scholarly journals Genetic Characterization of Brassica oleracea L. var. acephala DC cultivars from Bosnia and Herzegovina

2021 ◽  
Vol 5 (1) ◽  
pp. 40
Author(s):  
Jasmin Šutković ◽  
Petar Glamočija ◽  
Lutvija Karić ◽  
Ahmet Yildirim
Keyword(s):  
Brassica Oleracea ◽  
Information Content ◽  
Genetic Characterization ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Group Method ◽  
Molecular Characteristics ◽  
Pair Group ◽  
Ssr Loci ◽  
Brassica Oleracea L

Fifteen Brassica oleracea L. var. acephala DC accessions were collected and evaluated for their genetic diversity and molecular characteristics using 10 previously developed and used codominant SSR markers. The SSR loci used revealed a total of 51 alleles. The domestic kale varieties were collected locally and the hybrids kales were found in markets. The averages of total heterozygosity (H) and polymorphic information content (PIC) was 0.6774 and 0.6201, respectively. The average number of alleles was 4.2 per locus, where 8 of 10 markers showed high polymorphic information content (PIC), being more than 0.5. The genetic relationships among the populations revealed by Unweighted Pair Group Method with Arithmetic mean (UPGMA), showed a clear clustering into three distinct groups. As expected, all local varieties were separated within two separated clusters, whereas only two domestic varieties shared one cluster with the group of hybrids, indicating similar genetic background shared by domestic and hybrid varieties. These results indicate and confirm the regional and physiological differences between the kale varieties and confirm the SSR marker efficiency for genetic characterization assays

scholarly journals Genetic diversity in table grapes based on RAPD and microsatellite markers

2011 ◽  
Vol 46 (9) ◽  
pp. 1035-1044 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Sérgio Yoshimitsu Motoike
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Similarity Index ◽  
Genetic Distances ◽  
Table Grape ◽  
Group Method ◽  
Molecular Characteristics ◽  
Table Grapes ◽  
Pair Group

The objective of this work was to analyze the genetic diversity of 47 table grape accessions, from the grapevine germplasm bank of Embrapa Semiárido, using 20 RAPD and seven microsatellite markers. Genetic distances between pairs of accessions were obtained based on Jaccard's similarity index for RAPD data and on the arithmetic complement of the weighted index for microsatellite data. The groups were formed according to the Tocher's cluster analysis and to the unweighted pair‑group method with arithmetic mean (UPGMA). The microsatellite markers were more efficient than the RAPD ones in the identification of genetic relationships. Information on the genetic distance, based on molecular characteristics and coupled with the cultivar agronomic performance, allowed for the recommendation of parents for crossings, in order to obtain superior hybrids in segregating populations for the table grape breeding program of Embrapa Semiárido.

scholarly journals Polymorphism and Genetic Relationships among Tea Genotypes from Turkey Revealed by Amplified Fragment Length Polymorphism Markers

2009 ◽  
Vol 134 (4) ◽  
pp. 428-434 ◽  
Author(s):  
Salih Kafkas ◽  
Sezai Ercişli ◽  
Yıldız Doğan ◽  
Yaşar Ertürk ◽  
Ayhan Haznedar ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Group Method ◽  
Aflp Analysis ◽  
Black Sea Region ◽  
Pair Group

Individuals in most countries around the world drink tea (Camellia sinensis). Tea drinking has attained ceremonial status in many places as a social and medicinal beverage. Although tea is of great importance in Turkey's economy, little is known about the pattern of genetic variation among the various tea genotypes grown in Turkey. A total of 32 tea genotypes found at the Ataturk Tea and Horticulture Research Institute in the eastern Black Sea region of Turkey were sampled. Fluorescent dye amplified fragment length polymorphism (AFLP) markers and capillary electrophoresis were applied for molecular characterization. The AFLP analysis with six primer combinations generated 835 fragments of which 567 were polymorphic, corresponding to 69.8% polymorphism. Resolving powers of the AFLP primers ranged from 62.6 to 81.9, yielding a total of 437.8; the polymorphic information content (PIC) ranged from 0.76 to 0.83, with an average of 0.79. Genetic similarity values ranged from 0.68 to 0.92, with an average of 0.76. The dendrogram derived by unweighted pair group method with arithmetic mean algorithm (UPGMA) and principal coordinate analysis (PCoA) revealed that all tea genotypes could be clearly divided into four distinct clusters. The results of this study will provide valuable information to the tea cultivar breeding program for the purpose of parental selection.

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.

