ArticleBMC genetics2015
Genome-wide distribution comparative and composition analysis of the SSRs in Poaceae.
Article in BMC genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- In silico mining of microsatellites from the Phlebotomus argentipes (Diptera: Psychodidae) scaffold-level genome assembly and validation of eleven genotyping markers.Research square · 2026Article
- Comprehensive analysis of chloroplast genome evolution in Poaceae: codon usage patterns, selection pressures, and phylogenomic relationships.BMC genomics · 2026Article
- Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants.Genomics, proteomics & bioinformatics · 2021Article
- Genomic approach for conservation and the sustainable management of endangered species of the Amazon.PloS one · 2021Article
- Rapid identification and characterization of genetic loci for defective kernel in bread wheat.BMC plant biology · 2019Article
- Comparative analyses of simple sequence repeats (SSRs) in 23 mosquito species genomes: Identification, characterization and distribution (Diptera: Culicidae).Insect science · 2019Article
- Identification of massive molecular markers inPlant diversity · 2017Article
- Genome-wide mapping and characterization of microsatellites in the swamp eel genome.Scientific reports · 2017Article
- Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses.Frontiers in plant science · 2017Review
- De novo assembly, functional annotation, and analysis of the giant reed (Biotechnology for biofuels · 2017Article
- In Silico Approach for Characterization and Comparison of Repeats in the Genomes of Oil and Date Palms.Bioinformatics and biology insights · 2017Article
- Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda).BMC genetics · 2015Article
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7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThe Poaceae family is of great importance to human beings since it comprises the cereal grasses which are the main sources for human food and animal feed. With the rapid growth of genomic data from Poaceae members, comparative genomics becomes a convinent method to study genetics of diffierent species. The SSRs (Simple Sequence Repeats) are widely used markers in the studies of Poaceae for their high abundance and stability.
resultsIn this study, using the genomic sequences of 9 Poaceae species, we detected 11,993,943 SSR loci and developed 6,799,910 SSR primer pairs. The results show that SSRs are distributed on all the genomic elements in grass. Hexamer is the most frequent motif and AT/TA is the most frequent motif in dimer. The abundance of the SSRs has a positive linear relationship with the recombination rate. SSR sequences in the coding regions involve a higher GC content in the Poaceae than that in the other species. SSRs of 70-80 bp in length showed the highest AT/GC base ratio among all of these loci. The result shows the highest polymorphism rate belongs to the SSRs ranged from 30 bp to 40 bp. Using all the SSR primers of Japonica, nineteen universal primers were selected and located on the genome of the grass family. The information of SSR loci, the SSR primers and the tools of mining and analyzing SSR are provided in the PSSRD (Poaceae SSR Database, http://biodb.sdau.edu.cn/pssrd/).
conclusionsOur study and the PSSRD database provide a foundation for the comparative study in the Poaceae and it will accelerate the study on markers application, gene mapping and molecular breeding.
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