Eco-Geographical, Morphological and Molecular Characterization of a Collection of the Perennial Endemic Species Medicago tunetana (Murb.) A.W. Hill (Fabaceae) from Tunisia

In order to characterize and conserve the endemic pastoral species Medicago tunetana, many prospecting missions were carried out in mountainous regions of the Tunisian ridge. Twenty-seven eco-geographical and morphological traits were studied for six M. tunetana accessions and followed by molecular analysis using seven Simple Sequence Repeat (SSR). Only five markers were polymorphic and reproductible in the six M. tunetana populations. A total of 54 alleles were observed with an average of 10.8 bands/primer/genotype. Mean Polymorphism Information Content (PIC), Nei gene diversity (h) Shannon’s information index (I) indicated the high level of polymorphism. The generated dendrogram with hierarchical UPGMA cluster analysis grouped accessions into two main groups with various degree of subclustring. All the studied accessions shared 57% of genetic similarity. Analysis of variance showed high significant difference between morphological traits among M. tunetana populations where MT3 from Kesra showed different morphological patterns regarding leaf, pod and seeds traits. Canonical correspondence analysis (CCA) showed two principal groups of M. tunetana populations based on potassium, total and active lime contents in soil. Our results suggest that SSR markers developed in M. truncatula could be a valuable tool to detect polymorphism in M. tunetana. Furthermore, the studied morphological markers showed a large genetic diversity among M. tunetana populations. This approach may be applicable for the analysis of intra specific variability in M. tunetana accessions. Our study could help in the implementation of an effective and integrated conservation programs of perennial endemic Medicago.

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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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Assessment of relationships among and within Helichrysum Mill. (Asteraceae) species by using ISSR markers and morphological traits

Hacquetia ◽

10.2478/hacq-2018-0014 ◽

2019 ◽

Vol 18 (1) ◽

pp. 105-118 ◽

Cited By ~ 2

Author(s):

Narjes Azizi ◽

Masoud Sheidai ◽

Valiollah Mozaffarian ◽

Mitra Arman ◽

Zahra Noormohammadi

Keyword(s):

Genetic Similarity ◽

Morphological Traits ◽

Morphological Analysis ◽

Gene Diversity ◽

Molecular Data ◽

Issr Markers ◽

Diagnostic Features ◽

Analysis Of Molecular Variance ◽

Information Index ◽

Expected Heterozygosity

Abstract This study conducted to determine relationship among and within Iranian Helichrysum species (Asteraceae). In this study based on ISSR markers, the highest percentage of ISSR loci polymorphism (54.7%) occurred in H. armenium. The highest gene diversity over loci (1.224), Shannon’s Information Index (0.224%) and Expected Heterozygosity (0.142%) occurred in H. armenium (0.18) and the lowest of these parameters (0%) were observed in H. araxinum, H. graveolens, H. persicum and H. psychrophilum. The highest genetic similarity occurred between H. armenium and H. rubicundum (0.989), while the lowest was between H. polyphyllum and H. graveolens (0.213). The analysis of molecular variance (AMOVA), showed significant genetic variation among (24%) and within (76%) species. In morphological analysis traits such as indumentum, resting bud, achene length, achenial papillae, dimension of receptacle and form and apex of phyllaries were main diagnostic features. Results obtained from the morphological cluster were greatly consistent with the molecular data, to elucidating taxonomic relationships, as well as both attributed the higher diversity in H. armenium and H. rubicundum in comparison with other species and also indicated that H. persicum is a member of H. oocephalum species. Totally we confirmed the presence of 18 species in Iran.

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Genetic Diversity and Population Structure of Endangered Catfish Rita rita (Hamilton, 1822) Revealed by Heterologous DNA Microsatellite Markers

Asian Fisheries Science ◽

10.33997/j.afs.2021.34.2.007 ◽

2021 ◽

Vol 34 (2) ◽

Author(s):

MUHAMMAD FORHAD ALI ◽

◽

MD. RAFIQUL ISLAM SARDER ◽

MOHAMMAD MATIUR RAHMAN ◽

MD. FAZLUL AWAL MOLLAH ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Genetic Difference ◽

