scholarly journals  Genetic diversity of Czech apple cultivars inferred from microsatellite markers analysis

2012 ◽  
Vol 39 (No. 4) ◽  
pp. 149-157 ◽  
Author(s):  
J. Patzak ◽  
F. Paprštein ◽  
A. Henychová ◽  
J. Sedlák
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Simple Sequence Repeat ◽  
Cultivar Identification ◽  
Genetic Relationships ◽  
Similarity Coefficient ◽  
Collection Management ◽  
Apple Cultivars ◽  
Repeat Primer ◽  
Simple Sequence

Genetic diversity and genetic relationships of Czech apple cultivars were evaluated. Trees of 33 Czech apple cultivars and 97 reference foreign cultivars were analysed using the set of 10 SSR (simple sequence repeat) primer pairs. The total of 89 polymorphic alleles were amplified, while the number of alleles per locus ranged from 4 to 14. The SSR dendrogram, based on the Jaccard’s similarity coefficient, divided apple cultivars into three major groups: Cox’s Orange Pippin, McIntosh and Golden Delicious ancestries. The clustering highly depended on pedigree and origin of apple cultivars. Spontaneous mutated cultivars were identical with their progenitors. We proved that microsatellite markers were useful for evaluation of genetic resources, collection management and cultivar identification.  

Genetic diversity among silkworm (Bombyx mori L., Lep., Bombycidae) germplasms revealed by microsatellites

Genome ◽  
2005 ◽  
Vol 48 (5) ◽  
pp. 802-810 ◽  
Author(s):  
Muwang Li ◽  
Li Shen ◽  
Anying Xu ◽  
Xuexia Miao ◽  
Chengxiang Hou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Bombyx Mori ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Group Method ◽  
Sequence Repeat ◽  
Bombyx Mori L ◽  
Simple Sequence ◽  
Silkworm Bombyx Mori

To determine genetic relationships among strains of silkworm, Bombyx mori L., 31 strains with different origins, number of generations per year, number of molts per generation, and morphological characters were studied using simple sequence repeat (SSR) markers. Twenty-six primer pairs flanking microsatellite sequences in the silkworm genome were assayed. All were polymorphic and unambiguously separated silkworm strains from each other. A total of 188 alleles were detected with a mean value of 7.2 alleles/locus (range 2–17). The average heterozygosity value for each SSR locus ranged from 0 to 0.60, and the highest one was 0.96 (Fl0516 in 4013). The mean polymorphism index content (PIC) was 0.66 (range 0.12–0.89). Unweighted pair group method with arithmetic means (UPGMA) cluster analysis of Nei's genetic distance grouped silkworm strains based on their origin. Seven major ecotypic silkworm groups were analyzed. Principal components analysis (PCA) for SSR data support their UPGMA clustering. The results indicated that SSR markers are an efficient tool for fingerprinting cultivars and conducting genetic-diversity studies in the silkworm.Key words: silkworm, Bombyx mori L., microsatellites, simple sequence repeat (SSR), genetic diversity.

scholarly journals Genetic Diversity in Spanish and Foreign Almond Germplasm Assessed by Molecular Characterization with Simple Sequence Repeats

2009 ◽  
Vol 134 (5) ◽  
pp. 535-542 ◽  
Author(s):  
Àngel Fernández i Martí ◽  
José M. Alonso ◽  
María T. Espiau ◽  
María J. Rubio-Cabetas ◽  
Rafel Socias i Company
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Geographical Origin ◽  
Cultivar Identification ◽  
Prunus Amygdalus ◽  
Allele Size ◽  
Successful Amplification ◽  
Genetic Closeness ◽  
Simple Sequence

Genetic diversity of the Spanish national almond (Prunus amygdalus Batsch) collection was characterized with 19 simple sequence repeat (SSR) markers selected because of their polymorphism in almond and other Prunus L. species. A total of 93 almond genotypes, including 63 Spanish cultivars from different growing regions, as well as some international cultivars and breeding releases were analyzed. All primers produced a successful amplification, giving a total of 323 fragments in the genotypes studied, with an average of 17 alleles per SSR, ranging from 4 (EPDCU5100) to 33 (BPPCT038). Allele size ranged from 88 bp at locus PMS40 to 260 bp at locus CPPCT022. The heterozygosity observed (0.72) was much higher not only than in other Prunus species, but also than in other almond pools already studied. The dendrogram generated using the variability observed classified most of the genotypes according to their geographical origin, confirming the particular evolution of different almond ecotypes. The SSR markers have consequently shown their usefulness for cultivar identification in almond, for establishing the genetic closeness among its cultivars, and for establishing genealogical relationships.

