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

S Islam; MS Haque; RM Emon; MM Islam; SN Begum

doi:10.3329/bjar.v37i3.12082

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

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.

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.

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

Science Journal of University of Zakho ◽

10.25271/sjuoz.2020.8.3.732 ◽

2020 ◽

Vol 8 (3) ◽

pp. 80-87

Author(s):

Yousif M. Fattah ◽

Nergiz N. Tayib

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Triticum Aestivum L ◽

Wheat Varieties ◽

Discriminating Power ◽

Triticum Spp ◽

Cultivated Species ◽

The Common ◽

Diversity Studies

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.

Analysis of Genetic Diversity and Population Structure of Some Bangladeshi Rice Landraces and HYV

Journal of Scientific Research ◽

10.3329/jsr.v4i3.10416 ◽

2012 ◽

Vol 4 (3) ◽

pp. 757-767 ◽

Cited By ~ 1

Author(s):

M. M. Hassan ◽

A. K. M. Shamsuddin ◽

M. M. Islam ◽

K. Khatun ◽

J. Halder

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Distance ◽

Gene Diversity ◽

Allele Number ◽

Rice Landraces ◽

Efficient Management ◽

Ssr Loci ◽

Pattern Of Variation ◽

Rice Improvement

Information on the patterns of genetic variation and population structure is essential for rational use and efficient management of germplasms. It helps in monitoring germplasm and can also be used to predict potential genetic gains. Therefore, in the present study genetic diversity of 59 rice genotypes were assessed using 8 simple sequence repeat (SSR) primers. By the DNA profiling, a total of 114 alleles were detected. Allele number per/locus ranged from 9 to 27, with an average of 14.25. Average polymorphism information content (PIC) value was 0.857 with lowest 0.767 to highest 0.857. Mean gene diversity over all SSR loci was 0.870 with a range from 0.792 to 0.948. Fst values for each locus varied from 0.071 to 0.262. Genetic distance between the variety pair ranged from 0.33 to 1.0. The lowest genetic distance was found between Rajashili and Kumragori (2). Cluster and principal coordinate analysis (PCoA) analysis revealed similar pattern of variation. Marker RM11300 was found most polymorphic and robust among the accessions and can be widely used for rice germplasm characterization. The exclusive variability and unique feature of germplasm found in this study can be a gateway for both domestic and global rice improvement.© 2012 JSR Publications. ISSN: 2070-0237 (Print); 2070-0245 (Online). All rights reserved.doi: http://dx.doi.org/10.3329/jsr.v4i3.10416 J. Sci. Res. 4 (3), 757-767 (2012)

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.

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.

Molecular Assessment of Genetic Diversity among Egyptian Landraces of Wheat (Triticum aestivum L.) Using Microsatellite Markers

Asian Journal of Biochemistry, Genetics and Molecular Biology ◽

10.9734/ajbgmb/2020/v3i430094 ◽

2020 ◽

pp. 46-58 ◽

Cited By ~ 1

Author(s):

Ahmed Medhat Mohamed Al-Naggar ◽

Mohamed Abd El-Maboud Abd El-Shafi ◽

Mohamed Helmy El-Shal ◽

Ali Hassan Anany

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Microsatellite Markers ◽

Ssr Markers ◽

Triticum Aestivum L ◽

Genetic Progress ◽

High Genetic Diversity ◽

Breeding Programs ◽

High Polymorphism Information Content ◽

Wheat Landraces

To increase the genetic progress in wheat (Triticum aestivum L.) yield, breeders search for germplasm of high genetic diversity, one of them is the landraces. The present study aimed at evaluating genetic diversity of 20 Egyptian wheat landraces and two cultivars using microsatellite markers (SSRs). Ten SSR markers amplified a total of 27 alleles in the set of 22 wheat accessions, of which 23 alleles (85.2%) were polymorphic. The majority of the markers showed high polymorphism information content (PIC) values (0.67-0.94), indicating the diverse nature of the wheat accessions and/or highly informative SSR markers used in this study. The genotyping data of the SSR markers were used to assess genetic variation in the wheat accessions by dendrogram. The highest genetic distance was found between G21 (Sakha 64; an Egyptian cultivar) and the landrace accession No. 9120 (G11). These two genotypes could be used as parents in a hybridization program followed by selection in the segregating generations, to identify some transgressive segregates of higher grain yield than both parents. The clustering assigned the wheat genotypes into four groups based on SSR markers. The results showed that the studied SSR markers, provided sufficient polymorphism and reproducible fingerprinting profiles for evaluating genetic diversity of wheat landraces. The analyzed wheat landraces showed a good level of genetic diversity at the molecular level. Molecular variation evaluated in this study of wheat landraces can be useful in traditional and molecular breeding programs.

Genetic diversity of Cameroonian bread wheat (Triticum aestivum L.) cultivars revealed by microsatellite markers

AFRICAN JOURNAL OF BIOTECHNOLOGY ◽

10.5897/ajb2017.16090 ◽

2017 ◽

Vol 16 (36) ◽

pp. 1832-1839 ◽

Cited By ~ 1

Author(s):

Tekeu Honore ◽

M. L. Ngonkeu Eddy ◽

P. Djocgoue Francois ◽

Ellis Aletta ◽

Lendzemo Venasius ◽

...

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Microsatellite Markers ◽

Bread Wheat ◽

Triticum Aestivum L

Assessing genetic diversity of Egyptian hexaploid wheat (Triticum aestivum L.) using microsatellite markers

Genetic Resources and Crop Evolution ◽

10.1007/s10722-014-0159-5 ◽

2014 ◽

Vol 62 (3) ◽

pp. 377-385 ◽

Cited By ~ 8

Author(s):

Khaled F. M. Salem ◽

Marion S. Röder ◽

Andreas Börner

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Microsatellite Markers ◽

Hexaploid Wheat ◽

Triticum Aestivum L

Assessing genetic diversity of wheat (Triticum aestivum L.) germplasm using microsatellite markers

Theoretical and Applied Genetics ◽

10.1007/s00122-002-0959-4 ◽

2002 ◽

Vol 105 (5) ◽

pp. 699-707 ◽

Cited By ~ 215

Author(s):

X. Huang ◽

A. Börner ◽

M. Röder ◽

M. Ganal

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Microsatellite Markers ◽

Triticum Aestivum L