scholarly journals Identification of hypothetical duplicate accessions of plums (Prunus domestica L.) within the slovene plant gene bank collection using molecular markers

Agricultura ◽  
2016 ◽  
Vol 13 (1-2) ◽  
pp. 57-64 ◽  
Author(s):  
Metka Šiško
Keyword(s):  
Molecular Markers ◽  
Microsatellite Markers ◽  
Life Sciences ◽  
Genetic Distances ◽  
Gene Bank ◽  
Prunus Domestica ◽  
Dice Coefficient ◽  
Plant Materials ◽  
Plant Gene ◽  
Traditional Cultivars

Abstract The main goal of the Slovene Plant Gene Bank is preservation, maintenance and evaluation of traditional cultivars and other useful genotypes. The Faculty of Agriculture and Life Sciences houses among other plant materials also numerous accessions of plums (Prunus domestica L.). Duplicates among 15 accessions were studied using six microsatellite primer pairs. These microsatellite markers revealed an average of 7.67 alleles per locus, and a range of 4 to 10 different alleles per locus. The genetic distances between studied accessions were calculated using the Dice coefficient to form a dendrogram. The six SSRs were found to be adequate for differentiating among genotypes within the collection. Among the analysed accessions no duplicates were found.

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 Bulked Segregant Analysis Identifies Molecular Markers Linked to Melampsora medusae Resistance in Populus deltoides

2000 ◽  
Vol 90 (9) ◽  
pp. 1039-1042 ◽  
Author(s):  
G. M. Tabor ◽  
T. L. Kubisiak ◽  
N. B. Klopfenstein ◽  
R. B. Hall ◽  
H. S. McNabb McNabb
Keyword(s):  
Molecular Markers ◽  
Leaf Rust ◽  
Populus Deltoides ◽  
Bulked Segregant Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Distances ◽  
Resistance Locus ◽  
The North ◽  
Melampsora Medusae ◽  
Central United States

In the north central United States, leaf rust caused by Melampsora medusae is a major disease problem on Populus deltoides. In this study we identified molecular markers linked to a M. medusae resistance locus (Lrd1) that was segregating 1:1 within an intraspecific P. deltoides family (C9425DD). Previous field results were confirmed in the controlled environment of a growth chamber through an excised whole-leaf inoculation method. Using bulked segregant analysis we identified two random amplified polymorphic DNA (RAPD) markers (OPG10340 and OPZ191800) that are linked to Lrd1. Based on segregation in a total of 116 progeny, the genetic distances between OPG10340 and OPZ191800 and the resistance locus were estimated as 2.6 and 7.4 Haldane centimorgans (cM), respectively. Multipoint linkage analyses strongly suggest the most likely order for these loci is Lrd1, OPG10340, and OPZ191800. These markers may prove to be instrumental in the eventual cloning of Lrd1, as well as for marker-assisted selection of leaf-rust resistant genotypes.

scholarly journals Evaluation of genetic variability and genetic distances between eight chicken lines using microsatellite markers

1998 ◽  
Vol 77 (6) ◽  
pp. 783-790 ◽  
Author(s):  
T Vanhala ◽  
M Tuiskula-Haavisto ◽  
K Elo ◽  
J Vilkki ◽  
A Maki-Tanila
Keyword(s):  
Genetic Variability ◽  
Microsatellite Markers ◽  
Genetic Distances

scholarly journals Microsatellite Markers in Olives (Olea europaea L.): Utility in the Cataloging of Germplasm, Food Authenticity and Traceability Studies

Foods ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1907
Author(s):  
Shambhavi Yadav ◽  
Joana Carvalho ◽  
Isabel Trujillo ◽  
Marta Prado
Keyword(s):  
Molecular Markers ◽  
Oleic Acid ◽  
Microsatellite Markers ◽  
Genetic Resources ◽  
Mediterranean Region ◽  
Food Authenticity ◽  
Food Authentication ◽  
Organoleptic Characteristics ◽  
Olive Cultivars ◽  
Molecular Information

