scholarly journals High-throughput retrotransposon-based genetic diversity of maize germplasm assessment and analysis

2020 ◽  
Vol 47 (3) ◽  
pp. 1589-1603 ◽  
Author(s):  
Marwa Ghonaim ◽  
Ruslan Kalendar ◽  
Hoda Barakat ◽  
Nahla Elsherif ◽  
Naglaa Ashry ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
High Throughput ◽  
Genetic Similarity ◽  
Maize Genome ◽  
Ltr Retrotransposons ◽  
Maize Germplasm ◽  
Phylogeny Analysis ◽  
Generating Method ◽  
Polymerase Chain Reaction Primers ◽  
Hybrid Lines

AbstractMaize is one of the world’s most important crops and a model for grass genome research. Long terminal repeat (LTR) retrotransposons comprise most of the maize genome; their ability to produce new copies makes them efficient high-throughput genetic markers. Inter-retrotransposon-amplified polymorphisms (IRAPs) were used to study the genetic diversity of maize germplasm. Five LTR retrotransposons (Huck, Tekay, Opie, Ji, and Grande) were chosen, based on their large number of copies in the maize genome, whereas polymerase chain reaction primers were designed based on consensus LTR sequences. The LTR primers showed high quality and reproducible DNA fingerprints, with a total of 677 bands including 392 polymorphic bands showing 58% polymorphism between maize hybrid lines. These markers were used to identify genetic similarities among all lines of maize. Analysis of genetic similarity was carried out based on polymorphic amplicon profiles and genetic similarity phylogeny analysis. This diversity was expected to display ecogeographical patterns of variation and local adaptation. The clustering method showed that the varieties were grouped into three clusters differing in ecogeographical origin. Each of these clusters comprised divergent hybrids with convergent characters. The clusters reflected the differences among maize hybrids and were in accordance with their pedigree. The IRAP technique is an efficient high-throughput genetic marker-generating method.

scholarly journals Genetic Diversity of Local Maize Germplasm of Tana Toraja South Sulawesi Using SSR (Simple Sequence Repeat) Markers

2018 ◽  
Vol 2 (3) ◽  
pp. 144
Author(s):  
Ramlah Ramlah ◽  
Isna Rasdianah Aziz ◽  
Cut Muthiadin ◽  
Mashuri Masri ◽  
Muhammad Khalifah Mustami ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Simple Sequence Repeat ◽  
Genetic Similarity ◽  
Agricultural Research ◽  
Similarity Coefficient ◽  
Sequence Repeat ◽  
Maize Germplasm ◽  
South Sulawesi ◽  
Simple Sequence

Plant genetic diversity is an emerging variation in a crop group caused by its genetic factors. Local corn germplasm as a source of plant genes that are able to adapt to the local environment. The purpose of this research is to obtain information on genetic variation of Tana Toraja local maize germ plasm using SSR (Simple Sequence Repeat) marker. This research was conducted at Balitsereal Molecular Biology Laboratory, Agricultural Research Agency in Maros Regency, South Sulawesi. A total of 4 local maize populations were analyzed by laboratory experimental method with observation with NTSYS pc 2.1 program. The results showed that the average number of alleles was 3.72 alleles per locus and the polymorphism rate of 0.53 with the genetic similarity coefficient was in the range of 0.47 to 0.85. 2 main clusters formed in the genetic similarity coefficient 0.47. Klaster I is Local DallePondan and Local Purple. Klaster II is Local Bebo and Kandora. The genetic distance is in the range of 0.15 to 0.74 with an average genetic distance of 0.46. From the data obtained shows that the 4th germplasm of the population of Tana Toraja Local maize diteleti has a very informative level of genetic diversity. Genetic diversity of local maize germplasm of Tana Toraja, can be used as a source of genes in the assembly of improved varieties in the future.

scholarly journals Keragaman Genetik Inbrida Jagung QPM dan Provit-A Berdasarkan Marka SSRs (Simple Sequence Repeats)

2016 ◽  
Vol 35 (2) ◽  
pp. 133
Author(s):  
Nining Nurini Andayani ◽  
M. Yasin H.G ◽  
Marcia B. Pabendon
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Simple Sequence Repeats ◽  
Genetic Similarity ◽  
Genetic Distances ◽  
Large Variability ◽  
Maize Germplasm ◽  
High Level ◽  
Biology Laboratory ◽  
Simple Sequence

