Assessment of Genetic Diversity and Population Structure of Some Soft and Hard Wheat Varieties Based on SSR Marker

Wheat (Triticum spp.) is one of the most important cereal crops in Iraq and the world. It includes many species and varieties. The two major cultivated species of wheat are, durum wheat (Tritium durum Desf.) which is tetraploid (2n= 28) and the common wheat (Triticum aestivum L.) which is hexaploid (2n = 42). Ten wheat varieties from both species were examined using ten Simple sequence repeat (SSR) markers (WMC17, WMC20, WMC21, WMC24, WMC25, WMC48, WMC50, WMC283, Xgwm11 and Xgwm626). Various genetic parameters were calculated using Power Marker V3.25 software. A total of 156 alleles were detected in both species. The gene diversity in wheat varieties from both species collectively varied from 0.85 to 1.00, which indicates considerable genetic diversity in the examined varieties. All markers used in this study were highly informative and the polymorphic information content (PIC) values were higher than 0.50 in all loci. Hence all markers are considered useful for genetic diversity studies in wheat’s populations. The dendrogram separated the populations into two main clades and many subgroups. Azadi variety was simplicifolious. This study confirms the discriminating power of SSR typing and its usefulness for comparison within hard and soft wheat populations.

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

Bangladesh Journal of Agricultural Research ◽

10.3329/bjar.v37i3.12082 ◽

2012 ◽

Vol 37 (3) ◽

pp. 389-398 ◽

Cited By ~ 3

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

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AFLP and SSR analysis of genetic diversity among landraces of bread wheat (Triticum aestivum L. em. Thell) from different geographic regions

Australian Journal of Agricultural Research ◽

10.1071/ar05015 ◽

2005 ◽

Vol 56 (7) ◽

pp. 691 ◽

Cited By ~ 15

Author(s):

B. J. Stodart ◽

M. Mackay ◽

H. Raman

Keyword(s):

Genetic Diversity ◽

Middle East ◽

Bread Wheat ◽

Ssr Markers ◽

North Africa ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Triticum Aestivum L ◽

Southern Europe ◽

Germplasm Collections

A set of 44 bread wheat landraces was used to determine the efficacy of 16 amplifed fragment length polymorphism (AFLP) primers and 63 wheat simple sequence repeat (SSR) markers in identifying polymorphisms between accessions. The SSR markers detected approximately 10 alleles per locus with a mean gene diversity (Hz) of 0.63, whereas AFLP primers identified approximately 147 fragments per primer with a mean gene diversity of 0.25. A set of 54 SSR markers and 11 AFLP primers was identified as highly polymorphic (polymorphic information content (PIC) ≥ 0.5 and 0.3 for SSR and AFLP, respectively), and suitable for molecular characterisation of germplasm. Principle coordinate analysis suggested that the AFLP and SSR loci could be used to discriminate among accessions collected from North Africa and southern Europe from those collected from the Middle East. Both marker types indicate that accessions from North Africa and southern Europe, the Middle East, and southern and eastern Asia are genetically diverse. The results indicate the usefulness of the molecular markers to assess genetic diversity present within germplasm collections.

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Genetic diversity within local and introduced cultivars of wheat (Triticum aestivum L.) grown under Mediterranean environment as revealed by AFLP markers

Acta Biologica Szegediensis ◽

10.14232/abs.2019.1.25-30 ◽

2019 ◽

Vol 63 (1) ◽

pp. 25-30

Author(s):

Mohammed Imad Eddin Arabi ◽

Amina Shoaib ◽

Eyad Al-Shehadah ◽

Mohammed Jawhar

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Principal Component ◽

Triticum Aestivum L ◽

Wheat Breeding ◽

Aflp Markers ◽

Group Method ◽

Wheat Cultivars ◽

Arithmetic Means

Information on genetic diversity among cultivars is critical in wheat improvement. In this work, heterogeneity within local and introduced cultivars of bread wheat grown in Syria was investigated using amplified fragment length polymorphism (AFLP) markers. The eight primer pairs were used to detect 177 polymorphic bands among the 21 cultivars resulting in an average of 22.13 (57.3%) polymorphic loci per primer pair. Major allelic frequency ranged from 0.50 to 0.75 with a mean 0.64, and estimated gene diversity was 0.45. Values of average polymorphic information content (PIC) for these markers were estimated to be 0.34. This low value might be attributed to the rigorous selection pressure aimed at cultivar purity and associated breeding practices. Dissimilarity values ranged from 0.32 to 0.66 with an average of 0.54, indicating that such techniques sample distinct genome regions. Three major subgroups of wheat cultivars were identified using the unweighted pair-group method with arithmetic means analysis (UPGMA), with all local cultivars falling into one cluster, which was confirmed by a principal component analysis (PCA). The narrow genetic diversity observed among Syrian wheat cultivars suggests the need of broadening the genetic base of wheat breeding materials, including local landraces.

