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

Yi Wang,Chao Yang,Qiaojun Jin,Yuanjie Yu,Long Yang,Shuangshuang Wang,Dongjie Zhou

doi:10.1186/s12863-015-0178-z

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.

Highlights

The 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
Statistics of the Simple sequence repeats (SSR) loci and primers In total, 11,993,943 SSR loci with a minimum length of 12 bp were detected from the nine grass species, and were categorized into seven types according to the unit length: monomer, dimer, trimer, tetramer, pentamer, hexamer, and heptamer (Table 1)
There are no significant differences in the SSR abundance composition within the nine species

Summary

Introduction

The 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. The SSRs (Simple Sequence Repeats) are widely used markers in the studies of Poaceae for their high abundance and stability. The Poaceae (Grass family) is one of the largest families of flowering plants, comprised of approximately 600 genera and 10,000 species [1]. The Poaceae plants are the world's most important food source for human beings. SSRs (Simple Sequence Repeats) are short tandem repetitive (at least 2-7) sequences of a basic unit with less than seven base pairs [2]. SSR markers are co-dominant, abundant, multiallelic, uniformly distributed, and can be detected by simple reproducible assays [5,6].

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Results

Discussion

Conclusion