Genetic diversity of Canadian elite summer rape (Brassica napus L.) cultivars from the pre- to post-canola quality era

2010 ◽  
Vol 90 (1) ◽  
pp. 23-33 ◽  
Author(s):  
Y -B. Fu ◽  
R K Gugel
Keyword(s):  
Genetic Diversity ◽  
Brassica Napus ◽  
Erucic Acid ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Gene Pools ◽  
Sequence Repeat ◽  
Low Erucic Acid ◽  
Simple Sequence ◽  
Canola Quality

The development of canola quality Brassica napus oilseed cultivars was a major achievement of Canadian public oilseed breeding programs. Simple sequence repeat (SSR) markers were applied to assess the genetic diversity of 300 plants representing one landrace introduced from Argentina in 1943, seven Canadian elite cultivars developed and released by Agriculture and Agri-Food Canada since 1954, and two European cultivars that were the source of the low erucic acid and low glucosinolate traits that define canola quality. Application of 22 SSR primer pairs from eight linkage groups detected 88 polymorphic alleles from 33 likely loci. The allelic frequencies in 300 samples ranged from 0.003 to 0.993 and averaged 0.388. The estimates of mean heterozygosity for these cultivars ranged from 0.055 to 0.203 and averaged 0.139. The most SSR variation was detected in the cultivars Argentine, Golden and Oro. A trend of decline in SSR variation was observed over the years of breeding effort. The proportion of total SSR variation residing among the cultivars was 51.4%; between high vs. low erucic acid cultivars 15% and between high vs. low glucosinolate cultivars 21.2%. Pairwise genetic differentiations among these cultivars ranged from 0.140 to 0.819 and averaged 0.500. Cluster analysis revealed that the genetic relationships of these cultivars were consistent with their known pedigrees. These findings are useful for broadening the genetic base of improved B. napus gene pools, selecting genetically diverse genotypes for hybrid combinations, and conserving summer rape germplasm.Key words: Simple sequence repeat, summer rape, Brassica napus, genetic diversity, genetic relationship, genetic structure

Genetic relatedness among cultivated and wild mulberry (Moraceae: Morus) as revealed by inter-simple sequence repeat analysis in China

2006 ◽  
Vol 86 (1) ◽  
pp. 251-257 ◽  
Author(s):  
Zhao Weiguo ◽  
Zhou Zhihua ◽  
Miao Xuexia ◽  
Wang Sibao ◽  
Zhang Lin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Pair Group ◽  
Simple Sequence

The genetic diversity of 27 mulberry (Morus spp.) genotypes mainly from China was investigated using inter-simple sequence repeat (ISSR) markers to assist in addressing breeding objectives and conserving existing genetic resources. Of the 22 primers screened, 15 produced highly reproducible ISSR bands. Using these 15 primers, 138 discernible DNA fragments were generated with 126 (91.3%) being polymorphic, indicating considerable genetic variation among the mulberry genotypes studied. Genetic similarity ranged from 0.6014 between Yu 2 and Yu 711 to 0.9493 between Cuizhisang and Dejiang 10. The phenetic dendrogram based on ISSR data generated by the unweighed pair group method with arithmetical averages (UPGMA) method grouped the 27 accessions into two major clusters: cluster I, cultivated mulberry species (M. multicaulis Perr., M. alba Linn., M. atropurpurea oxb., M. bombycis Kiodz., M. australis Poir., M. rotundiloba Kiodz., M. alba var. pendula Dipp., M. alba var. macrophylla Loud., and M. alba var. venose Delile.); and cluster II, wild mulberry species (M. cathayana Hemsl., M. laevigata Wall., M. wittiorum Hand-Mazz., M. nigra Linn., and M. mongolica Schneid.). Our molecular analyses agree with the existing morphological classification of Morus and clarify the genetic relationships among mulberry species. Key words: Morus L., genetic diversity, inter-simple sequence repeat, relatedness

Genetic diversity analysis of yam cultivars (Dioscorea rotundata Poir.) in Benin using simple sequence repeat (SSR) markers