Molecular Profiling of Chilli Germplasm By Using SSR Marker

2021 ◽  
Vol 19 (1) ◽  
pp. 1-13
Author(s):  
MI Haque ◽  
S Ishtiaque ◽  
MM Islam ◽  
TA Mujahidi ◽  
MA Rahim
Keyword(s):  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Similarity Index ◽  
Group Method ◽  
Arithmetic Means ◽  
Average Value ◽  
Pair Group ◽  
Index Matrix ◽  
Ssr Primers ◽  
Ssr Loci

The molecular characterization of chilli germplasm was done based on estimation of genetic diversity among the germplasm by using SSR markers. Forty chilli germplasms were analyzed using eight SSR primers. The SSR primers produced 30 SSR loci with an average value of 3.75 alleles per SSR locus. The similarity index matrix ranged from zero to 2.74. Polymorphic information content (PIC) of the SSR primers ranged from 0.543 to 0.735 with an average value of 0.658. The highest number (five) of allele was observed in primer CAMS-647, whereas the primers CAMS-864, CAMS-880 and CAMS-885 showed lowest number (three) of allele. The smallest allele was found in case of primer CAMS- 236 (176 bp), while the longest allele was detected for the primer CAMS- 864 (288 bp). Based on similarity matrix using the un-weighed Pair Group Method of Arithmetic Means (UPGMA) dendrogram, chilli germplasms were grouped into four main clusters. SSR markers showed genetic variability in the studied chilli germplasm.  SAARC J. Agric., 19(1): 1-13 (2021)

scholarly journals Genetic divergence in Tunisian castor bean genotypes based on trap markers

10.5219/1292 ◽  
2020 ◽  
Vol 14 ◽  
pp. 510-518
Author(s):  
Martin Vivodí­k ◽  
Zdenka Gálová ◽  
Želmí­ra Balážová
Keyword(s):  
Information Content ◽  
Ricinus Communis ◽  
Polymorphic Information Content ◽  
Pcr Amplification ◽  
Distance Matrix ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Genetic Distance Matrix ◽  
Amplicon Size

In the present study, the representatives of the genus Ricinus communis collected from 12 different parts of Tunisia were differentiated by the DNA fingerprinting patterns using 30 TRAP primers. The efficacy of the TRAP technique in this study is further supported by the obtained PIC values of the primers used in the analysis. PCR amplification of DNA using 30 primers for TRAP analysis produced 490 DNA fragments that could be scored in all 56 genotypes of Tunisian castor. The number of amplified fragments varied from 3 (TRAP 04 x arb 1, TRAP 22 x arb 3 and TRAP 23 x arb 3) to 13 (TRAP 56 x arb 2), and the amplicon size ranged from 100 to 1600 bp. Of the 490 amplified bands, 377 were polymorphic, with an average of 5.71 polymorphic bands per primer. To determine the level of polymorphism in the analysed group of Tunisian castor genotypes polymorphic information content (PIC) was calculated. The lowest values of polymorphic information content were recorded for TRAP 10 x arb 1 (0.555) and the highest PIC values were detected for TRAP 44 x arb 2 (0.961) with an average of 0.770. A dendrogram was constructed from a genetic distance matrix based on profiles of the 30 TRAP primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 56 Tunisian castor genotypes were clustered into five main clusters. Moreover, functional TRAP markers would be efficiently useful in genetic studies for castor genetic improvement.

scholarly journals Development of RNA-Seq SSR Markers and Application to Genetic Relationship Analysis among Sea Buckthorn Germplasm

2017 ◽  
Vol 142 (3) ◽  
pp. 200-208 ◽  
Author(s):  
He Li ◽  
Cheng-Jiang Ruan ◽  
Li Wang ◽  
Jian Ding ◽  
Xing-Jun Tian
Keyword(s):  
Ssr Markers ◽  
Genetic Relationships ◽  
Sea Buckthorn ◽  
The Other ◽  
Group Method ◽  
Rna Seq ◽  
Arithmetic Average ◽  
Relationship Analysis ◽  
Pair Group ◽  
Ssr Loci

