Genome-wide distribution comparative and composition analysis of the SSRs in Poaceae

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.

Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda)

“…yeast [31] as well as higher organisms e.g. model plant systems like Arabidopsis [32, 33] and also in more complex organisms like human beings [34]. Trimers and hexamers are predominant as they are favoured by the selective pressures compared to the other repeats (e.g.…”

Comparative analyses of simple sequence repeats (SSRs) in 23 mosquito species genomes: Identification, characterization and distribution (Diptera: Culicidae)

“…The density (SSR quantity per Mb of genomic sequence) and abundance (proportion of a given type of SSR among total SSRs) were used to measure the frequency of SSR in genomes (Wang et al, 2015b). The length of SSRs was divided into 10 groups with 10 bp intervals, namely 10-20, 21-30, 31-40, 41-50, 51-60, 61-70, 71-80, 81-90, 91-100 and 101+ bp (Zhao et al, 2015).…”

Genome-Wide Mining, Characterization and Development of miRNA-SSRs inArabidopsis thaliana

“…SSRs are co-dominant, and multi-allelic by nature and due to constant variation in the number of tandem repeats; they are known to be, robust, highly polymorphic (Brandstrom et al 2008, Heesacker et al 2008), locus-specific and co-dominant, thus becoming the markers of choice. (Gupta et al 1996; Ni et al 2002; Lightfoot and Iqbal, 2013; Senan et al 2014; Wang et al 2015). Previous reports show that SSRs are selectively neutral and are randomly distributed in the eukaryotic genome (Schlotterer, 2000; Schlotterer, 2004).…”