The olive fruit, a symbol of Mediterranean diets, is a rich source of antioxidants and oleic acid (55–83%). Olive genetic resources, including cultivated olives (cultivars), wild olives as well as related subspecies, are distributed widely across the Mediterranean region and other countries. Certain cultivars have a high commercial demand and economical value due to the differentiating organoleptic characteristics. This might result in economically motivated fraudulent practices and adulteration. Hence, tools to ensure the authenticity of constituent olive cultivars are crucial, and this can be achieved accurately through DNA-based methods. The present review outlines the applications of microsatellite markers, one of the most extensively used types of molecular markers in olive species, particularly referring to the use of these DNA-based markers in cataloging the vast olive germplasm, leading to identification and authentication of the cultivars. Emphasis has been given on the need to adopt a uniform platform where global molecular information pertaining to the details of available markers, cultivar-specific genotyping profiles (their synonyms or homonyms) and the comparative profiles of oil and reference leaf samples is accessible to researchers. The challenges of working with microsatellite markers and efforts underway, mainly advancements in genotyping methods which can be effectively incorporated in olive oil varietal testing, are also provided. Such efforts will pave the way for the development of more robust microsatellite marker-based olive agri-food authentication platforms.

scholarly journals Genetic Diversity Analysis of Indonesian Pigmented Rice Accessions Based on Functional Molecular Markers

2021 ◽  
Vol 17 (1) ◽  
pp. 25
Author(s):  
Andari Risliawati ◽  
Yusi N. Andarini ◽  
Rerenstradika T. Terryana ◽  
Kristianto Nugroho ◽  
Puji Lestari
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Gene Bank ◽  
Diversity Analysis ◽  
Anthocyanin Content ◽  
Local Varieties ◽  
Pigmented Rice ◽  
Health Studies ◽  
Pericarp Color ◽  
Functional Molecular Markers

Pigmented rice is functional staple food that becomes popular because of its anthocyanin content which is beneficial for health. Studies on the diversity of the local variety of Indonesian pigmented rice accessions have been carried out, but are still limited to one region of germplasm origin. This study aimed to analyze the genetic diversity of local varieties of pigmented rice collections of the IAARD-ICABIOGRAD Gene Bank. A total of 93 pigmented rice accessions from 16 provinces in Indonesia were analyzed using 15 functional molecular markers of SSR, STS, and indel. The total alleles detected were 115 with an average per locus of genetic diversity value of 0.71. There were five markers with PIC values >0.75, i.e. RM167, RM223, R8M33, R10M10, and GBSS1. The accessions were divided into two main groups based on their pericarp color. It is necessary to analyze the physicochemical content of the local rice accessions to complement the existing diversity information and identify potential pigmented rice accessions with high palatability.

scholarly journals Genetic diversity and differentiation in reef-buildingMilleporaspecies, as revealed by cross-species amplification of fifteen novel microsatellite loci

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2936 ◽  
Author(s):  
Caroline E. Dubé ◽  
Serge Planes ◽  
Yuxiang Zhou ◽  
Véronique Berteaux-Lecellier ◽  
Emilie Boissin
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Natural Populations ◽  
454 Sequencing ◽  
Genetic Distances ◽  
Null Alleles ◽  
Future Research ◽  
Significant Linkage ◽  
Pacific Species

Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coralMillepora platyphylla, an important reef-builder of Indo-Pacific reefs.We tested the cross-species amplification of these loci in five other species of the genusMilleporaand analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target speciesM. platyphylla,among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five otherMilleporaspecies revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean speciesM. complanatadue to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species ofMillepora.Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoanMilleporaspecies creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

scholarly journals High Genetic Diversity but Absence of Population Structure in Local Chickens of Sri Lanka Inferred by Microsatellite Markers

2021 ◽  
Vol 12 ◽  
Author(s):  
Amali Malshani Samaraweera ◽  
Ranga Liyanage ◽  
Mohamed Nawaz Ibrahim ◽  
Ally Mwai Okeyo ◽  
Jianlin Han ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sri Lanka ◽  
Microsatellite Markers ◽  
Allelic Diversity ◽  
Genetic Distances ◽  
Population Substructure ◽  
High Genetic Diversity ◽  
Naked Neck ◽  
Local Chicken ◽  
Local Chickens

