Microsatellite markers useful throughout the genus Dianthus

Genome ◽  
2000 ◽  
Vol 43 (1) ◽  
pp. 208-210 ◽  
Author(s):  
MJM Smulders ◽  
W Rus-Kortekaas ◽  
B Vosman
Keyword(s):  
Simple Sequence Repeat ◽  
Repeat Unit ◽  
Natural Populations ◽  
Acc Synthase ◽  
Sequence Repeat ◽  
Site Analysis ◽  
Coding Regions ◽  
Wide Range ◽  
Simple Sequence ◽  
Allele Series

Using repeats found in sequences from Dianthus species present in the EMBL database, primers for STMS (sequence-tagged microsatellite site) analysis were developed and tested. Five loci were polymorphic and amplified products of sufficient quality in nearly all of the 26 Dianthus species tested, except MS-DINGSTA, which amplified in only one-third of the species. Loci MS-DINMADSBOX and MS-DCDIA30 produced allele series that were mostly two nucleotides (the repeat unit) apart. MS-DCAMCRBSY and MS-DINCARACC also amplified regular series of alleles, but more than two fragments per individual were detected in a number of species. Both loci code for a member of the ACC synthase gene family. The observation that the loci amplified across a wide range of Dianthus species may imply that the different species within the genus are relatively closely related. Alternatively, it may indicate that the regions selected for primer design (some of which are in coding regions) are well conserved. These microsatellites will be useful for the measurement of genetic diversity in natural populations of Dianthus species and the identification of carnation varieties. Key words: SSR, simple sequence repeat, identification, STMS, sequence-tagged microsatellite site.

Microsatellite polymorphism in Dioscorea tokoro, a wild yam species

Genome ◽  
1994 ◽  
Vol 37 (5) ◽  
pp. 794-801 ◽  
Author(s):  
Ryohei Terauchi ◽  
Akihiro Konuma
Keyword(s):  
Microsatellite Loci ◽  
Simple Sequence Repeat ◽  
Population Genetic ◽  
Natural Populations ◽  
Allozyme Analysis ◽  
Sequence Repeat ◽  
Expected Heterozygosity ◽  
Simple Sequence ◽  
Paternity Exclusion ◽  
Wild Yam

Six microsatellite loci were characterized in Dioscorea tokoro, a wild yam species in East Asia. All six loci were polymorphic in a sample of 23 individuals from natural populations in Japan. The microsatellite loci displayed many alleles (6.2 alleles per locus on average), and the observed heterozygosity (Ho = 0.54) as well as expected heterozygosity (He = 0.68) were high. The heterozygosities were far more than that previously detected by allozyme analysis of D. tokoro (Ho = 0.23, He = 0.28). Five microsatellite loci were sufficient to provide a paternity exclusion rate (Q) of Q = 0.98, which enables monitoring of the pollen-mediated gene flow between plants in a population. Microsatellite loci are abundant and highly polymorphic in D. tokoro and other plants and are therefore ideal markers for plant population genetic studies.Key words: microsatellite, simple sequence repeat, population genetics, Dioscorea tokoro.

Molecular phylogeny of genus Musa determined by simple sequence repeat markers

2015 ◽  
Vol 14 (3) ◽  
pp. 192-199 ◽  
Author(s):  
Huimin Feng ◽  
You Chen ◽  
Bo Li ◽  
Yaoting Wu
Keyword(s):  
Simple Sequence Repeat ◽  
Polymorphic Information Content ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Sequence Repeat ◽  
Wide Range ◽  
Molecular Marker Analysis ◽  
High Level ◽  
Simple Sequence

Musa L. was previously separated into five sections (Eumusa, Rhodochlamys, Callimusa, Australimusa and Ingentimusa) based on basic chromosome numbers and morphological characters. However, several molecular analyses currently support restructuring of Musa species into two sections, Musa and Callimusa. The application of simple sequence repeat molecular marker analysis to Musa phylogeny provided valuable, supplemental information about the classification of, and relationships between, Musa species and subspecies. Totally, 28 accessions of Musa acuminata Colla subspecies and varieties and 25 accessions of other Musa species were evaluated; 12 primers produced 91 polymorphic bands, polymorphic information content ranged from 0.4473 to 0.8394 (average = 0.7226), indicating that the primers showed a high level of polymorphism. Our results generally agreed with previous phylogenetic analyses based on molecular data. One clade comprised species of sections Australimusa and Callimusa (X= 10/9); most species of sections Eumusa and Rhodochlamys (X= 11) formed the other clade. The relationships between most species were as expected; however, some species did not conform to findings of previous studies. A wide range of variability was observed in the M. acuminata complex. M. acuminata var. chinensis and M. acuminata subsp. 522 showed the most distant relationships to other subspecies: Musa laterita, Musa ornata and Musa velutina clustered with M. acuminata var. chinensis, suggesting that they may constitute a secondary gene pool for the improvement of cultivated bananas. Molecular data indicated that Musa tongbiguanensis Chen You & Yao-Ting Wu, which was observed and described by our research group in Yunnan, China, was a distinct, new species.

scholarly journals Strawberry GenBank-derived and Genomic Simple Sequence Repeat (SSR) Markers and Their Utility with Strawberry, Blackberry, and Red and Black Raspberry

2005 ◽  
Vol 130 (1) ◽  
pp. 102-115 ◽  
Author(s):  
K.S. Lewers ◽  
S.M.N. Styan ◽  
S.C. Hokanson ◽  
N.V. Bassil
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Gene Sequence ◽  
Genomic Library ◽  
Black Raspberry ◽  
Sequence Repeat ◽  
Coding Regions ◽  
Polymorphism Detection ◽  
Mining Methods ◽  
Simple Sequence

