Genome-Wide Distribution and Organization of Microsatellites in Plants: An Insight into Marker Development in Brachypodium

Humira Sonah,Tilak R Sharma,Deepak K Gupta,Rupesh K Deshmukh,Jai C Rana,Anshul Sharma,Nagendra K Singh,Raju N Gacche,Vinay P Singh,Ying Xu

doi:10.1371/journal.pone.0021298

Abstract

Plant genomes are complex and contain large amounts of repetitive DNA including microsatellites that are distributed across entire genomes. Whole genome sequences of several monocot and dicot plants that are available in the public domain provide an opportunity to study the origin, distribution and evolution of microsatellites, and also facilitate the development of new molecular markers. In the present investigation, a genome-wide analysis of microsatellite distribution in monocots (Brachypodium, sorghum and rice) and dicots (Arabidopsis, Medicago and Populus) was performed. A total of 797,863 simple sequence repeats (SSRs) were identified in the whole genome sequences of six plant species. Characterization of these SSRs revealed that mono-nucleotide repeats were the most abundant repeats, and that the frequency of repeats decreased with increase in motif length both in monocots and dicots. However, the frequency of SSRs was higher in dicots than in monocots both for nuclear and chloroplast genomes. Interestingly, GC-rich repeats were the dominant repeats only in monocots, with the majority of them being present in the coding region. These coding GC-rich repeats were found to be involved in different biological processes, predominantly binding activities. In addition, a set of 22,879 SSR markers that were validated by e-PCR were developed and mapped on different chromosomes in Brachypodium for the first time, with a frequency of 101 SSR markers per Mb. Experimental validation of 55 markers showed successful amplification of 80% SSR markers in 16 Brachypodium accessions. An online database ‘BraMi’ (Brachypodium microsatellite markers) of these genome-wide SSR markers was developed and made available in the public domain. The observed differential patterns of SSR marker distribution would be useful for studying microsatellite evolution in a monocot–dicot system. SSR markers developed in this study would be helpful for genomic studies in Brachypodium and related grass species, especially for the map based cloning of the candidate gene(s).

Highlights

Microsatellites or simple sequence repeats (SSRs) are codominant, abundant, multi-allelic, and uniformly distributed over the genome, and can be detected by simple reproducible assays [1]
SSR markers were developed from expressed sequence tags (ESTs) and bacterial artificial chromosome (BAC) end sequences in most plant species
Whole genome sequencing has led to the identification of numerous SSR markers that are distributed over the entire genomes of rice and Arabidopsis

Summary

Introduction

Microsatellites or simple sequence repeats (SSRs) are codominant, abundant, multi-allelic, and uniformly distributed over the genome, and can be detected by simple reproducible assays [1]. The present study deals with a genome-wide comparative analysis of microsatellite distribution in the nuclear and chloroplast genomes of monocot and dicot species, the development of genome-wide SSR markers, and the validation of a subset of these new markers in Brachypodium. Microsatellite distribution in monocot and dicot species A total of 797,863 SSRs were identified among six plant genomes — three monocot (Brachypodium, sorghum and rice) and three dicot (Arabidopsis, Medicago and Populus) plant species (Table 1).

Results

Conclusion