Information on genetic diversity of QPM and Provit-A maize germplasm is important to support breeding program, in order to form a high yielding maize hybrid. Simple sequence repeats (SSR) have been extensively utilized as genetic markers to study the genetic diversity, cultivar identification, and gene mapping. The objectives of this research were to investigate the genetic diversity and to obtain information the genetic relationship among 20 maize accessions using 29 SSRs. The research was carried out at the Moleculer Biology Laboratory of Indonesian Cereals Research Institute (ICERI) in Maros, South Sulawesi. Twenty nine polymorphic primers that covered the 10 maize chromosomes were used to fingerprint the genotype of the lines, detecting 83 allels, with an average allel number of 3 allels per locus, ranging from 2 to 6 alleles per locus. The results indicated that polymorphism information content (PIC) ranged from 0.10 (nc133 and phi072) to 0.74 (phi064) with the average of 0.45. Genetic distance based on genetic similarity estimate ranged from 0.39 to 0.92. The high level of PIC values and wide genetic distances indicated the large variability among maize germplasm. Cluster analysis divided the 20 maize accessions into three groups. Coefficient cofenetic value (r) was 0.85 indicated a good fit based on the genetic similarity value. As many as 30 inbred heterotic recombinants were derived by incorporating 20 QPM and Provit-A with genetic distance of ≤0.65. The SSRs proved to be reliable and is practical technique for revealing the relationship among specialty maize genotypes.

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 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.

AFLP-based assessment of genetic diversity among nine alfalfa germplasms using bulk DNA templates

Genome ◽  
2003 ◽  
Vol 46 (1) ◽  
pp. 51-58 ◽  
Author(s):  
A Segovia-Lerma ◽  
R G Cantrell ◽  
J M Conway ◽  
I M Ray
Keyword(s):  
Genetic Diversity ◽  
Medicago Sativa ◽  
High Throughput ◽  
Genetic Distances ◽  
Group Method ◽  
Aflp Analysis ◽  
Dna Templates ◽  
Arithmetic Average ◽  
Pair Group ◽  
Large Numbers

Improving commercial utilization of perennial Medicago collections requires developing approaches that can rapidly and accurately characterize genetic diversity among large numbers of populations. This study evaluated the potential of using amplified fragment length polymorphism (AFLP) DNA markers, in combination with DNA bulking over multiple genotypes, as a strategy for high-throughput characterization of genetic distances (D) among alfalfa (Medicago sativa L.) accessions. Bulked DNA templates from 30 genotypes within each of nine well-recognized germplasms (African, Chilean, Flemish, Indian, Ladak, Medicago sativa subsp. falcata, Medicago sativa subsp. varia, Peruvian, and Turkistan) were evaluated using 34 primer combinations. A total of 3754 fragments were identified, of which 1541 were polymorphic. The number of polymorphic fragments detected per primer combination ranged from 20 to 85. Pairwise D estimates among the nine germplasms ranged from 0.52 to 1.46 with M. sativa subsp. falcata being the most genetically dissimilar. Unweighted pair-group method arithmetic average (UPGMA) analysis of the marker data produced two main clusters, (i) M. sativa subsp. sativa and M. sativa subsp. varia, and (ii) M. sativa subsp. falcata. Cluster-analysis results and D estimates among the Chilean, Peruvian, Flemish, and M. sativa subsp. varia germplasms supported the hypothesis that Peruvian was more similar to original Spanish introductions into Central and South America than Chilean. Hierarchical arrangement of the nine germplasms was supported by their respective geographic, subspecific, and intersubspecific hybrid origins. Subsets of as few as seven highly informative primer pairs were identified that produced comparable D estimates and similar heirarchical arrangements compared with the complete dataset. The results indicate that use of primer-pair subsets for AFLP analysis of bulk DNA templates could serve as a high-throughput system for accurately characterizing genetic diversity among large numbers of alfalfa populations.Key words: Medicago sativa, DNA bulking, genetic distance.

scholarly journals Analysis of genetic relationships of genotypes of the genus Rosa L. from the collection of Nikita Botanical Gardens using ISSR and IRAP DNA markers

2020 ◽  
Vol 24 (5) ◽  
pp. 474-480
Author(s):  
I. I. Suprun ◽  
S. A. Plugatar ◽  
I. V. Stepanov ◽  
T. S. Naumenko
Keyword(s):  
Genetic Diversity ◽  
Bayesian Methods ◽  
Dna Markers ◽  
Wild Species ◽  
Genetic Similarity ◽  
Genetic Relationships ◽  
Issr Markers ◽  
The Other ◽  
Clustering Methods ◽  
Botanical Gardens