2007 ◽  
Vol 5 (02) ◽  
pp. 71-81 ◽  
Author(s):  
Serge Tostain ◽  
Clément Agbangla ◽  
Nora Scarcelli ◽  
Cédric Mariac ◽  
Ogoubi Daïnou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Management Practices ◽  
Genetic Relationships ◽  
Sequence Repeat ◽  
Dioscorea Rotundata ◽  
Tuber Crop ◽  
The Mean ◽  
Simple Sequence

Guinea yam (Dioscorea rotundataPoir.) is a dioecious vegetatively propagated tuber crop. It is widely cultivated by traditional techniques in West Africa, its area of origin. The genetic diversity of 146 accessions from Benin was analysed using 10 polymorphic simple sequence repeat (SSR) nuclear markers and agromorphological traits. An average of 8.4 alleles per locus was detected. The mean heterozygosity was 0.57 and the mean polymorphism information content (PIC) for polymorphic markers was 0.51. Some cultivars (23%) were found to have an identical genotype for the 10 markers. The structure of the genetic diversity observed in Benin is the result of farmers' crop management practices and their know-how. The cultivar diversity had a geographical component. We also noted major differentiation between early and late cultivars, with higher diversity in the early ones. Cultivars from northern Benin and early cultivars had the greatest allelic richness. SSR markers proved to be powerful tools for fingerprinting each cultivar and analysing their genetic relationships. The results of this study could be useful for defining a strategy for the conservation of genetic diversity in yams.

Genetic diversity analysis using simple sequence repeat markers in soybean

2014 ◽  
Vol 12 (S1) ◽  
pp. S87-S90 ◽  
Author(s):  
Zhenbin Hu ◽  
Guizhen Kan ◽  
Guozheng Zhang ◽  
Dan Zhang ◽  
Derong Hao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Wild Soybean ◽  
Sequence Repeat ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Cultivated Soybean ◽  
Simple Sequence ◽  
Nei's Genetic Distance

To evaluate the genetic diversity (GD) of wild and cultivated soybeans and determine the genetic relationships between them, in this study, 127 wild soybean accessions and 219 cultivated soybean accessions were genotyped using 74 simple sequence repeat (SSR) markers. The results of the study revealed that the GD of the wild soybeans exceeded that of the cultivated soybeans. In all, 924 alleles were detected in the 346 soybean accessions using 74 SSRs, with an average of 12.49 alleles per locus. In the 219 cultivated soybean accessions, 687 alleles were detected, with an average of 9.28 alleles per locus; in the 127 wild soybean accessions, 835 alleles were detected, with an average of 11.28 alleles per locus. We identified 237 wild-soybean-specific alleles and 89 cultivated-soybean-specific alleles in the 346 soybean accessions, and these alleles accounted for 35.28% of all the alleles in the sample. Principal coordinates analysis and phylogenetic analysis based on Nei's genetic distance indicated that all the accessions could be classified into two major clusters, corresponding to wild and cultivated soybeans. These results will increase our understanding of the genetic differences and relationships between wild and cultivated soybeans and provide information to develop future breeding strategies to improve soybean yield.

Simple sequence repeat diversity in diploid and tetraploid Coffea species

Genome ◽  
2004 ◽  
Vol 47 (3) ◽  
pp. 501-509 ◽  
Author(s):  
Pilar Moncada ◽  
Susan McCouch
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Simple Sequence Repeat ◽  
Plant Material ◽  
Diploid Species ◽  
Allelic Diversity ◽  
Germplasm Bank ◽  
East African ◽  
In The Wild ◽  
Simple Sequence

Thirty-four fluorescently labeled microsatellite markers were used to assess genetic diversity in a set of 30 Coffea accessions from the CENICAFE germplasm bank in Colombia. The plant material included one sample per accession of seven East African accessions representing five diploid species and 23 wild and cultivated tetraploid accessions of Coffea arabica from Africa, Indonesia, and South America. More allelic diversity was detected among the five diploid species than among the 23 tetraploid genotypes. The diploid species averaged 3.6 alleles/locus and had an average polymorphism information content (PIC) value of 0.6, whereas the wild tetraploids averaged 2.5 alleles/locus and had an average PIC value of 0.3 and the cultivated tetraploids (C. arabica cultivars) averaged 1.9 alleles/locus and had an average PIC value of 0.22. Fifty-five percent of the alleles found in the wild tetraploids were not shared with cultivated C. arabica genotypes, supporting the idea that the wild tetraploid ancestors from Ethiopia could be used productively as a source of novel genetic variation to expand the gene pool of elite C. arabica germplasm.Key words: Coffea spp., microsatellite markers, genetic diversity.