Information Index ◽

Hardy Weinberg Equilibrium ◽

High Gene ◽

High Level ◽

Dna Microsatellite

Genetic information is essential for conservation and future aquaculture development of the endangered catfish Rita rita (Hamilton, 1822). Two hundred catfish, R. rita, 50 from four rivers, the Old Brahmaputra, Jamuna, Meghna and Kangsa were collected and analysed to evaluate the genetic diversity and population structure using five microsatellite primers (Cba06-KUL, Cba08-KUL, Cba09-KUL, Phy03-KUL and Phy07-KUL). Four of the five amplified loci were found polymorphic (P95) in all the populations and 46 alleles were recorded with 9 to 14 alleles per locus. Differences were observed in the total number of alleles ranging from 41 to 44, effective number of alleles from 29.96 to 37.46, observed heterozygosity from 0.57 to 0.76, Shannon’s information index from 2.09 to 2.30 and polymorphic information content from 0.84 to 0.88 among the four populations. Results exposed the highest levels of genetic diversity in the Meghna population while the lowest in the Kangsa population of R. rita. All the populations were significantly deviated (P < 0.001) from the Hardy-Weinberg equilibrium for all the loci. Nei’s genetic distance between populations ranged 0.007 to 0.017 with low overall genetic difference FST = 0.011 and high gene flow Nm = 24.333, indicating that R. rita populations were not subdivided. This study revealed a high level of gene diversity with deficiency in genetic heterogeneity in all the populations of R. rita, emphasising natural management, conservation and rehabilitation measures of this species.

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Characterization of simple sequence repeat loci for Peltigera membranacea (lichenized Ascomycota) and its Nostoc photobiont

The Lichenologist ◽

10.1017/s0024282921000384 ◽

2021 ◽

Vol 53 (6) ◽

pp. 457-465

Author(s):

Silke Werth ◽

Stefán Þór Pálsson ◽

Ólafur S. Andrésson

Keyword(s):

Simple Sequence Repeat ◽

Population Genetic ◽

Common Ground ◽

Gene Diversity ◽

Similar Species ◽

Sequence Repeat ◽

Genetic Studies ◽

Unbiased Gene ◽

Simple Sequence

AbstractTo facilitate population-genetic studies, we developed simple sequence repeat (SSR) markers and a molecular species identification assay for Peltigera membranacea (Ascomycota, Peltigerales), a common ground-dwelling lichen of forest and tundra ecosystems. Additional markers were developed for its Nostoc photobiont. Twenty-one fungal markers for P. membranacea were found to be polymorphic, with the number of alleles ranging from 3–21. Nei's unbiased gene diversity ranged from 0.588 to 0.640 in four significantly structured (FST = 0.059) mycobiont populations. For the Nostoc photobiont, 14 polymorphic SSR were developed, yielding 4–14 alleles each, with gene diversity ranging from 0.062 to 0.771 in four populations showing substantial population structure (FST = 0.278). The new markers developed are suitable for population genetic studies of Peltigera membranacea and of its cyanobiont, and at the same time allowed us to distinguish 98.5% of P. membranacea specimens from morphologically similar species of Peltigera.

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DNA Fingerprinting of Tetraploid Cherry Germplasm Using Simple Sequence Repeats

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.126.2.205 ◽

2001 ◽

Vol 126 (2) ◽

pp. 205-209 ◽

Cited By ~ 93

Author(s):

Claudio Cantini ◽

Amy F. Iezzoni ◽

Warren F. Lamboy ◽

Manuela Boritzki ◽

Darush Struss

Keyword(s):

Simple Sequence Repeats ◽

Agricultural Research ◽

Gene Diversity ◽

Sour Cherry ◽

Department Of Agriculture ◽

Global Database ◽

Usda Agricultural Research ◽

The Individual ◽

High Level ◽

Simple Sequence

The U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS) tetraploid cherry (Prunus L. sp.) collection at Geneva, N.Y., contains ≈75 accessions of sour cherry (P. cerasus L.), ground cherry (P. fruticosa Pall.), and their hybrids. Accurate and unambiguous identification of these accessions is essential for germplasm preservation and use. Simple sequence repeats (SSRs) are currently the markers of choice for germplasm fingerprinting because they characteristically display high levels of polymorphism. Recently SSR primer pairs from sweet cherry (P. avium L.), sour cherry, and peach [(P. persica L. Batsch (Peach Group)] have been reported. Ten SSR primer pairs were tested on 59 tetraploid cherry accessions to determine if they could differentiate among the accessions. Scorable SSR fragments were produced with all primer-accession combinations. The cherry accessions exhibited high levels of polymorphism with 4 to 16 different putative alleles amplified per primer pair. Most of the putative alleles were rare with frequencies <0.05. Heterozygosity values ranged from 0.679 to 1.00, while gene diversity values ranged from 0.655 to 0.906. The primer pairs differentiated all but two of the 59 cherry accessions. Based upon the ability of the SSR data to differentiate the cherry accessions and the high level of gene diversity, we propose that all the tetraploid cherry accessions in the USDA/ARS collection be fingerprinted to provide a mechanism to verify the identity of the individual accessions. The fingerprinting data are available on the World Wide Web (http://www.ars-grin.gov/gen/cherry.html) so that other curators and scientists working with cherry can verify identities and novel types in their collections and contribute to a global database.

