Genetic diversity analysis in blackgram (Vigna mungo (L.) Hepper) using AFLP and transferable microsatellite markers from azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi)

Genome ◽  
2009 ◽  
Vol 52 (2) ◽  
pp. 120-129 ◽  
Author(s):  
S. K. Gupta ◽  
T. Gopalakrishna
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Information Content ◽  
Principal Components ◽  
Polymorphic Information Content ◽  
Mantel Test ◽  
Vigna Mungo ◽  
Azuki Bean ◽  
Vigna Angularis ◽  
Aflp Data

Genetic diversity in 20 elite blackgram ( Vigna mungo (L.) Hepper) genotypes was studied using microsatellite and AFLP markers. Thirty-six microsatellite markers from azuki bean ( Vigna angularis (Willd.) Ohwi & Ohashi) were successfully amplified across the 20 blackgram genotypes and 33 microsatellite markers showed polymorphism. A total of 137 microsatellite alleles were generated with an average of 4.1 alleles per locus. The number of alleles ranged from two to nine and the polymorphic information content value for the microsatellite markers varied from 0.10 to 0.87 with an average of 0.49. Microsatellite markers were highly informative and a combination of only three microsatellite markers (CEDG264, CEDG173, and CEDG044) was sufficient to discriminate all 20 blackgram genotypes. In the case of AFLP, 11 primer pairs generated 324 polymorphic marker fragments. The polymorphic information content values for AFLP primer combinations ranged from 0.21 to 0.34 with an average of 0.29. Similarity measures and clustering analyses were made using microsatellite and AFLP data separately. The resulting dendrograms distributed the 20 blackgram genotypes into five main clusters. The dendrograms were comparable with each other with the Mantel test between the cophenetic matrices of microsatellite data and AFLP data showing moderate correlation (r = 0.64). The results of the principal components analysis were well congruent with the dendrograms. In the dendrograms as well as in the principal components analyses, genotype Trombay wild (Vigna mungo var. silvestris) was placed separately from rest of the genotypes. This study demonstrated that the azuki bean microsatellite markers are highly polymorphic and informative and can be successfully used for genome analysis in blackgram. Results indicate that sufficient variability is present in the blackgram genotypes and would be helpful in the selection of suitable parents for breeding purposes and gene mapping studies.

scholarly journals Genetic diversity and population structure of date palms (Phoenix dactylifera L.) in Ethiopia using microsatellite markers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Workia Ahmed ◽  
Tileye Feyissa ◽  
Kassahun Tesfaye ◽  
Sumaira Farrakh
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Information Content ◽  
Date Palm ◽  
Polymorphic Information Content ◽  
Phoenix Dactylifera ◽  
Mean Value ◽  
Date Palms ◽  
Expected Heterozygosity

Abstract Background Date palm tree (Phoenix dactylifera L.) is a perennial monocotyledonous plant belonging to the Arecaceae family, a special plant with extraordinary nature that gives eminent contributions in agricultural sustainability and huge socio-economic value in many countries of the world including Ethiopia. Evaluation of genetic diversity across date palms at DNA level is very important for breeding and conservation. The result of this study could help to design for genetic improvement and develop germplasm introduction programmes of date palms mainly in Ethiopia. Results In this study, 124 date palm genotypes were collected, and 10 polymorphic microsatellite markers were used. Among 10 microsatellites, MPdCIR085 and MPdCIR093 loci showed the highest value of observed and expected heterozygosity, maximum number of alleles, and highest polymorphic information content values. A total of 112 number of alleles were found, and the mean number of major allele frequency was 0.26, with numbers ranging from 0.155 (MPdCIR085) to 0.374 (MPdCIR016); effective number of alleles with a mean value of 6.61, private alleles ranged from 0.0 to 0.65; observed heterozygosity ranged from 0.355 to 0.726; expected heterozygosity varied from 0.669 to 0.906, polymorphic information content with a mean value of 0.809; fixation index individuals relative to subpopulations ranged from 0.028 for locus MPdCIR032 to 0.548 for locus MPdCIR025, while subpopulations relative to total population value ranged from − 0.007 (MPdCIR070) to 0.891 (MPdCIR015). All nine accesstions, neighbour-joining clustering analysis, based on dissimilarity coefficient values were grouped into five major categories; in population STRUCTURE analysis at highest K value, three groups were formed, whereas DAPC separated date palm genotypes into eight clusters using the first two linear discriminants. Principal coordinate analysis was explained, with a 17.33% total of variation in all populations. Generally, the result of this study revealed the presence of allele variations and high heterozygosity (> 0.7) in date palm genotypes. Conclusions Microsatellites (SSR) are one of the most preferable molecular markers for the study of genetic diversity and population structure of plants. In this study, we found the presence of genetic variations of date palm genotypes in Ethiopia; therefore, these genetic variations of date palms is important for crop improvement and conservation programmes; also, it will be used as sources of information to national and international genbanks.