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 Simple Sequence Repeat Marker Analysis of Genetic Relationships within Hydrangea macrophylla

2007 ◽  
Vol 132 (3) ◽  
pp. 341-351 ◽  
Author(s):  
Sandra M. Reed ◽  
Timothy A. Rinehart
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Allelic Diversity ◽  
Sequence Repeat ◽  
Hydrangea Macrophylla ◽  
Total Genetic Diversity ◽  
Ssr Loci ◽  
Diversity Studies ◽  
Simple Sequence

Genetic diversity studies using 39 simple-sequence repeat (SSR) markers were carried out with 114 taxa of Hydrangea macrophylla (Thunb.) Ser., including 87 H. macrophylla ssp. macrophylla cultivars and 20 members of H. macrophylla ssp. serrata (Thunb.) Makino. The SSR loci were highly variable among the taxa, producing a mean of 8.26 alleles per locus. Overall allelic richness was relatively high at 5.12 alleles per locus. H. macrophylla ssp. serrata contained nearly twice the allelic diversity of H. macrophylla ssp. macrophylla. The majority of genetic diversity was found to reside within the subspecies, with only 12% of the total genetic diversity observed occurring between subspecies. Although the elevation of H. macrophylla ssp. serrata to species level has recently been recommended by several hydrangea authorities, these data support the subspecies designation. Four cultivars (Preziosa, Pink Beauty, Tokyo Delight, and Blue Deckle) appeared to be hybrids between the two subspecies. Genetic similarities were found among five remontant cultivars (Bailmer, Oak Hill, David Ramsey, Decatur Blue, and Penny Mac) and several nonremontant cultivars, including General Vicomtesse de Vibraye, Nikko Blue, All Summer Beauty, and La France. No close genetic relationship was found between the remontant cultivar Early Sensation and other remontant cultivars. Genetic similarities were found among variegated and double-flower cultivars. Within H. macrophylla ssp. macrophylla, cultivars with mophead inflorescences clustered separately from most lacecap cultivars. This indicates the cultivars with lacecap inflorescences that were among some of the earliest introductions to Europe were not widely used in the breeding of mophead forms. Some presumed synonyms were found to be valid (‘Preziosa’ and ‘Pink Beauty’, ‘Rosalba’ and ‘Benigaku’, ‘Geoffrey Chadbund’ and ‘Mowe’), whereas others were not (‘Harlequin’ and ‘Monrey’, ‘Nigra’ and ‘Mandschurica’). This study identified potentially unexploited sources of germplasm within H. macrophylla and relationships between existing cultivars of this popular shrub. This information should be of value when selecting parents for breeding programs.

scholarly journals Molecular characterization of indigenous olive genotypes based on SSR analysis

Genetika ◽  
2016 ◽  
Vol 48 (3) ◽  
pp. 1017-1025
Author(s):  
Hulya Unver ◽  
Ebru Sakar ◽  
Mehmet Ulas ◽  
Sezai Ercisli ◽  
Bekir Ak
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Ssr Analysis ◽  
Olive Cultivars ◽  
Ssr Loci ◽  
Similarity Ratio ◽  
Repeat Primer ◽  
Simple Sequence

Trees of 25 widely grown olive genotypes were analyzed using a set of 10 SSR (simple sequence repeat) primer pairs and to evaluate genetic diversity and reveal inter-cultivar relationships. Two well-known international olive cultivars (Chetoni and Manzanilla) and four widely grown Turkish standard cultivars (Aycalik, Edincik Su, Gemlik, Kilis Yaglik) are also included in the study to compare Kilis genotypes. The 10 polymorphic SSR loci exhibited 4 (UDO4) to 17 alleles (UDO43), with expected heterozygozity (He) ranging from 0.510 to 0.887 and a mean of 0.692 presenting high polymorphism. In this study we did not determine identical genotypes and Polateli4 and Kilis Ya?l?k (0.75), Polateli3 and Polateli7 (0.75) and Polateli6 and Manzanilla (0.70) revealed the highest similarity ratio each other. The most genetically divergent cultivars were Elbeyli8 and Musabeyli5 (0.10); Elbeyli3 and Musabeyli7 (0.15) and Musabeyli6 and Elbeyli7 (0.15), respectively.

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