Genetic mapping and variability of seven soybean simple sequence repeat loci

Genome ◽  
1994 ◽  
Vol 37 (5) ◽  
pp. 763-769 ◽  
Author(s):  
M. Morgante ◽  
A. Rafalski ◽  
P. Biddle ◽  
S. Tingey ◽  
A. M. Olivieri
Keyword(s):  
Simple Sequence Repeats ◽  
Simple Sequence Repeat ◽  
Allelic Variation ◽  
Glycine Soja ◽  
Wild Soybean ◽  
Rflp Markers ◽  
Sequence Motifs ◽  
Sequence Repeat ◽  
Rflp Map ◽  
Simple Sequence

Microsatellites or simple sequence repeats are stretches of short tandemly repeated DNA sequence motifs, dispersed throughout the genomes of most eukaryotes. Simple sequence repeat polymorphisms (SSRPs) have recently been reported in plants. Here we present the genetic map position of seven different soybean (Glycine max (L.) Merr. and Glycine soja Sieb. and Zucc.) SSRPs contained in sequenced genes, four of which represent newly mapped positions for these genes. The other three SSRPs coincided with independently established RFLP map positions for the corresponding genes. When a set of 61 soybean accessions was screened at four of these loci by using agarose gels, the average number of alleles per locus was 7.75, the effective number of alleles (ne) was 2.57, and the level of allele differentiation (δT) was 0.62. Allelic variation decreased sharply with increasing levels of domestication, with the level of differentiation going from 84% in the wild soybean to 43% in the elite germplasm. Variation levels observed on a subset made of 19 of the 61 lines were always higher for SSRPs than for RFLP markers, with the average number of alleles per locus going from 4.25 to 2.15. In comparison with RFLP markers, SSRPs are more informative and are easier to analyse but require more effort to develop.Key words: simple sequence repeats, soybean, variability, mapping, domestication, microsatellites.

Mapping of digested and undigested random amplified microsatellite polymorphisms in barley

Genome ◽  
1995 ◽  
Vol 38 (5) ◽  
pp. 991-998 ◽  
Author(s):  
Jörg Becker ◽  
Manfred Heun
Keyword(s):  
Simple Sequence Repeats ◽  
Dna Markers ◽  
Simple Sequence Repeat ◽  
Sequence Data ◽  
Linkage Maps ◽  
Sequence Repeat ◽  
Rflp Map ◽  
Alternative Approach ◽  
Microsatellite Mapping ◽  
Simple Sequence

The broad use of microsatellites as a tool for constructing linkage maps in plants has been limited by the need for sequence data to detect the underlying simple sequence repeats. Therefore, random amplified microsatellite polymorphisms (RAMPs) were studied as an alternative approach for barley mapping. Labelled (GA)n simple sequence repeat primers were combined with RAPD primers of different length and sequence to generate RAMPs. To get additional polymorphisms (called dRAMPs), the obtained products were also analysed after digestion with MseI. There were 0–11 polymorphisms found per primer combination. Sixty RAMPs/dRAMPs identifying 40 new loci were mapped onto a barley RFLP map. The new DNA markers are found on all chromosomes and they increased the length of the barley map by 174 cM to a total of 1270 cM. Interestingly, the RAMPs/dRAMPs caused stretching effects in genome areas where stretching was also observed for AFLPs.Key words: barley, microsatellite, mapping, RAMP, RFLP.

scholarly journals Analysis of allelic variation in wild potato (Solanum) species by simple sequence repeat (SSR) markers

3 Biotech ◽  
2019 ◽  
Vol 9 (7) ◽  
Author(s):  
Jagesh Kumar Tiwari ◽  
Nilofer Ali ◽  
Sapna Devi ◽  
Rasna Zinta ◽  
Vinod Kumar ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Allelic Variation ◽  
Solanum Species ◽  
Wild Potato ◽  
Sequence Repeat ◽  
Simple Sequence

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.