Local chicken populations belonging to five villages in two geographically separated provinces of Sri Lanka were analyzed using 20 microsatellite markers to determine the genetic diversity of local chickens. Population genetic parameters were estimated separately for five populations based on geographic locations and for eight populations based on phenotypes, such as naked neck, long legged, crested or crown, frizzle feathered, Giriraj, commercial layer, crossbreds, and non-descript chicken. The analysis revealed that there was a high genetic diversity among local chickens with high number of unique alleles, mean number of alleles per locus (MNA), and total number of alleles per locus per population. A total of 185 microsatellite alleles were detected in 192 samples, indicating a high allelic diversity. The MNA ranged from 8.10 (non-descript village chicken) to 3.50 (Giriraj) among phenotypes and from 7.30 (Tabbowa) to 6.50 (Labunoruwa) among village populations. In phenotypic groups, positive inbreeding coefficient (FIS) values indicated the existence of population substructure with evidence of inbreeding. In commercial layers, a high expected heterozygosity He = 0.640 ± 0.042) and a negative FIS were observed. The positive FIS and high He estimates observed in village populations were due to the heterogeneity of samples, owing to free mating facilitated by communal feeding patterns. Highly admixed nature of phenotypes was explained as a result of rearing many phenotypes by households (58%) and interactions of chickens among neighboring households (53%). A weak substructure was evident due to the mating system, which disregarded the phenotypes. Based on genetic distances, crown chickens had the highest distance to other phenotypes, while the highest similarity was observed between non-descript village chickens and naked neck birds. The finding confirms the genetic wealth conserved within the populations as a result of the breeding system commonly practiced by chicken owners. Thus, the existing local chicken populations should be considered as a harbor of gene pool, which can be readily utilized in developing locally adapted and improved chicken breeds in the future.

scholarly journals DArT-based evaluation of soybean germplasm from Polish Gene Bank

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Elzbieta Czembor ◽  
Jerzy H. Czembor ◽  
Radoslaw Suchecki ◽  
Nathan S. Watson-Haigh
Keyword(s):  
Chlorophyll Fluorescence ◽  
Flower Colour ◽  
Significant Snps ◽  
Gene Bank ◽  
Eastern European ◽  
Phenotypic Data ◽  
High Quality Snps ◽  
Traditional Cultivars ◽  
Materials Used ◽  
Eastern European Countries

Abstract Objective Soybean is an important plant used for food, feed and many industrial purposes. Interest in soybean breeding is growing in Central Europe, including Poland. A very large number of soybean accessions are stored in gene banks, but less than 1% of them have been used for breeding. Here, we present genotypic data as well as phenotypic data on plant and seed performance, including seed chlorophyll fluorescence traits, and on yield components within a collection of soybean accessions that are conserved in the Polish Gene Bank at the Plant Breeding and Acclimatization Institute-National Research Institute. Results The materials used consisted of sub-collections: 79 Polish genotypes, including old traditional cultivars, 24 Canadian, 21 American, 21 Swedish and 31 from Central and Eastern European Countries, 9 from France and 6 from Japan. In total, 9602 high quality SNPs were derived from DArTseq, a method utilising GBS technology. GWAS, performed with the BLINK model, revealed that a total of 41 significant SNPs were mapped for days to flowering, flower colour, plant height, days to pod formation, 100 seed weight, pod colour, seeds and hilum colour and steady-state chlorophyll fluorescence under light (Ft_Lss). This is the first report about the diversity of traditional old Polish soybean cultivars.

