A genome-wide analysis of simple sequence repeats in maize and the development of polymorphism markers from next-generation sequence data

Jingtao Qu,Jian Liu

doi:10.1186/1756-0500-6-403

Abstract

BackgroundMaize (Zea mays ssp. mays L.), as the most important plant for staple food of several million people, animal feed and bioenergy productions, is widely cultivated around the world. Simple sequence repeats (SSRs) are widely used as molecular markers in maize genetics and breeding, but only two thousands pairs of SSRs have been published currently, which hardly satisfies for the increasing needs of geneticists and breeders. Furthermore, the increasing studies have revealed that SSRs also play a vital role in functional regulation and evolution. It is fortunate that the development of sequencing technology and bio-software provides the basis for characterization and development of SSRs in maize.ResultsIn this study, MISA was applied to identify overall 179,681 SSRs in maize reference genome B73, with an average distance of 11.46 Kbp. Their distributions within the genome in different regions were non-random, and the density followed in a descending order of UTR, promotor, intron, intergenic and CDS. Meanwhile, 82,694 (46.02%) SSRs with unique flanking sequences were selected, and then applied to analyze the polymorphism of next-generation sequencing data from 345 maize inbred lines and data from maize reference genome B73. There were 58,946 SSRs with length information results in ten or more than ten genomes, accounting for 71.28% of SSRs with unique flanking sequences, while 55,621 SSRs had polymorphism, with an average PIC value of 0.498. 250 pairs of SSR primers in different genomic regions covering all maize chromosomes were randomly chosen for the experimental validation, with an average PIC value of 0.63 in 11 elite maize inbred lines.ConclusionsOur work provided insight into the non-random distribution spatterns and compositions of SSRs in different regions of maize genome, and also developed more polymorphic SSR markers using next-generation sequencing reads. The genome-wide SSRs polymorphism markers could be useful for genetic analysis and marker-assisted selection in breeding practice, and it was also proved to be high efficient for molecular marker development via next-generation sequencing reads.

Highlights

Maize (Zea mays ssp. mays L.), as the most important plant for staple food of several million people, animal feed and bioenergy productions, is widely cultivated around the world
Simple sequence repeats (SSRs) markers based on the repeat number variation were showing significant advantages over the variety of other molecular markers, including restriction fragment length polymorphisms (RFLPs), random amplification of polymorphic DNA (RAPD), and amplified fragment length polymorphisms (AFLPs) [5,6,7]
The genome-wide SSRs polymorphism markers could be useful for genetic analysis and marker-assisted selection in breeding practice

Summary

Introduction

Maize (Zea mays ssp. mays L.), as the most important plant for staple food of several million people, animal feed and bioenergy productions, is widely cultivated around the world. Simple sequence repeats (SSRs) are widely used as molecular markers in maize genetics and breeding, but only two thousands pairs of SSRs have been published currently, which hardly satisfies for the increasing needs of geneticists and breeders. SSRs have proven to be highly polymorphic, reproducible, low costing, facility amplified, and not linked to gene loci of immediate interest [8]. Just for these reasons, SSRs markers turned out to be ideal molecular markers which were widely used in genetic and evolution researches, even as the preferred marker system for many breeding applications. SSRs located in the 5’UTR of rice waxy gene were correlated with amylase content [13]

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