Investigation of IRAP transposon-based molecular markers for analysis of genetic diversity in pea germplasm

2018 ◽  
Author(s):  
Sajjad Ahmad ◽  
Rajvinder Kaur ◽  
Mark Lefsrud ◽  
Jaswinder Singh
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Dna Polymorphism ◽  
Breeding Programs ◽  
Molecular Analyses ◽  
Marker System ◽  
Varietal Identification ◽  
D Values ◽  
Mean Similarity ◽  
Germplasm Accessions

Retrotransposons diversity has been extensively studied in monocots, but it is not well documented in dicot species. Transposition activity of transposons creates DNA polymorphism and their abundant presence in genomes is making transposons a promising marker system for varietal identification and fingerprinting. In this study, four transposon-based markers (two DNA- and two RNA-transposons) were employed to evaluate the effectiveness of Inter-Retrotransposon Amplified Polymorphism (IRAP) transposon system in assessing genetic diversity in pea germplasm accessions. A total of 28 alleles were detected across the 35 pea accessions with number of alleles per locus ranged from 5 (Mutator) to 9 (Cyclops). RNA transposons produced a higher number of polymorphic alleles (Ogre: 8, Cyclops: 9) than DNA transposon markers (Mutator: 5, MITE: 6). Overall mean PIC value and D values for these transposon markers were 0.810 and 0.817 respectively. Genetic similarity values ranged from 0.143 to 0.823 with a mean similarity value of 0.403. Cluster analysis classified pea genotypes into six major groups that were somewhat consistent with their geographical origins. The molecular analyses differentiated all the 35 accessions and generated higher PIC and D values that can be useful for MAS-based breeding programs in pea.

scholarly journals Genetic Similarity of Avena sativa L. Varieties as an Example of a Narrow Genetic Pool of Contemporary Cereal Species

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1424
Author(s):  
Magdalena Cieplak ◽  
Sylwia Okoń ◽  
Krystyna Werwińska
Keyword(s):  
Genetic Diversity ◽  
Avena Sativa ◽  
Genetic Similarity ◽  
Breeding Programs ◽  
Central European ◽  
Cereal Species ◽  
Genetic Pool ◽  
Selection Of ◽  
High Genetic Similarity

The assessment of the genetic diversity of cultivated varieties is a very important element of breeding programs. This allows the determination of the level of genetic differentiation of cultivated varieties, their genetic distinctiveness, and is also of great importance in the selection of parental components for crossbreeding. The aim of the present study was to determine the level of genetic diversity of oat varieties currently grown in Central Europe based on two marker systems: ISSR and SCoT. The research conducted showed that both these types of markers were suitable for conducting analyses relating to the assessment of genetic diversity. The calculated coefficients showed that the analyzed cultivars were characterized by a high genetic similarity. However, the UPGMA and PCoA analyses clearly indicated the distinctiveness of the breeding programs conducted in Central European countries. The high genetic similarity of the analyzed forms allow us to conclude that it is necessary to expand the genetic pool of oat varieties. Numerous studies show that landraces may be the donor of genetic variation.

scholarly journals Genetic Variability of 21 Tea Genotypes [Camellia sinensis (L.) O. Kuntze] Based on RAPD Markers

2018 ◽  
Vol 5 (2) ◽  
pp. 77
Author(s):  
Budi Martono ◽  
Syafaruddin Syafaruddin
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Similarity ◽  
Binary Data ◽  
Rapd Markers ◽  
Group Method ◽  
Breeding Programs ◽  
Pair Group ◽  
Monomorphic Band ◽  
And Cluster Analysis

<em>Knowing the genetic diversity in the tea germplasms collection is one of important conditions for assembling new superior varieties. Information of genetic diversity can be obtained through analysis using RAPD molecular markers. The study aimed to determine the genetic diversity of 21 tea genotypes based on RAPD markers. The research was conducted in Integrated Laboratory, Seameo Biotrop, Bogor, from July to September 2013. Genomic DNA was isolated from 21 tea genotypes leaf samples, then amplified with primer OPA 03, OPA 05, OPB 04, OPB 06, OPC 06, and OPD 08. Electrophoresis result was converted into binary data. The genetic similarity and cluster analysis calculation was done using NTSYS-pc version 2.10. In this research, 50 polymorphic bands (94,34%) and 3 monomorphic band (5,66%) were obtained. Cluster analysis based on Nei's genetic distance using the unweighted pair-group method with arithmatic (UPGMA) divided 21 tea genotypes into two groups at a genetic similarity value of 0,48. Group 1 consisted of 20 tea genotypes, while the second group comprised only a one genotype (Sin 27). The range of genetic similarity matrix was between 28%–92%, the lowest genetic similarity (28%) was found between GMB 4 and Sin 27 genotypes, while the highest (92%) was found between AS 2 and AS 1 genotypes. The information obtained can be utilized in breeding programs with the support of agronomic characters as well as in the conservation of tea germplasm.</em>

scholarly journals (235) Genetic Diversity Analysis of Five Passiflora Genotypes

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1002A-1002
Author(s):  
Eric Stafne ◽  
Jon Lindstrom ◽  
John Clark
Keyword(s):  
Genetic Diversity ◽  
North American ◽  
Genetic Similarity ◽  
The Other ◽  
Diversity Analysis ◽  
Breeding Programs ◽  
Genetic Diversity Analysis ◽  
Native North American ◽  
Cold Hardy ◽  
High Degree