scholarly journals Simple Sequence Repeat Markers Reveal Hungarian Plum (Prunus domestica L.) Germplasm as a Valuable Gene Resource

HortScience ◽  
2017 ◽  
Vol 52 (12) ◽  
pp. 1655-1660 ◽  
Author(s):  
Noémi Makovics-Zsohár ◽  
Magdolna Tóth ◽  
Dezső Surányi ◽  
Szilvia Kovács ◽  
Attila Hegedűs ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Allelic Variation ◽  
Genetic Relationships ◽  
Principal Component ◽  
Bootstrap Support ◽  
Limited Information ◽  
Sequence Repeat ◽  
Prunus Domestica ◽  
Simple Sequence

The hexaploid European plum (Prunus domestica L.) is an economically important fruit species with limited information on its genetic structure. Our objective was to fingerprint 55 cultivars using seven simple sequence repeat (SSR) markers to estimate the polymorphism level and determine allelic variation and genetic relationships among local and international cultivars. The primer pairs amplified a total of 135 alleles ranging from six to 27 alleles per locus, displaying high polymorphism. All genotypes were clearly distinguished with the seven SSRs used in this study. In a neighbor-joining cluster analysis, cultivars belonging to the same species did not group together. Foreign modern cultivars clustered together, and Hungarian landraces positioned distantly from those. STRUCTURE analysis indicated three genetically distinct groups of the studied genotypes. Each cluster of Hungarian landrace cultivars received strong bootstrap support (89% to 100%). Most genotypes kept under identical name showed different DNA fingerprints. A principal component analysis (PCA) confirmed the information provided by the dendrogram and clarified the origin of ʻFehérszilva’. Our results confirmed the potential of the application of SSR markers in plum breeding.

Simple sequence repeats for germplasm analysis and mapping in maize

Genome ◽  
1996 ◽  
Vol 39 (2) ◽  
pp. 277-287 ◽  
Author(s):  
Graziana Taramino ◽  
Scott Tingey
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Trinucleotide Repeats ◽  
High Rate ◽  
Rflp Markers ◽  
Sequence Motifs ◽  
Genomic Libraries ◽  
Expected Heterozygosity ◽  
Germplasm Analysis ◽  
Simple Sequence

Simple sequence repeats (SSRs) are a relatively new class of DNA markers consisting of short runs of tandemly repeated sequence motifs evenly distributed throughout eukaryotic genomes. Owing to the high rate of variation in the number of repeat units, the polymorphism level shown by SSRs is high. Furthermore, they are easy to analyze by means of the polymerase chain reaction, using flanking unique sequence primers. In order to establish the utility of SSR markers for genetic mapping and for the analysis of corn germplasm, corn genomic libraries were constructed and screened for clones containing dinucleotide and trinucleotide repeats. One hundred and fifty clones were isolated and 34 of them were used in this study to analyze 15 (AG)n repeats, 15 (AC)n repeats, and 4 trinucleotide repeats. Twelve corn inbred lines, representing 87% of the RFLP alleles present in a collection of public corn cultivars, were used to assess the information content of the SSR markers. The expected heterozygosity of each SSR marker was compared with the expected heterozygosity of 100 different RFLP markers. The stability of SSRs was also tested through segregation analysis on an existing mapping population. Key words : simple sequence repeats, microsatellites, maize, germplasm analysis, mapping.

scholarly journals Allelic variation on DcAOX1 gene in carrot (Daucus carota L.): An interesting simple sequence repeat in a highly variable intron

Plant Gene ◽  
2016 ◽  
Vol 5 ◽  
pp. 49-55 ◽  
Author(s):  
Amaia Nogales ◽  
Tânia Nobre ◽  
Helia G. Cardoso ◽  
Luz Muñoz-Sanhueza ◽  
Vera Valadas ◽  
...  
Keyword(s):  
Daucus Carota ◽  
Simple Sequence Repeat ◽  
Allelic Variation ◽  
Sequence Repeat ◽  
Daucus Carota L ◽  
Simple Sequence
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