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Breeding potential and genetic diversity of "Híbrido do Timor" coffee evaluated by molecular markers

Cropp Breeding and Applied Biotechnology ◽

10.1590/s1984-70332010000400003 ◽

2010 ◽

Vol 10 (4) ◽

pp. 298-304 ◽

Cited By ~ 12

Author(s):

Tesfahun Alemu Setotaw ◽

Eveline Teixeira Caixeta ◽

Guilherme Ferreira Pena ◽

Eunize Maciel Zambolim ◽

Antonio Alves Pereira ◽

...

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Molecular Markers ◽

Genetic Structure ◽

Gene Diversity ◽

High Genetic Diversity ◽

Breeding Programs ◽

Information Index ◽

Upgma Cluster Analysis ◽

Potential Use

AFLP, RAPD and SSR molecular markers were used to study the genetic diversity and genetic structure of the Híbrido de Timor germplasm. The principal coordinate analysis, UPGMA cluster analysis based on genetic dissimilarity of Jaccard, Bayesian model-based cluster analysis, percentage of polymorphic loci, Shannon's information index and Nei gene diversity were employed to assess the genetic diversity. The analyses demonstrated a high genetic diversity among Híbrido de Timor accessions. UPGMA and Bayesian cluster analyses grouped the accessions into three clusters. The genetic structure of Híbrido de Timor is reported. The management of Híbrido de Timor germplasm variability and its potential use in breeding programs are discussed.

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Diversity Among a Wide Asian Collection of Bitter Gourd Landraces and their Genetic Relationships with Commercial Hybrid Cultivars

Journal of the American Society for Horticultural Science ◽

10.21273/jashs03748-16 ◽

2016 ◽

Vol 141 (5) ◽

pp. 475-484 ◽

Cited By ~ 10

Author(s):

Narinder P.S. Dhillon ◽

Supannika Sanguansil ◽

Roland Schafleitner ◽

Yen-Wei Wang ◽

James D. McCreight

Keyword(s):

Genetic Relationships ◽

Geographic Origin ◽

Bitter Gourd ◽

Breeding Lines ◽

Ssr Loci ◽

Geographical Group ◽

Dark Green ◽

High Level ◽

Simple Sequence

We report here the genetic characterization of bitter gourd (Momordica charantia) based on polymorphisms of 50 simple sequence repeat (SSR) loci in 114 accessions that included landraces, breeding lines, and commercial open-pollinated and F1 hybrid cultivars widely grown in Asia. Neighbor-joining tree analysis revealed a high level of genetic variability in the collection. The 114 accessions formed three subpopulations represented by five clusters. Distribution of accessions across the five clusters reflected their geographic origin to a large extent. South Asian accessions originating from India, Bangladesh, and Pakistan were more closely related to each other than to any other geographical group. Likewise, southeast Asian accessions that originated from Cambodia, Vietnam, Indonesia, and Philippines were grouped together. Accessions that originated from Taiwan were genetically distinct and grouped separately. A landrace from Laos was genetically close to the accessions from Thailand and genetically distinct from the rest of the accessions. White-fruited genotypes were genetically distinct from green- and dark green–fruited genotypes. Low- and medium-bitter accessions were more similar to each other than to the high-bitter genotypes. Accessions with cylindrical fruit were genetically distinct from those with spindle or elongated fruit. Commercial cultivars in each cluster were closely related, which indicated a narrowing of the bitter gourd genetic base in Asia in response to market demands for uniformity and yield. Use of diverse germplasm resources in bitter gourd breeding will help in sustainable breeding and production.

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Genetic Dissection of New Genotypes of Drumstick Tree (Moringa oleiferaLam.) Using Random Amplified Polymorphic DNA Marker

BioMed Research International ◽

10.1155/2013/604598 ◽

2013 ◽

Vol 2013 ◽

pp. 1-6 ◽

Cited By ~ 6

Author(s):

Shamsuddeen Rufai ◽

M. M. Hanafi ◽

M. Y. Rafii ◽

S. Ahmad ◽

I. W. Arolu ◽

...