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Molecular characterization and genetic diversity in some Egyptian wheat (Triticum aestivum L.) using microsatellite markers

Potravinarstvo Slovak Journal of Food Sciences ◽

10.5219/978 ◽

2019 ◽

Vol 13 (1) ◽

pp. 100-108

Author(s):

Ayman El-Fiki ◽

Mohamed Adly

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Microsatellite Markers ◽

Bread Wheat ◽

Polymorphic Information Content ◽

Triticum Aestivum L ◽

Cereal Crop ◽

Font Size ◽

Wheat Varieties ◽

Marker Index

Wheat (Triticum aestivum L.) is the most important and strategic cereal crop in Egypt and has many bread wheat varieties. Seventeen Egyptian bread wheat varieties used in this study with a set of sixteen wheat microsatellite markers to examine their utility in detecting DNA polymorphism, estimating genetic diversity and identifying genotypes. A total of 190 alleles were detected at 16 loci using 16 microsatellite primer pairs. The number of allele per locus ranged from 8 to 20, with an average of 11.875. The polymorphic information content (PIC) and marker index (MI) average values were 0.8669, 0.8530 respectively. The (GA) n microsatellites were the highest polymorphic (20 alleles). The Jaccard's Coefficient for genetic similarity was ranged from 0.524 to 0.109 with average of 0.375. A dendrogram was prepared based on similarity matrix using UPGMA algorithm, divided the cultivars into two major clusters. The results proved the microsatellite markers utility in detecting polymorphism due to the discrimination of cultivars and estimating genetic diversity.

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Molecular diversity analysis in hexaploid wheat (Triticum aestivum L.) and two Aegilops species (Aegilops crassa and Aegilops cylindrica) using CBDP and SCoT markers

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-021-00157-8 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Ghazal Ghobadi ◽

Alireza Etminan ◽

Ali Mehras Mehrabi ◽

Lia Shooshtari

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Crop Improvement ◽

Wild Relatives ◽

Resolving Power ◽

Start Codon ◽

Aegilops Cylindrica ◽

Aegilops Crassa

Abstract Background Evaluation of genetic diversity and relationships among crop wild relatives is an important task in crop improvement. The main objective of the current study was to estimate molecular variability within the set of 91 samples from Triticum aestivum, Aegilops cylindrica, and Aegilops crassa species using 30 CAAT box–derived polymorphism (CBDP) and start codon targeted (SCoT) markers. Results Fifteen SCoT and Fifteen CBDP primers produced 262 and 298 fragments which all of them were polymorphic, respectively. The number of polymorphic bands (NPB), polymorphic information content (PIC), resolving power (Rp), and marker index (MI) for SCoT primers ranged from 14 to 23, 0.31 to 0.39, 2.55 to 7.49, and 7.56 to 14.46 with an average of 17.47, 0.34, 10.44, and 5.69, respectively, whereas these values for CBDP primers were 15 to 26, 0.28 to 0.36, 3.82 to 6.94, and 4.74 to 7.96 with a mean of 19.87, 0.31, 5.35, and 6.24, respectively. Based on both marker systems, analysis of molecular variance (AMOVA) indicated that the portion of genetic diversity within species was more than among them. In both analyses, the highest values of the number of observed (Na) and effective alleles (Ne), Nei’s gene diversity (He), and Shannon’s information index (I) were estimated for Ae. cylindrica species. Conclusion The results of cluster analysis and population structure showed that SCoT and CBDP markers grouped all samples based on their genomic constitutions. In conclusion, the used markers are very effective techniques for the evaluation of the genetic diversity in wild relatives of wheat.

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Assessment of Genetic Diversity of Promising Castor Been (Ricinus communis L.) Genotypes in Nigeria

Notulae Scientia Biologicae ◽

10.15835/nsb11310346 ◽

2019 ◽

Vol 11 (3) ◽

pp. 467-474

Author(s):

Bolaji Zuluqurineen SALIHU ◽

Olamide Ahmed FALUSI ◽

Adeyinka Olufemi ADEPOJU ◽

Ibrahim Wasiu AROLU ◽

Oladipupo Yusuf DAUDU ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Index ◽

Gene Diversity ◽

Ricinus Communis ◽

Polymorphic Information Content ◽

Block Design ◽

Genetic Material ◽

Morphological Data ◽

Research Attention ◽

Ricinus Communis L

Castor oil plant (Ricinus communis L.) is an important oil crop with little research attention in Nigeria. In the present research, extent of genetic diversity among 20 Nigerian castor genotypes was determined using morphological descriptors and molecular markers. The genotypes were laid out on a randomized complete block design with three replicated plots. Molecular genotyping of the genotypes was carried out using genomic Simple Sequence Repeats (SSR). The genotypes revealed high divergence in seed colour, seed shape, seed mottle, seed caruncle and seed sizes. Seedling establishment varied from 70.18% (in Acc. 006) to 93.25% (Acc. 001) with average mean of 81.53%. Raceme length ranged from 15.90 cm to 29.54 cm with population mean of 20.80 cm. The highest seed yield (1222.98 kg/ha) was recorded in Acc. 001 and the least (611.46 kg/ha) was observed in Acc. 006. Seed oil content varied between 32.15% in Acc. 042 and 54.03% in Acc. 006. Agglomerative cluster dendrogram constructed from morphological data showed random distribution of the genotypes into three cluster groups irrespective of the sources/collection points. The genetic diversity based on SSR Marker Analysis revealed high average expected heterozygosity (0.74), Polymorphic information content (0.68), Nei’s gene diversity index (0.72) and Shannon's Information index (1.43). The dendrogram constructed from molecular data grouped the twenty genotypes into three groups at coefficient of 0.34. From these findings, it showed that the twenty genotypes evaluated are divergent in nature and they could serve as good genetic material for castor breeding in Nigeria.

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

Asian Journal of Agriculture ◽

10.13057/asianjagric/g010109 ◽

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.

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

Archives Animal Breeding ◽

10.5194/aab-60-183-2017 ◽

2017 ◽

Vol 60 (3) ◽

pp. 183-189 ◽

Cited By ~ 9

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.

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Molecular genetic diversity and conservation priorities of Egyptian rabbit breeds

World Rabbit Science ◽

10.4995/wrs.2019.8923 ◽

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>

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