scholarly journals Using microsatellite markers to analyze genetic diversity in 14 sheep types in Iran

2017 ◽  
Vol 60 (3) ◽  
pp. 183-189 ◽  
Author(s):  
Mohammad Taghi Vajed Ebrahimi ◽  
Mohammadreza Mohammadabadi ◽  
Ali Esmailizadeh
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Information Content ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Extraction Procedure ◽  
Shannon Index ◽  
Group Method ◽  
Salting Out ◽  
Pair Group

Abstract. Investigation of genetic relationship among populations has been traditionally based on the analysis of allele frequencies at different loci. The prime objective of this research was to measure the genetic polymorphism of five microsatellite markers (McMA2, BM6444, McMA26, HSC, and OarHH35) and study genetic diversity of 14 sheep types in Iran. Genomic DNA was extracted from blood samples of 565 individuals using an optimized salting-out DNA extraction procedure. The polymerase chain reaction (PCR) was successfully performed with the specific primers. Some locus–population combinations were not at Hardy–Weinberg equilibrium (P < 0. 05). The microsatellite analysis revealed high allelic and gene diversity in all 14 breeds. Pakistani and Arabi breeds showed the highest mean number of alleles (11.8 and 11 respectively), while the highest value for polymorphic information content was observed for the Arabi breed (0.88). A UPGMA (unweighted pair group method with arithmetic mean) dendrogram based on the Nei's standard genetic distance among studied breeds showed a separate cluster for Arabi and Pakistani breeds and another cluster for other breeds. The Shannon index (H0) for McMA2, BM6444, McMA26, HSC, and OarHH35 was 2.31, 2.17, 2.27, 2.04 and 2.18, respectively, and polymorphic information content (PIC) values were 0.88, 0.92, 0.87, 0.84, and 0.86 for McMA2, BM6444, McMA26, HSC, and OarHH35, respectively. The high degree of variability demonstrated within the studied sheep types implies that these populations are rich reservoirs of genetic diversity that must be preserved.

scholarly journals Evaluation of genetic variations and phylogeny of the most popular pear (Pyrus communis L.) cultivars in Duhok city using AFLP markers

2018 ◽  
Vol 6 (1) ◽  
pp. 1-10
Author(s):  
Shaymaa H. Ali ◽  
Hemin E. Othman ◽  
Payman A. Abdullah-Zibari ◽  
Jaladet M.S. Jubrael
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Distance ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Pyrus Communis ◽  
Aflp Markers ◽  
Aflp Data ◽  
Powerful Technique ◽  
Pyrus Communis L

Introduction: Genotyping and evaluation of genetic variation and polymorphic information content of the locally cultivated pear (Pyrus communis L.) might play an important role in building the genetic bank. These are also immensely important for present and future pear breeding program in the region. Methods: In the current study, AFLP markers have been employed to estimate the level of genetic diversity and to assess the phylogeny among the seven most popular pear cultivars in Duhok city. Results: Eight selective primer combinations generated a total of 653 AFLP fragments from which 445 (68.2%) fragments were polymorphic. The number of visible amplified products per primer combination were varied and ranged from 66 to 96 bands. The highest percentage of polymorphism (78.4%) was observed by the primer pair P174/M182, while the lowest percentage of polymorphism (58.6%) was observed by the primer pair P174/M100. The highest PIC (0.85) was obtained with the primer combination P174/M182, while, the lowest PIC (0.49) was obtained by the primer combination P174/M307. The genetic distance was ranged from 0.1348 (between Danimarki and Amreki cultivars) to 0.3131 (between Italy and Zaafaran2 cultivars). Based on the AFLP data, all the seven pear genotypes were successfully clustered into two separate clusters (C1 and C2) with an out-group of Itali cultivar. Conclusions: Overall, it can be concluded that there was high polymorphism among the studied genotypes. Also, it can be stated that the AFLP was a reliable and a powerful technique in genotyping and discriminating of respective pear cultivars.