Genetic diversity analysis of the Greek lentil (Lens culinaris) landrace ‘Eglouvis’ using morphological and molecular markers

2018 ◽  
Vol 16 (5) ◽  
pp. 469-477 ◽  
Author(s):  
Georgios F. Tsanakas ◽  
Photini V. Mylona ◽  
Katerina Koura ◽  
Anthoula Gleridou ◽  
Alexios N. Polidoros
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Variability ◽  
Morphological Analysis ◽  
Phenotypic Variability ◽  
Market Price ◽  
Genetic Distances ◽  
Reaction Products ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates

AbstractThe Greek lentil landrace ‘Eglouvis’ is cultivated continuously at the Lefkada island for more than 400 years. It has great taste, high nutritional value and high market price. In the present study, we used morphological and molecular markers to estimate genetic diversity within the landrace. Morphological analysis was based on characteristics of the seed. Molecular analysis was performed using simple sequence repeat (SSR) molecular markers in a high-resolution melting (HRM) approach. ‘Samos’ and ‘Demetra’, two of the most widely cultivated commercial lentil varieties in Greece, were used for comparisons. Morphological analysis was performed with 584 seeds randomly selected from a lot. Analysis of seed dimensions and colour distributed the samples in different categories and highlighted the phenotypic variability in ‘Eglouvis’ lentil seeds. Genetic variability was estimated from 91 individual DNA samples with 11 SSR markers using HRM analysis. Genotyping was based upon the shape of the melting curves and the difference plots; all polymerase chain reaction products were also run on agarose gels. Genetic distances of individuals and principal coordinates analysis suggested that ‘Eglouvis’ landrace has a unique genetic background that significantly differs from ‘Samos’ and ‘Demetra’ and no overlapping could be detected. Genetic variability within the ‘Eglouvis’ landrace can be considered in targeted breeding programs as a significant phytogenetic resource of lentils in Greece.

scholarly journals Identifying Pollen Donors and Success Rate of Individual Pollinizers in European Plum (Prunus domestica L.) Using Microsatellite Markers

Agronomy ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 264
Author(s):  
Meland ◽  
Frøynes ◽  
Fotiric Akšić ◽  
Pojskić ◽  
Kalamujić Stroil ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Success Rate ◽  
Genetic Characterization ◽  
Prunus Domestica ◽  
Tissue Samples ◽  
Self Pollination ◽  
Self Fertilization ◽  
High Level ◽  
Very High ◽  
Simple Sequence

European plum cultivars (Prunus domestica L.) are hexaploid and partially self-fertile or self-sterile requiring compatible pollinizers with overlapping bloom times. Therefore, inter-planting of different pollinizer cultivars is recommended. In order to identify successful pollinizers of the plum cultivars ‘Edda’, ‘Opal’ (self-fertile), ‘Jubileum’, ‘Reeves’, ‘Mallard’, ‘Avalon’, ‘Cacanska Lepotica’ (self-fertile), and ‘Valor’, 60 fruits per cultivar were collected from nine orchards in 2017 and 2018, all of which were located in Ullensvang, western Norway. DNA extraction was subsequently conducted from the obtained embryos, followed by genetic characterization using seven microsatellite markers. Tissue samples from all possible pollinizers were collected during the summer of 2017 and the same DNA approach was conducted. Results showed that ‘Opal’ was the most successful pollinizer among the investigated plum cultivars. The main exception was ‘Cacanska Lepotica’, which consistently displayed very high level of self-pollination. The most successful foreign pollinizer of ‘Opal’ was ‘Mallard’. However, in more than two thirds of embryos extracted from ‘Opal’ fruits self-fertilization was determined. ‘Reeves’ was identified as the most successful pollinizer among embryos collected from ‘Valor’. Among the five cultivars (‘Edda’, ‘Jubileum’, ‘Reeves’, ‘Mallard’, and ‘Avalon’) that did not display self-pollination, the pollinizer success rate of ‘Opal’, ranged from 36.5% (‘Mallard’) to 93.5% (‘Edda’) in 2017, while in 2018 this rate ranged from 43.5% (‘Jubileum’ and ‘Reeves’) up to 96.5% (‘Edda’). Overall, genotyping embryos using SSRs (simple sequence repeats) proved an effective method in determining the success rate of individual pollinizers among European plum cultivars.

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