Passiflora is an important ornamental genus, mainly within tropical zones. However, two cold-hardy, North American Passiflora species exist. Previous work has been done to incorporate these species into breeding programs with some success. The intent of this study was to evaluate the extent of genetic diversity among five different Passiflora genotypes, including the two native North American species, P. incarnata L. and P. lutea L. Results indicate low genetic similarity among all genotypes with none at 50% or greater. P. incarnata and the ornamental cultivar `Lady Margaret' displayed the highest relationship at 49%. P. incarnata averaged 35.5% similarity with the other genotypes and P. lutea was 29.5%. Average overall similarity among all genotypes was 31.1%. These and other results show that the Passiflora genus has a high degree of genetic variation and breeding efforts could expand interest within North America.

Genetic variation between several species of sections Extranervosae, Caulorrhizae, Heteranthae, and Triseminatae (genus Arachis) estimated by DNA polymorphism

Genome ◽  
1998 ◽  
Vol 41 (3) ◽  
pp. 445-454 ◽  
Author(s):  
Leticia Galgaro ◽  
Catalina Romero Lopes ◽  
Marcos Gimenes ◽  
José FM Valls ◽  
Gary Kochert
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Similarity ◽  
Dna Polymorphism ◽  
Rapd Markers ◽  
Rflp Markers ◽  
The Third ◽  
Rflp Rapd ◽  
High Degree ◽  
A New Species

Genetic variation within and among accessions of the genusArachis representing sections Extranervosae, Caulorrhizae, Heteranthae, and Triseminatae was evaluated using RFLP and RAPD markers. RAPD markers revealed a higher level of genetic diversity than did RFLP markers, both within and among the species evaluated. Phenograms based on various band-matching algorithms revealed three major clusters of similarity among the sections evaluated. The first group included the species from section Extranervosae, the second group consisted of sections Triseminatae, Caulorrhizae, and Heteranthae, and the third group consisted of one accession of Arachis hypogaea, which had been included as a representative of section Arachis. The phenogramsobtained from the RAPD and RFLP data were similar but not identical. Arachis pietrarellii, assayed only by RAPD, showed a high degree of genetic similarity with Arachis villosulicarpa. This observation supported the hypothesis that these two species are closely related. It was also shown that accession V 7786, previously considered to be Arachis sp. aff.pietrarellii, and assayed using both RFLPs and RAPDs, was possibly a new species from section Extranervosae, but very distinct from A. pietrarellii.Keywords: Arachis, RFLP, RAPD, genetic similarity, genetic distance.

scholarly journals DNA POLYMORPHISM AND GENETIC DIVERSITY OF MANGO (Mangifera sp.) GERMPLASM IN TROPICAL ISLAND

2020 ◽  
Vol 7 (1) ◽  
pp. 45
Author(s):  
Putu Suwardike ◽  
I Nyoman Rai ◽  
Rindang Dwiyani ◽  
Eniek Kriswiyanti
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Dna Polymorphism ◽  
Microsatellite Analysis ◽  
Similarity Coefficient ◽  
Test Results ◽  
Tropical Island ◽  
Similar Coefficient ◽  
Group A ◽  
Group B

Creation of new superior varieties of mango through the empowerment of local genetic resources requires information about the potential properties of mango germplasm, including DNA polymorphism and its genetic diversity. This research aimed to obtain basic data on DNA polymorphism, genetic relationship, genetic similarity level, and molecular accession of Bali’s unique local mango. Sampling was conducted in four regencies in the Province of Bali. DNA preparation, PCR, and microsatellite analysis were carried out at the Laboratory of Genetics and Plant Breeding, Faculty of Agriculture, Gadjah Mada University. It found 44accessions of mangoes in Bali. The test results with 10 pairs of SSR markers showed that all primers produced polymorphic loci. There were 825 amplified DNA bands. Primer of AY31 produced the highest number of loci, which were 14 loci, while AY21 produced the fewest loci, i.e., 3 loci. Forty-four mango accessions showed a genetic similarity coefficient of 0.27 to 0.97. At a coefficient of 0.27, accessions were divided into 2 major groups: group A and group B. Group A consisted of two accessions, namely, KRA-005 and BDG-006 (Mangifera foetida Lour.), which had a similar coefficient of 0.657. Group B was divided into twosmaller groups, namely, groups B1 and B2, at a similarity coefficient of 0.342. Group B1 consisted of 39 accessions, while group B2 consisted of 3 accessions. Accessions Madu Anggur, Gading, Sambuk Mengwi, Kakul and Pakel Sulangai were identified as having unique alleles.