Keyword(s):

Genetic Diversity ◽

Dna Marker ◽

Diversity Index ◽

Gene Diversity ◽

Random Amplified Polymorphic Dna ◽

Genetic Dissection ◽

Improvement Program ◽

Information Index ◽

Upgma Cluster Analysis ◽

Genetic Diversity Study

The knowledge of genetic diversity of tree crop is very important for breeding and improvement program for the purpose of improving the yield and quality of its produce. Genetic diversity study and analysis of genetic relationship among 20Moringa oleiferawere carried out with the aid of twelve primers from, random amplified polymorphic DNA marker. The seeds of twentyM. oleiferagenotypes from various origins were collected and germinated and raised in nursery before transplanting to the field at University Agricultural Park (TPU). Genetic diversity parameter, such as Shannon's information index and expected heterozygosity, revealed the presence of high genetic divergence with value of 1.80 and 0.13 for Malaysian population and 0.30 and 0.19 for the international population, respectively. Mean of Nei's gene diversity index for the two populations was estimated to be 0.20. In addition, a dendrogram constructed, using UPGMA cluster analysis based on Nei's genetic distance, grouped the twentyM. oleiferainto five distinct clusters. The study revealed a great extent of variation which is essential for successful breeding and improvement program. From this study,M. oleiferagenotypes of wide genetic origin, such as T-01, T-06, M-01, and M-02, are recommended to be used as parent in future breeding program.

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Assessment of genetic diversity in Narbon vetch (Vicia narbonensis L.) germplasm using morphological and molecular markers

Crop and Pasture Science ◽

10.1071/cp18086 ◽

2018 ◽

Vol 69 (9) ◽

pp. 904 ◽

Cited By ~ 1

Author(s):

Siwar Bouabid ◽

H. Chennaoui Kourda ◽

A. Boussaha ◽

M. Ben Naceur ◽

A. Zoghlami Khélil

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Morphological Traits ◽

Polymorphic Information Content ◽

Genetic Distances ◽

Germplasm Management ◽

Vicia Narbonensis ◽

High Level ◽

Differentiation Index ◽

Simple Sequence

Narbon vetch (Vicia narbonensis L.) is a promising forage legume with good resistance to cold and drought. The assessment of genetic diversity of Narbon vetch is an essential component in germplasm management. In this study, we analysed the genetic diversity of 13 local and introduced Narbon vetch accessions from three continents using 27 morphological traits and 13 simple sequence repeat (SSR) markers. Significant differences among accessions for morphological and phenological traits were observed. The SSR markers showed a total of 126 alleles with a mean number of two alleles per locus. Polymorphic information content values were in the range of 0.772–0.915 with an average of 0.858. A high level of diversity (Nei’s genetic differentiation index of 59) was observed among accessions. Analysis of genetic distances separated the studied accessions into three groups based on both morphological and SSR markers. Cluster analysis of the SSR markers separated the accessions into three groups according to geographical origin. The Tunisian populations shared the same morphological traits but differed genetically from each other and were similar to those from Lebanon. A significant correlation was detected between morphological traits and SSR markers. The results suggested that SSR markers can be used to efficiently distinguish Narbon vetch accessions and estimate their genetic diversity.

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Morphomolecular Characterization of Local Boro Rice (Oryza Sativa L.) Germplasm

Bangladesh Journal of Plant Breeding and Genetics ◽

10.3329/bjpbg.v29i2.33941 ◽

2016 ◽

Vol 29 (2) ◽

pp. 01-09

Author(s):

T. Halder ◽

M. E. Hoque ◽

M. M. Islam ◽

L. Ali ◽

A. K. Chowdhury

Keyword(s):

Oryza Sativa ◽

Morphological Traits ◽

Oryza Sativa L ◽

Polymorphic Information Content ◽

Growth Duration ◽

Allele Number ◽

Simple Sequence ◽

1000 Grain Weight ◽

Boro Rice

An investigation was carried out to analysis the genetic diversity of 12 Bangladeshi local Boro rice (Oryza sativa L.) germplasm using morphological traits and molecular markers. Eight morphological traits (viz., days to 50 percent flowering, growth duration, plant height, filled grain/panicle, 1000 grain weight and grain yield) and eight Simple Sequence Repeat (SSR) markers were used for this analysis. The plant morphological traits exhibited more variation among the genotypes tested. Several traits were found to be significantly positive in correlation coefficient analysis and thus those traits can be considered stable as demonstrated by their coefficient of variability. A set of eight SSR primer pairs was used for molecular characterization resulting 49 alleles, where average of allele number was 6.13. The polymorphic information content (PIC) values ranged from 0.67 (RM1) to 0.86 (RM314) with an average of 0.76. The highest PIC value (0.86) was obtained for RM314 which also gave maximum alleles. The PIC value revealed that RM314 was the best marker for 12 genotypes tested. The cluster analysis based on UPGMA system grouped 12 genotypes into four clusters.

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