scholarly journals Assessment of genetic diversity of selected cowpea landraces from Nigeria based on simple sequence repeat markers

2020 ◽  
Vol 36 (2) ◽  
pp. 33-44
Author(s):  
I.O. Iseghohi ◽  
A.I. Adesoye ◽  
D.A. Oludare ◽  
F.V. Agunbiade ◽  
N. Unachukwu
Keyword(s):  
Genetic Diversity ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Mantel Test ◽  
Ex Situ ◽  
Breeding Programs ◽  
Ecological Zones ◽  
Landrace Diversity ◽  
Savannah Zone ◽  
Simple Sequence

Understanding the genetic diversity of cowpea (Vigna unguiculata L. Walp.) landraces is useful for effective characterization and ex-situ conservation of germplasm. The analysis of genetic diversity of eighteen cowpea landraces collected from five agro-ecological zones in Nigeria was reported in this study. Five individuals per landrace were genotyped with six polymorphic microsatellite markers. Three to 5 alleles with a mean of 3.833 were detected. Mean Polymorphic information content (PIC) and observed heterozygosity of the markers were 0.5721 and 0.2433, respectively. Analysis of Molecular Variance (AMOVA) showed that variation due to agroecological zone constituted 24%, while variations among and within landraces as well as within individuals constituted 25%, 17% and 33%, respectively. Landraces collected from the humid rainforest zone showed high within landrace diversity and were not significantly different (P ≥ 0.001) from other landraces collected from the same zone. Landraces from the savannah zones showed low within landrace diversity and homozygous across all loci. Consequently, among landrace diversity was higher in the savannah zone with landraces collected from guinea savannah been the most diverse, followed by landraces from the derived savannah and Sudan savannah. Mantel test showed positive and significant correlation (r= 0.377, p= 0.01) between genetic and geographical distance of landrace collections. The findings are important for up-to-date characterizations of cowpea germplasm in Nigeria for improved breeding programs. Keywords: Genetic diversity, cowpea, Alleles, Polymorphic information content, AMOVA,

scholarly journals Diversity and genetic relatedness among genotypes of Vitis spp. using microsatellite molecular markers

2013 ◽  
Vol 35 (3) ◽  
pp. 799-808 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Cosme Damião Cruz ◽  
Sérgio Yoshimitsu Motoike
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Molecular Markers ◽  
Microsatellite Markers ◽  
Information Content ◽  
Genetic Relatedness ◽  
Polymorphic Information Content ◽  
Germplasm Bank ◽  
Expected Heterozygosity ◽  
Vitis Spp

The purpose of this research was to study the genetic diversity and genetic relatedness of 60 genotypes of grapevines derived from the Germplasm Bank of Embrapa Semiárido, Juazeiro, BA, Brazil. Seven previously characterized microsatellite markers were used: VVS2, VVMD5, VVMD7, VVMD27, VVMD3, ssrVrZAG79 and ssrVrZAG62. The expected heterozygosity (He) and polymorphic information content (PIC) were calculated, and the cluster analysis were processed to generate a dendrogram using the algorithm UPGMA. The He ranged from 81.8% to 88.1%, with a mean of 84.8%. The loci VrZAG79 and VVMD7 were the most informative, with a PIC of 87 and 86%, respectively, while VrZAG62 was the least informative, with a PIC value of 80%. Cluster analysis by UPGMA method allowed separation of the genotypes according to their genealogy and identification of possible parentage for the cultivars 'Dominga', 'Isaura', 'CG 26916', 'CG28467' and 'Roni Redi'.

scholarly journals Review: Genetic diversity studies using microsatellite markers and their contribution in supporting sustainable sheep breeding programs

2017 ◽  
Vol 1 (01) ◽  
pp. 46-51
Author(s):  
OUMER SHERIFF ◽  
KEFYALEW ALEMAYEHU
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Domestic Sheep ◽  
Breeding Programs ◽  
Sheep Breeding ◽  
Population Structures ◽  
The Mean ◽  
Tree Building ◽  
Diversity Studies