Although simple sequence repeat (SSR) markers have been developed for species in the closely related genera Fragaria L. (strawberry) and Rubus L. (raspberry and blackberry), the number of SSRs available is insufficient for genetic mapping. Our objective was to use and compare multiple approaches for developing additional SSRs for Fragaria and Rubus. The approaches included: the development of SSRs from GenBank sequences from species of varied relatedness to Fragaria and Rubus and identified with two different data-mining methods (BLAST and SSRIT); the evaluation of some previously published SSRs designed from related species; and the development of SSRs from a genomic library made from F. ×ananassa Duschene ex Rozier `Earliglow'. When an SSR was developed from a known gene sequence, the location of the repeat in the gene was determined to evaluate the effect on amplification and polymorphism detection. Cross-generic amplification between closely related Fragaria and Rubus as well as transference from species of varied relatedness to Fragaria and Rubus also was evaluated and indicated limited transference within the subfamily Rosoideae. However, development of SSRs for Fragaria and Rubus from Rosa L. (rose) and Rosaceae genera outside Rosoideae was not efficient enough to be practical for new map development. SSRIT was superior to BLAST for identifying GenBank sequences containing repeats. SSRs developed from repeats found in either the 5′UTR (80% polymorphic) or 3′UTR (85% polymorphic) were most likely to detect polymorphisms, compared with those developed from coding regions (30%). SSRs developed from the genomic library were only slightly superior to GenBank-derived SSRs in their ability to detect polymorphisms.

scholarly journals An Extended Linkage Map for Watermelon Based on SRAP, AFLP, SSR, ISSR, and RAPD Markers

2006 ◽  
Vol 131 (3) ◽  
pp. 393-402 ◽  
Author(s):  
A. Levi ◽  
C.E. Thomas ◽  
T. Trebitsh ◽  
A. Salman ◽  
J. King ◽  
...  
Keyword(s):  
Linkage Map ◽  
Simple Sequence Repeat ◽  
Citrullus Lanatus ◽  
Average Distance ◽  
Acc Synthase ◽  
Segregation Ratio ◽  
Issr Markers ◽  
Sequence Repeat ◽  
Linkage Groups ◽  
Simple Sequence

Seventy-one amplified fragment length polymorphism (AFLP), 93 sequence related amplified polymorphism (SRAP), and 14 simple sequence repeat (SSR) markers were used to extend an initial genetic linkage map for watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai]. The initial map was based on 151 randomly amplified polymorphic DNA (RAPD) and 30 and inter-simple sequence repeat (ISSR) markers. A testcross population previously used for mapping of RAPD and ISSR markers was used in this study: {plant accession Griffin 14113 [C. lanatus var. citroide (L.H. Bailey) Mansf.] × the watermelon cultivar New Hampshire Midget (C. lanatus var. lanatus)} × PI 386015 [C. colocynthis (L.) Schrad.]. The linkage map contains 360 DNA markers distributed on 19 linkage groups, and covers a genetic distance of 1976 cM with an average distance of 5.8 cM between two markers. A genomic DNA clone representing 1-amino-cyclopropane-1-carboxylic acid (ACC-) synthase gene, involved in ethylene biosynthesis, was also mapped. As in previous mapping studies for watermelon, a large number of AFLP and SRAP markers were skewed away from the 1:1 segregation ratio, and had to be excluded from the final mapping analysis. The stringent mapping criteria (JoinMap 3.0 mapping program) produced linkage groups with marker order consistent with those reported in previous mapping study for watermelon.

scholarly journals Impact of Plant Breeding on the Genetic Diversity of Cultivated Strawberry as Revealed by Expressed Sequence Tag-derived Simple Sequence Repeat Markers

2009 ◽  
Vol 134 (3) ◽  
pp. 337-347 ◽  
Author(s):  
David Jesús Gil-Ariza ◽  
Iraida Amaya ◽  
José Manuel López-Aranda ◽  
José Federico Sánchez-Sevilla ◽  
Miguel Ángel Botella ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Natural Populations ◽  
Group Method ◽  
Sequence Repeat ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Strawberry Cultivars

Unlike other important crops analyzed so far for genetic diversity and population structure, the brief history and particularities of the genetics of the cultivated strawberry (Fragaria ×ananassa Duchesne) have limited its genetic characterization. The genomic composition and the pattern of inheritance have not been fully elucidated, although a number of studies have suggested a highly diploidized genome. In this study, the similarity relationships and structure of 92 selected strawberry cultivars with widely diverse origins have been established using simple sequence repeat (SSR) markers derived from expressed sequence tags (EST-SSR markers). Genetic analysis performed by the unweighted pair group method with arithmetic mean clustering revealed a distribution according to both date of cultivar release and breeding for a specific climatic adaptation. Additionally, a model-based clustering approach identified three populations among the strawberry cultivars with an overall FST value of 0.15 to 0.16. Both analyses support a limited differentiation of modern cultivars, most probably as a consequence of the methodology of strawberry breeding. Interestingly, the collection of strawberry cultivars here analyzed showed comparable genetic differentiation to that observed in natural populations of Fragaria chiloensis (L.) Mill., one of its wild ancestors. Our results suggest that breeding has produced a small but significant reduction on the genetic diversity of F. ×ananassa. The panel of 10 EST-SSRs described in this work provided an extremely low probability of confusion (less than 10−11), offering an efficient and accurate method for cultivar identification.

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