scholarly journals Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Grimar Abdiel Perez ◽  
Pumipat Tongyoo ◽  
Julapark Chunwongse ◽  
Hans de Jong ◽  
Anucha Wongpraneekul ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Fixation Index ◽  
Breeding Programs ◽  
Total Fixation ◽  
Unrooted Phylogenetic Tree ◽  
Luffa Acutangula ◽  
Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS =  − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

scholarly journals Molecular Analysis of a Plum pox virus W Isolate in Plum Germplasm Hand Carried into the USA from the Ukraine Shows a Close Relationship to a Latvian Isolate

Plant Disease ◽  
2013 ◽  
Vol 97 (1) ◽  
pp. 44-52 ◽  
Author(s):  
Vessela Mavrodieva ◽  
Delano James ◽  
Karen Williams ◽  
Sarika Negi ◽  
Aniko Varga ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
The United States ◽  
Common Source ◽  
Plum Pox Virus ◽  
High Genetic Diversity ◽  
Close Relationship ◽  
The Usa ◽  
Sequence Identities ◽  
Germplasm Accessions

Four of 19 Prunus germplasm accessions hand carried from the Ukraine into the United States without authorization were found to be infected with Plum pox virus (PPV). Of the three isolates characterized, isolates UKR 44189 and UKR 44191 were confirmed to be isolates of PPV strain W, and UKR 44188 was confirmed to be an isolate of PPV strain D. UKR 44189 and UKR 44191 are very closely related to the PPV strain W isolate LV-145bt (HQ670748) from Latvia. Nucleotide and amino acid sequence identities between these three isolates were greater than 99%. This indicates that the isolates are very closely related and likely originated from a common source. The high genetic diversity among PPV-W strain isolates allowed the identification of potential recombination events between PPV isolates. It appears also that GF 305 peach and Prunus tomentosa are not hosts for the PPV isolate UKR 44189.

scholarly journals Genetic diversity of table grape based on morphoagronomic traits

2011 ◽  
Vol 68 (1) ◽  
pp. 42-49 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Cosme Damião Cruz ◽  
Sérgio Yoshimitsu Motoike
Keyword(s):  
Genetic Diversity ◽  
Clustering Analysis ◽  
Germplasm Collection ◽  
Table Grape ◽  
Cluster Method ◽  
Breeding Programs ◽  
Method Analysis ◽  
Vitis Spp ◽  
Grape Cultivars

The conservation and characterization of grape (Vitis spp) genetic resources in germplasm banks have been the basis of its use in breeding programs that result in development of new cultivars. There are at least 10,000 grape cultivars kept in germplasm collection. The genetic diversity in 136 table grape accessions from the state of Bahia, Brazil, was evaluated. Continuous and discrete morphoagronomic traits were assessed. The clustering analysis by the Tocher otimization method resulted in 30 clusters (considering continuous morphoagronomic traits), and 9 clusters (taking into consideration multicategorical traits). There was no agreement between clusters obtained by both, continuous or discrete phenotypic descriptors, independent of the cluster method analysis used. A satisfactory genetic variability among the table grape accessions was observed.

scholarly journals Genetic diversity of Avena strigosa Schreb. ecotypes on the basis of isoenzyme markers

2009 ◽  
Vol 15 (1) ◽  
pp. 23-28 ◽  
Author(s):  
Katarzyna Kubiak
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Avena Strigosa ◽  
Total Genetic Diversity ◽  
Geographical Regions ◽  
The World ◽  
Total Variability ◽  
The Mean ◽  
Intrapopulation Diversity ◽  
Very High

Genetic diversity ofAvena strigosaSchreb. ecotypes on the basis of isoenzyme markersGenetic diversity was analyzed in 19 ecotypes of the diploid oatA. strigosaoriginating from various geographical regions of the world. Six isoenzyme systems (AAT, ACP, EST, LAP, MDH, PX) were studied and 16 loci were identified. Only two loci (Est4andMdh2) were polymorphic. Ecotypes were characterized by the percentage of polymorphic loci (P=3.3%), the mean number of alleles per locus (A=1.04) and intrapopulation diversity (HS=0.013). Total genetic diversity (HT=0.07) and interpopulation diversity (DST=0.057) were examined as well. The value of the coefficient of gene differentiation (GST=0.821) indicated that diversity among populations was an important contributor to total variability. Genetic similarity betweenA. strigosapopulations was very high (IN=0.94). Cluster analysis did not demonstrate strongly differentiated groups among the ecotypes examined.

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