Sheriff O, Alemayehu K. 2017. Review: Genetic diversity studies using microsatellite markers and their contribution in supporting sustainable sheep breeding programs. Asian J Agric 1: 46-51. Microsatellites have been widely accepted and employed as useful molecular markers for measuring genetic diversity and divergence within and among populations. The various parameters developed so far to measure genetic diversity within and among populations are observed and expected heterozygosities (Ho and He), the mean number of alleles per locus (MNA),polymorphic information content (PIC), genetic distance and phylogenetic or tree building approach.The objective of thisreview was therefore to quantifythe genetic diversity studies of domestic sheep populations using microsatellite markersand their contribution in supporting sustainable sheep breeding programs. From the review, it is possible to see that there was high within population genetic variations in all the studied sheep populations, poor level of population differentiations and high levels of inbreeding. On the other hand, low estimates of hetrozygosities and mean number of alleles and employing only few and weak markers were observed in some of the studies. The gaps observed in the previous genetic diversity studies of the sheep populations may demand further works to reveal more information on the population structures andto start appropriate and sustainable breeding programs.

scholarly journals Microsatellite development via next-generation sequencing in Acacia stenophylla (Fabaceae) and Duma florulenta (Polygonaceae): two ecologically important plant species of Australian dryland floodplains

2018 ◽  
Author(s):  
Bruce F Murray ◽  
Michael A Reid ◽  
Shu-Biao Wu
Keyword(s):  
Gene Flow ◽  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Extreme Variability ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing ◽  
Semi Arid

Duma florulenta and Acacia stenophylla are two ecologically important but understudied species that naturally occur on the floodplains and riverbanks of Australia’s arid and semi-arid river systems. This paper describes the discovery and characterization of 12 and 13 polymorphic microsatellite markers for D. florulenta and A. stenophylla respectively. The number of alleles per locus for D. florulenta ranged from 2-12 with an average of 6.1. Across all samples, observed and expected heterozygosities ranged from 0.026 to 0.784 and 0.026 to 0.824 respectively and mean polymorphic information content was equal to 0.453. For A. stenophylla, the number of alleles per locus ranged between 2 and 8 with an overall mean of 4.8. Across all samples, observed and expected heterozygosities ranged from 0.029 to 0.650 and 0.029 to 0.761 respectively and mean polymorphic information content was 0.388. The developed suites of 12 and 13 microsatellite markers for D. florulenta and A. stenophylla respectively provide opportunity for novel research into mechanisms of gene flow, dispersal and breeding system and how they operate under the extreme variability these species are exposed to in the environments in which they live.

scholarly journals Molecular characterization of wheat (Triticum aestivum L.) genotypes through SSR markers

2012 ◽  
Vol 37 (3) ◽  
pp. 389-398 ◽  
Author(s):  
S Islam ◽  
MS Haque ◽  
RM Emon ◽  
MM Islam ◽  
SN Begum
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Allelic Diversity ◽  
Triticum Aestivum L ◽  
Allele Number ◽  
Average Gene

A study was undertaken to examine the genetic diversity of 12 wheat (Triticum aestivum L.) genotypes, using 4 simple sequence repeats (SSRs). A total of 10 alleles were found. Allele number per locus ranged from 2 to 4 with an average of 2.5. The polymorphic information content (PIC) values ranged from 0.2755 to 0.5411 with an average of 0.3839. The average gene diversity over all SSR loci for the 12 wheat genotypes was 0.4688, ranging from 0.3299 to 0.6042. Cluster analysis based on microsatellite allelic diversity discriminated the varieties into different clusters. Genetic diversity was the highest between variety Gourab and Akbar as well as Gourab and BAW-1064, showing a genetic distance value of 0.4697. The genetic distance was lowest between Balaka and Aghrani as well as Triticale and BAW-1036. Positive correlations were found between gene diversity, number of alleles, the allele size range and the types of repeat motif of microsatellite markers. It was found from this study that microsatellite markers could characterize and discriminate all of the genotypes. More primers should be used for saturation of different regions in further studies. Bangladesh J. Agril. Res. 37(3): 389-398, September 2012 DOI: http://dx.doi.org/10.3329/bjar.v37i3.12082

scholarly journals Molecular genetic diversity and conservation priorities of Egyptian rabbit breeds

