scholarly journals Genomic sequence derived simple sequence repeats markers. A case study with Medicago spp.

2002 ◽  
Vol 5 (3) ◽  
Author(s):  
Rodomiro Ortiz ◽  
Viswanathan Mahalakshmi ◽  
P. Aparna ◽  
S. Ramadevi
Keyword(s):  
Simple Sequence Repeats ◽  
Genomic Sequence ◽  
Simple Sequence

scholarly journals Identification and Characterization of LaSCL6 Alleles in Larix kaempferi (Lamb.) Carr. Based on Analysis of Simple Sequence Repeats and Allelic Expression

Forests ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1296
Author(s):  
Qiao-Lu Zang ◽  
Xiang-Yi Li ◽  
Li-Wang Qi ◽  
Wan-Feng Li
Keyword(s):  
Simple Sequence Repeats ◽  
Genomic Sequence ◽  
Expression Patterns ◽  
Larix Kaempferi ◽  
Mature Trees ◽  
Vegetative Development ◽  
Genetic Studies ◽  
Identification And Characterization ◽  
Simple Sequence

Simple sequence repeats (SSRs) are widely used as markers for the assessment of genetic diversity and marker-assisted breeding. In a previous study, two SSRs (GCA and CCA), were found in the genomic sequence of Larix (La) SCL6, which plays important roles in the growth and development of Larix kaempferi (Lamb.) Carr. In this study, we analyzed the polymorphisms of these two SSRs in the L. kaempferi population. We found that each SSR had five different polymorphisms, among which (GCA)7 and (CCA)7 were predominant. In addition, 12 haplotypes were detected, with (GCA)7(CCA)7 having the highest frequency. Furthermore, we detected the haplotypes of LaSCL6 in mature trees and their seeds and analyzed the relationships between parents and offspring. The expression patterns of five LaSCL6 alleles were analyzed and they showed balanced expression during vegetative development. Taken together, these findings not only provide more genetic information on LaSCL6, but also provide a candidate marker for genetic studies and breeding.

scholarly journals LegumeSSRdb: A Comprehensive Microsatellite Marker Database of Legumes for Germplasm Characterization and Crop Improvement

2021 ◽  
Vol 22 (21) ◽  
pp. 11350
Author(s):  
Naveen Duhan ◽  
Rakesh Kaundal
Keyword(s):  
Simple Sequence Repeats ◽  
Genomic Sequence ◽  
Crop Improvement ◽  
Genomic Region ◽  
Web Interface ◽  
Genic Ssrs ◽  
Marker Selection ◽  
User Friendly ◽  
Simple Sequence ◽  
Crop Health

Microsatellites, or simple sequence repeats (SSRs), are polymorphic loci that play a major role as molecular markers for genome analysis and plant breeding. The legume SSR database is a webserver which contains simple sequence repeats (SSRs) from genomes of 13 legume species. A total of 3,706,276 SSRs are present in the database, 698,509 of which are genic SSRs, and 3,007,772 are non-genic. This webserver is an integrated tool to perform end-to-end marker selection right from generating SSRs to designing and validating primers, visualizing the results and blasting the genomic sequences at one place without juggling between several resources. The user-friendly web interface allows users to browse SSRs based on the genomic region, chromosome, motif type, repeat motif sequence, frequency of motif, and advanced searches allow users to search based on chromosome location range and length of SSR. Users can give their desired flanking region around repeat and obtain the sequence, they can explore the genes in which the SSRs are present or the genes between which the SSRs are bound design custom primers, and perform in silico validation using PCR. An SSR prediction pipeline is implemented where the user can submit their genomic sequence to generate SSRs. This webserver will be frequently updated with more species, in time. We believe that legumeSSRdb would be a useful resource for marker-assisted selection and mapping quantitative trait loci (QTLs) to practice genomic selection and improve crop health. The database can be freely accessed at http://bioinfo.usu.edu/legumeSSRdb/.

Polymorphism revealed by simple sequence repeats

1996 ◽  
Vol 1 (7) ◽  
pp. 215-222 ◽  
Author(s):  
W POWELL ◽  
G MACHRAY ◽  
J PROVAN
Keyword(s):  
Simple Sequence Repeats ◽  
Simple Sequence

scholarly journals Implications of genome simple sequence repeats signature in 98 Polyomaviridae species

3 Biotech ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rezwanuzzaman Laskar ◽  
Md Gulam Jilani ◽  
Safdar Ali
Keyword(s):  
Simple Sequence Repeats ◽  
Simple Sequence

Instability of simple sequence repeats in a mammalian cell line

1994 ◽  
Vol 3 (2) ◽  
pp. 253-256 ◽  
Author(s):  
Rosann A. Farber ◽  
Thomas D. Petes ◽  
Margaret Dominska ◽  
Sarah S. Hudgens ◽  
R.Michael Liskay
Keyword(s):  
Cell Line ◽  
Mammalian Cell ◽  
Simple Sequence Repeats ◽  
Mammalian Cell Line ◽  
Simple Sequence

scholarly journals A High-Density EST-SSR-Based Genetic Map and QTL Analysis of Dwarf Trait in Cucurbita pepo L.

2018 ◽  
Vol 19 (10) ◽  
pp. 3140 ◽  
Author(s):  
Chenggang Xiang ◽  
Ying Duan ◽  
Hongbo Li ◽  
Wei Ma ◽  
Sanwen Huang ◽  
...  
Keyword(s):  
Genetic Map ◽  
Simple Sequence Repeats ◽  
Cucurbita Pepo ◽  
Economic Value ◽  
High Density ◽  
Oxidase Gene ◽  
Phenotypic Polymorphism ◽  
The Rich ◽  
Expressed Sequence ◽  
Simple Sequence

As one of the earliest domesticated species, Cucurbita pepo (including squash and pumpkin) is rich in phenotypic polymorphism and has huge economic value. In this research, using 1660 expressed sequence tags-simple sequence repeats (EST-SSRs) and 632 genomic simple sequence repeats (gSSRs), we constructed the highest-density EST-SSR-based genetic map in Cucurbita genus, which spanned 2199.1 cM in total and harbored 623 loci distributed in 20 linkage groups. Using this map as a bridge, the two previous gSSR maps were integrated by common gSSRs and the corresponding relationships around chromosomes in three sets of genomes were also collated. Meanwhile, one large segmental inversion that existed between our map and the C. pepo genome was detected. Furthermore, three Quantitative Trait Loci (QTLs) of the dwarf trait (gibberellin-sensitive dwarf type) in C. pepo were located, and the candidate region that covered the major QTL spanned 1.39 Mb, which harbored a predicted gibberellin 2-β-oxidase gene. Considering the rich phenotypic polymorphism, the important economic value in the Cucurbita genus species and several advantages of the SSR marker were identified; thus, this high-density EST-SSR-based genetic map will be useful in Pumpkin and Squash breeding work in the future.

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