In connection with the development of breeding and the creation of new plant varieties, the problem of their genotyping and identification is becoming increasingly important, therefore the use of molecular methods to identify genetic originality and assess plant genetic diversity appears to be relevant. As part of the work performed, informative ISSR and IRAP DNA markers promising for the study of genetic diversity of the Rosa L. genus were sought and applied to analysis of genetic relationships among 26 accessions of the genus Rosa L. from the gene pool collection of Nikita Botanical Gardens. They included 18 cultivated varieties and 8 accessions of wild species. The species sample included representatives of two subgenera, Rosa and Platyrhodon. The subgenus Platyrhodon was represented by one accession of the species R. roxburghii Tratt. Cultivated roses were represented by varieties of garden groups hybrid tea, floribunda, and grandiflora. The tested markers included 32 ISSRs and 13 IRAPs. Five ISSR markers (UBC 824, ASSR29, 3A21, UBC 864, and UBC 843) and three IRAPs (TDK 2R, Сass1, and Сass2) were chosen as the most promising. They were used for genotyping the studied sample of genotypes. In general, they appeared to be suitable for further use in studying the genetic diversity of the genus Rosa L. The numbers of polymorphic fragments ranged from 12 to 31, averaging 19.25 fragments per marker. For markers UBC 864 and UBC 843, unique fingerprints were identified in each accession studied. The genetic relationships of the studied species and varieties of roses analyzed by the UPGMA, PCoA, and Bayesian methods performed on the basis of IRAP and ISSR genotyping are consistent with their taxonomic positions. The genotype of the species R. roxburghii of the subgenus Platyrhodon was determined genetically as the most distant. According to clustering methods, the representative of the species R. bengalensis did not stand out from the group of cultivated varieties. When assessing the level of genetic similarity among the cultivated varieties of garden roses, the most genetically isolated varieties were ‘Flamingo’, ‘Queen Elizabeth’, and ‘Kordes Sondermeldung’; for most of the other varieties, groups of the greatest genetic similarity were identified. This assessment reflects general trends in phylogenetic relationships, both among the studied species of the genus and among cultivated varieties.

scholarly journals Proteomic data from leaves of twenty-four sunflower genotypes underwater deficit

2020 ◽  
Author(s):  
Thierry Balliau ◽  
Harold Duruflé ◽  
Nicolas Blanchet ◽  
Mélisande Blein-Nicolas ◽  
Nicolas B. Langlade ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Water Deficit ◽  
High Throughput ◽  
Molecular Basis ◽  
Inbred Lines ◽  
Vegetative Stage ◽  
Valuable Resource ◽  
Proteomic Data ◽  
High Throughput Phenotyping

AbstractThis article describes how the proteomic data were produced on sunflower plants subjected to water deficit. Twenty-four sunflower genotypes were selected to represent genetic diversity within cultivated sunflower. They included both inbred lines and their hybridsWater deficit was applied to plants in pots at the vegetative stage using the high-throughput phenotyping platform Heliaphen. Here, we provide proteomic data from sunflower leaves corresponding to the identification of 3062 proteins and the quantification of 1211 of them in these 24 genotypes grown in two watering conditions. These data differentiate both treatment and the different genotypes and constitute a valuable resource to the community to study adaptation of crops to drought and the molecular basis of heterosis.

scholarly journals EVALUATION OF GENETIC DIVERSITY IN CACAO COLLECTED FROM KOLAKA, SOUTHEAST SULAWESI, USING SSR MARKERS

2016 ◽  
Vol 16 (2) ◽  
pp. 71
Author(s):  
Rubiyo Rubiyo ◽  
Nur Kholilatul Izzah ◽  
Indah Sulistiyorini ◽  
Cici Tresniawati
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gel Electrophoresis ◽  
Genetic Similarity ◽  
Similarity Coefficient ◽  
Breeding Program ◽  
New Variety ◽  
Average Value ◽  
The Third ◽  
Ctab Method

Kolaka, which is located in Southeast Sulawesi, has long been known as one of cacao production centers in Indonesia. Therefore, many different cacao germplasms can be found in this region. The study aimed to evaluate genetic diversity and relationships of 12 cacao genotypes collected from Kolaka. Genomic DNA was extracted by using a modified CTAB method. Meanwhile, genetic diversity was analyzed based on 16 SSR markers, which then separated by 6% non-denaturing polyacryl-amide gel electrophoresis. The result showed that all of those markers, 14 markers exhibited polymorphism and subsequently used for data analysis using NTSYS and PowerMarker program. About 70 different alleles were generated from 12 cacao genotypes analyzed with an average of 5 alleles per locus. Average value of polymorphism information content (PIC) resulted in this study was 0.59. The cluster analysis using UPGMA method based on the genetic similarity coefficient revealed that all cacao genotypes were separated into three major groups. The first group consisted of five cacao genotypes, the second one held four cacao genotypes, whereas the third group contained three genotypes. This result indicates that three genotypes that clustered separately from the others could be used as a good clonal candidate for cacao breeding program. The information resulted from this present study would be useful for future cacao breeding program, especially in efforts to release a new variety.

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