Sea buckthorn (Hippophae rhamnoides) is an ecologically and economically valuable species that has been widely cultivated as a new berry crop rich in nutritional and medicinal compounds. RNA Sequencing (RNA-Seq) simple sequence repeat (SSR) markers were developed to evaluate the genetic relationships among 91 plants of 31 cultivars from two subspecies, mongolica and sinensis, as well as intraspecific hybrids between them. A total of 7540 RNA-Seq SSRs were identified as potential molecular markers, in which AG/CT (27.57%) was the most abundant unit type. AT/AT (9.93%), and AAG/CTT (11.95%) are the other main repeat motifs. A total of 110 primer pairs were randomly selected for validation of amplification. Seventeen SSR loci, located in genes encoding metabolic processes and cellulose synthases, were identified to be polymorphic among different sea buckthorn cultivars. These SSR loci generated 48 alleles, ranging from 2 to 5 per locus. Cluster analysis based on the proportion of shared alleles and unweighted pair group method with arithmetic average (UPGMA) algorithm divided all the genotypes into two main groups, with all of the ssp. sinensis cultivars (native to China) and hybrids in one group and ssp. mongolica cultivars (introduced from Russia) in the other group, which was in good agreement with their taxonomic classification. The RNA-Seq SSRs developed in this study have a potential use in the conservation of sea buckthorn germplasm and marker-assisted breeding (MAB).

scholarly journals VALIDATION AND TRANSFERABILITY OF SIMPLE SEQUENCE REPEATS (SSR’S) FROM SOME SPECIES OF ACACIA GENUS TO ACACIA NILOTICA L.

2016 ◽  
Vol 8 (11) ◽  
pp. 95
Author(s):  
Amita Yadav ◽  
Manila Yadav ◽  
Sandeep Kumar ◽  
Dushyant Sharma ◽  
Jaya Parkash Yadav
Keyword(s):  
Genetic Diversity ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Climatic Conditions ◽  
Acacia Nilotica ◽  
Group Method ◽  
Acacia Species ◽  
Pair Group ◽  
High Level ◽  
Simple Sequence

Objective: In present study genetic transferability of SSR’s from related Acacia species to Acacia nilotica was evaluated along with its genetic diversity analysis from north Indian region. Methods: A total of 30 primers selected from 5 different Acacia species were screened for amplification and polymorphism. Dendrogram and 2 D Plot were constructed using NTSys PC version 2.02e. Different diversity parameters like Polymorphism information content (PIC), alleles per primer, number (no.) of amplicons were also calculated for each primer pair.Results: SSRs from Acacia tortilis, A. senegal and A. koa were highly transferable in A. nilotica. Out of 30, only twenty-two primers showed amplification with an average of 1.36 alleles per locus. Polymorphic information content (PIC) values ranged from 0.5 to 0.96 with an average of 0.81. Jaccard similarity coefficient (J) values ranged from 0.04 to 0.67 showing a high level of diversity. Un-weighted pair group method with arithmetic mean (UPGMA), based cluster analysis, divided all accessions into three main clusters.Conclusion: Geographical and climatic conditions showed a great impact on genetic diversity. The results indicated high transferability of genomic resources from related species and will facilitate more studies to characterize the relatively less studied Acacia niloticagenome. 

scholarly journals Optimal use of SSR markers for varietal identification of upland cotton

2015 ◽  
Vol 50 (7) ◽  
pp. 571-581 ◽  
Author(s):  
Guilherme da Silva Pereira ◽  
Ana Luíza Ramos Cazé ◽  
Michelle Garcia da Silva ◽  
Vanessa Cavalcante Almeida ◽  
Fernanda Oliveira da Cunha Magalhães ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Group Method ◽  
Discrimination Power ◽  
Arithmetic Average ◽  
Pair Group ◽  
Varietal Identification ◽  
The World ◽  
The Mean

Abstract: The objective of this work was to identify polymorphic simple sequence repeat (SSR) markers for varietal identification of cotton and evaluation of the genetic distance among the varieties. Initially, 92 SSR markers were genotyped in 20 Brazilian cotton cultivars. Of this total, 38 loci were polymorphic, two of which were amplified by one primer pair; the mean number of alleles per locus was 2.2. The values of polymorphic information content (PIC) and discrimination power (DP) were, on average, 0.374 and 0.433, respectively. The mean genetic distance was 0.397 (minimum of 0.092 and maximum of 0.641). A panel of 96 varieties originating from different regions of the world was assessed by 21 polymorphic loci derived from 17 selected primer pairs. Among these varieties, the mean genetic distance was 0.387 (minimum of 0 and maximum of 0.786). The dendrograms generated by the unweighted pair group method with arithmetic average (UPGMA) did not reflect the regions of Brazil (20 genotypes) or around the world (96 genotypes), where the varieties or lines were selected. Bootstrap resampling shows that genotype identification is viable with 19 loci. The polymorphic markers evaluated are useful to perform varietal identification in a large panel of cotton varieties and may be applied in studies of the species diversity.