2019 ◽  
Vol 27 (3) ◽  
pp. 135
Author(s):  
O.A.M. Badr ◽  
I.I.S. El-Shawaf ◽  
M.H.A. Khalil ◽  
M.H. Refaat ◽  
S.I.A. Ramadan
Keyword(s):  
Genetic Diversity ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Molecular Genetic ◽  
Vital Role ◽  
Conservation Priorities ◽  
Molecular Genetic Diversity ◽  
Hardy Weinberg Equilibrium ◽  
Diversity Studies ◽  
Nei's Genetic Distance

<p>The limited rabbit resources in Egypt are threatened by the danger of extinction, whereas genetic diversity studies of native breeds could play a vital role in conservation and improvement of these breeds. In this study, 3 native rabbit breeds: Gabali (G), Baladi Red (BR) and Baladi Black (BB), in addition to New Zealand White (NZW), were genotyped using 12 microsatellite markers. All the typed microsatellites were polymorphic by average number of alleles 5.25 per locus. Observed and expected heterozygosity per locus averaged 0.62 and 0.68, respectively. The average polymorphic information content was 0.71 and the highest polymorphic information content was recorded in locus SOL33 by 0.85. All the studied loci except SAT7 and SAT2 showed deviation from Hardy-Weinberg equilibrium with significant level. The inbreeding coefficient of the individuals relative to the total population was 0.07. The within-population heterozygote deficit averaged 0.07 and ranged from 0.141 in BR to 0.015 in BB breeds. The highest pairwise differentiation among the populations was recorded between BB and NZW (0.071), while the lowest value was recorded between BR and both of G (0.038) and BB (0.039). The lowest pairwise Nei’s genetic distance was recorded between BR and BB (0.190), while the highest was recorded between NZW and BB breeds (0.409). BR and G populations were clustered together forming an admixed mosaic cluster. BR recorded the highest contribution in the aggregate genetic diversity based on the three prioritisation methods used.</p>

scholarly journals Morphological Characterization and Genetic Diversity Analysis of a Tunisian Durum Wheat (Triticum Turgidum Var. Durum) Collection

2020 ◽  
Author(s):  
Maroua Ouaja ◽  
Bochra Amina Bahri ◽  
Lamia Aouini ◽  
Sahbi Ferjaoui ◽  
Maher Medini ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Durum Wheat ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Morphological Characterization ◽  
Genetic Variations ◽  
Mantel Test ◽  
Ex Situ ◽  
The South ◽  
Population Structure Analysis

Abstract Background: Tunisia is a center of genetic diversity of durum wheat and has a large number of abandoned old local landraces. An accurate investigation and characterization of the morphological and genetic features of these landraces would allow their rehabilitation and use for practical and beneficial purposes. In this context, a collection of 304 local accessions of durum wheat, collected from five regions and three climatic zones of central and southern Tunisia, was studied. Results: Morphological characterization was carried out using 12 spike-related traits and rendered a mean Shannon-Weaver Index (H') of 0.80 indicating the presence of a high level of polymorphism among accessions. Based on these traits 11 local landraces, namely Mahmoudi, Azizi, Jneh Khotifa, Mekki, Biskri, Taganrog, Biada, Badri, Richi, Roussia and Souri were identified. Spike length (H’=0.98) and shape (H’=0.86) with grains size (H’=0.94), form (H’=0.87) and color (H’=0.86) were the most polymorphic morphological traits. The genetic diversity was assessed using 10 SSR markers, with a polymorphic information content (PIC) of 0.69. Levels of genetic diversity were generally high, with a Shannon's Information Index (I) of 0.62 and a gene diversity (He) of 0.35. In addition, population structure analysis distinguished 11 genetic groups resulted from STRUCTURE and Mantel test showed a significant correlation between genetic and morphological distances. Analysis of molecular variance (AMOVA) showed high genetic variations within regions (81%) and wheat subpopulations (41%) showing a considerable amount of admixture between landraces realized by farmers; as well as a moderate (19%) and high (59%) genetic variations among regions and wheat subpopulations, indicating practices of selection pressure conducted by farmers. The Mahmoudi landrace showed spike densities significantly different between the center to the south of Tunisia; notably loose spikes with open glumes in the south and compact ones in the center, which may represent an adaptation form for tolerance to high temperature. Conclusion: Overall, this study highlights the genetic richness of local resources for better in situ or ex situ conservation and for their subsequent use in plant breeding programs.

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