides to the breeding of the species.

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Genetic diversity of grapevine (Vitis vinifera L.) cultivars in Al-Madinah Al-Munawara based on molecular markers and morphological traits

Bangladesh Journal of Plant Taxonomy ◽

10.3329/bjpt.v27i1.47573 ◽

2020 ◽

Vol 27 (1) ◽

pp. 113-127

Author(s):

Usama K Abdel Hameed ◽

Khawla Abdelaziz ◽

Nahla El Sherif

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Genetic Distance ◽

Fruit Trees ◽

Inter Simple Sequence Repeat ◽

Morphological Data ◽

Start Codon ◽

Vitis Vinifera L ◽

Plant Taxon ◽

Issr Primers

Grapevine is one of the major fruit trees in the Kingdom of Saudi Arabia. This study aims to discriminate and assess the genetic diversity in three grapevine cultivars in Al- Madinah through the combination of characterization using both classical ampelographic as well as ampelometric studies with molecular markers using Randomly Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeat (ISSR) and Start Codon Targeted Polymorphism (SCoT). For the ampelographic analysis, twelve OIV descriptors were used, and for the ampelometric analysis, the fully expanded mature leaves area were automatedly measured. The genetic distance among the three grapevines cultivars, calculated using Jaccard's coefficient, ranged from 0.7577 (between AL Nakheel and Banati) to 0.4501 (between AL Nakheel and Ahmer). The molecular analysis was based on the use of thirty-one primers; ten RAPD primers, seven ISSR primers and fourteen SCoT primers. RAPD primers generated the highest polymorphism (67%), while the level of polymorphism with ISSR primers was 36% and with SCoT 44%. All of the three markers generated similar dendrograms, and the genetic distance generated with RAPD was higher compared with SCoT and ISSR. The three markers RAPD, ISSR and SCoT were combined and amalgamated with the morphological data, and combined dendrogram was generated and discussed. AL Nakheel and Ahmer cultivars were found to be more closely related to each other than Banati which was separated in a different cluster. Both methods were effectively efficient for complete identification of grapevine and for studying the genetic diversity between closely related cultivars. Bangladesh J. Plant Taxon. 27(1): 113-127, 2020 (June)

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Assessment of genetic variability amongst cultivated populations of Khasi mandarin (Citrus reticulata Blanco) detected by ISSR

Plant Genetic Resources ◽

10.1017/s1479262121000162 ◽

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.

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

10.21203/rs.3.rs-666059/v1 ◽

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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