scholarly journals Genotyping oil flax varieties using the microsatellite DNA marker system

2020 ◽  
Vol 21 (5) ◽  
pp. 531-539
Author(s):  
S. Z. Guchetl ◽  
T. A. Tchelyustnikova
Keyword(s):  
Information Content ◽  
Genetic Relatedness ◽  
Polymorphic Information Content ◽  
Biotic And Abiotic Stresses ◽  
Crop Acreage ◽  
Marker System ◽  
Average Value ◽  
Ssr Loci ◽  
New Varieties ◽  
Microsatellite Dna Marker

The tendency to increase crop acreage of oil flax requires the development of new varieties with high indicators of ecological plasticity, productivity and resistance to biotic and abiotic stresses. The application of modern biotechnolog ical approaches based on the use of molecular markers can accelerate the assessment of genetic differences and the dete rmination of potential of the source material for breeding. The research was aimed at assessment of the genotyping parameters of some oil flax varieties of VNIIMK breeding using the system of microsatellite markers. Seventeen variety samples of flax were used as the material for the research. DNA was isolated using CTAB buffer. Eleven SSR loci were used for the identification of varieties. Ten polymorphic loci were identified during the research. The total number of counted alleles is 32. The size of alleles varied in the range of 111-210 bps. The number of alleles per locus ranged from 2 to 6 with an average value of 3.20. The value of the index of polymorphic information content (PIC) was from 0.29 to 0.75 with an average parameter value of 0.51. The effective number of alleles for different loci is determined in the range of 1.40-3.94 with an average value of 2.28. The level of information content of the marker system (PIC 0.51) corresponds to that for identifying sets of genotypes from collections with a limitation in geographical origin. There were established differences in the frequency of occurrence of alleles. The discriminatory potential of the used marker system allowed to identify 15 variety samples. Two genotypes with common origin were identical. The degree of genetic relatedness of the studied flax genotypes has been evaluated. The obtained results will serve as the basis for the subsequent construction of genetic passports of oil flax varieties of VNIIMK breeding.

scholarly journals Assessment of Genetic Relationships among Philodendron Cultivars Using AFLP Markers

2004 ◽  
Vol 129 (5) ◽  
pp. 690-697 ◽  
Author(s):  
Pachanoor S. Devanand ◽  
Jianjun Chen ◽  
Richard J. Henny ◽  
Chih-Cheng T. Chao
Keyword(s):  
Genetic Similarity ◽  
Near Infrared ◽  
Genetic Relationships ◽  
Aflp Markers ◽  
Group Method ◽  
Limited Information ◽  
Similarity Coefficients ◽  
Arithmetic Average ◽  
Ornamental Foliage Plants ◽  
Pair Group

Philodendrons (Philodendron Schott) are among the most popular tropical ornamental foliage plants used for interior decoration. However, limited information is available on the genetic relationships among popular Philodendron species and cultivars. This study analyzed genetic similarity of 43 cultivars across 15 species using amplified fragment length polymorphism (AFLP) markers with near infrared fluorescence labeled primers. Forty-eight EcoR I + 2/Mse I + 3 primer set combinations were screened, from which six primer sets were selected and used in this investigation. Each selected primer set generated 96 to 130 scorable fragments. A total of 664 AFLP fragments were detected, of which 424 (64%) were polymorphic. All cultivars were clearly differentiated by their AFLP fingerprints, and the relationships were analyzed using the unweighted pair-group method of arithmetic average cluster analysis (UPGMA) and principal coordinated analysis (PCA). The 43 cultivars were divided into five clusters. Cluster I comprises eight cultivars with arborescent growth style. Cluster II has only one cultivar, `Goeldii'. There are 16 cultivars in cluster III, and most of them are self-heading interspecific hybrids originated from R.H. McColley's breeding program in Apopka, Fla. Cluster IV contains 13 cultivars that exhibit semi-vining growth style. Cluster V has five cultivars that are true vining in morphology, and they have lowest genetic similarity with philodendrons in other clusters. Cultivated philodendrons are generally genetically diverse except the self-heading hybrids in cluster III that were mainly developed using self-heading and semi-vining species as parents. Seven hybrid cultivars have Jaccard's similarity coefficients of 0.88 or higher, suggesting that future hybrid development needs to select parents with diverse genetic backgrounds.

Sign in / Sign up

Export Citation Format

Share Document