CHLOROPLAST SIMPLE SEQUENCE REPEAT (CP-SSR) ANALYSIS FOR DETERMINING THE ORIGIN OF J. HOPEIENSIS

2014 ◽  
pp. 35-40
Author(s):  
J.X. Qi ◽  
C.L. Wu ◽  
N.G. Dong ◽  
Y.H. Chen ◽  
Y.B. Hao
Keyword(s):  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Ssr Analysis ◽  
Simple Sequence

scholarly journals Cultivation-Independent Analysis of Fungal Genotypes in Soil by Using Simple Sequence Repeat Markers

2007 ◽  
Vol 73 (20) ◽  
pp. 6519-6525 ◽  
Author(s):  
Kaspar Schwarzenbach ◽  
Franco Widmer ◽  
Jürg Enkerli
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Fungal Species ◽  
Sequence Repeat ◽  
Beauveria Brongniartii ◽  
Soil Dna ◽  
Ssr Analysis ◽  
Community Profiling ◽  
Independent Analysis ◽  
Simple Sequence

ABSTRACT Cultivation-independent analyses of fungi are used for community profiling as well as identification of specific strains in environmental samples. The objective of the present study was to adapt genotyping based on simple sequence repeat (SSR) marker detection for use in cultivation-independent monitoring of fungal species or strains in bulk soil DNA. As a model system, a fungal biocontrol agent (BCA) based on Beauveria brongniartii, for which six SSR markers have been developed, was used. Species specificity of SSR detection was verified with 15 fungal species. Real-time PCR was used to adjust for different detection sensitivities of the six SSR markers as well as for different template quantities. The limit for reliable detection per PCR assay was below 2 pg target DNA, corresponding to an estimated 45 genome copies of B. brongniartii. The cultivation-independent approach was compared to cultivation-dependent SSR analysis with soil samples from a B. brongniartii BCA-treated field plot. Results of the cultivation-independent method were consistent with cultivation-dependent genotyping and allowed for unambiguous identification and differentiation of the applied as well as indigenous strains in the samples. Due to the larger quantities of soil used for cultivation-dependent analysis, its sensitivity was higher, but cultivation-independent SSR genotyping was much faster. Therefore, cultivation-independent monitoring of B. brongniartii based on multiple SSR markers represents a rapid and strain-specific approach. This strategy may also be applicable to other fungal species or strains for which SSR markers have been developed.

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.

scholarly journals Simple Sequence Repeat (SSR) Analysis of 7 Chestnut Cultivars in the Korean Peninsula Using SSR Markers of Japanese Chestnut

2008 ◽  
Vol 7 (4) ◽  
pp. 475-480
Author(s):  
Eiichi Inoue ◽  
Lin Ning ◽  
Toshiya Yamamoto ◽  
Shuan Ruan ◽  
Yumi Matsuki ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Korean Peninsula ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Ssr Analysis ◽  
Simple Sequence

scholarly journals Identification of rare traditional grapevine cultivars using SSR markers and their geographical location within the Czech Republic

2020 ◽  
Vol 56 (No. 2) ◽  
pp. 71-78
Author(s):  
Kateřina Baránková ◽  
Radek Sotolář ◽  
Miroslav Baránek
Keyword(s):  
Czech Republic ◽  
Simple Sequence Repeat ◽  
Cultivar Identification ◽  
Geographical Location ◽  
Verbal Information ◽  
Sequence Repeat ◽  
The Czech Republic ◽  
Ssr Analysis ◽  
Ssr Loci ◽  
Simple Sequence

The designation of traditional varieties of grapevine is usually based on verbal information or very dated records. Old rare cultivars found in the Czech Republic were identified by Simple Sequence Repeat (SSR) analysis, a generally accepted method for cultivar identification. These cultivars are primarily maintained in a national collection of genetic resources. Finally a total of 102 candidate genotypes was selected where 49 traditional varieties were identified on the base of nine SSR loci compared with the European Vitis Database. Thirty-six items were registered under the correct designation. The remaining genotypes included four clones, and two genotypes could be described as synonyms. Seven genotypes were found to be incorrectly marked. For three of them, the correct name was found in the database under their SSR profile and four items were considered to be unique as no identical profile was found.

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