Development of Highly Informative Genome-Wide Single Sequence Repeat Markers for Breeding Applications in Sesame and Construction of a Web Resource: SisatBase.

Komivi Dossa,Xiurong Zhang,Ndiaga Cisse,Jingyin Yu,Boshou Liao

doi:10.3389/fpls.2017.01470

Abstract

The sequencing of the full nuclear genome of sesame (Sesamum indicum L.) provides the platform for functional analyses of genome components and their application in breeding programs. Although the importance of microsatellites markers or simple sequence repeats (SSR) in crop genotyping, genetics, and breeding applications is well established, only a little information exist concerning SSRs at the whole genome level in sesame. In addition, SSRs represent a suitable marker type for sesame molecular breeding in developing countries where it is mainly grown. In this study, we identified 138,194 genome-wide SSRs of which 76.5% were physically mapped onto the 13 pseudo-chromosomes. Among these SSRs, up to three primers pairs were supplied for 101,930 SSRs and used to in silico amplify the reference genome together with two newly sequenced sesame accessions. A total of 79,957 SSRs (78%) were polymorphic between the three genomes thereby suggesting their promising use in different genomics-assisted breeding applications. From these polymorphic SSRs, 23 were selected and validated to have high polymorphic potential in 48 sesame accessions from different growing areas of Africa. Furthermore, we have developed an online user-friendly database, SisatBase (http://www.sesame-bioinfo.org/SisatBase/), which provides free access to SSRs data as well as an integrated platform for functional analyses. Altogether, the reference SSR and SisatBase would serve as useful resources for genetic assessment, genomic studies, and breeding advancement in sesame, especially in developing countries.

Highlights

During the past years, the development in genetic studies and decrease of genotyping costs, have resulted in the rapid growth of the use of molecular markers (Kantartzi, 2013)
Based on the physical location of each simple sequence repeats (SSR) and the general feature format (GFF) files of genes or transcripts, we uncovered that 18.84% of the total mapped SSRs were located in genic regions
We estimated the relationship between the “chr” length and the number of SSRs harbored on each “chr” and found a high correlation (r2 = 0.94) (Figure 2)

Summary

Introduction

The development in genetic studies and decrease of genotyping costs, have resulted in the rapid growth of the use of molecular markers (Kantartzi, 2013). Simple sequence repeats (SSR) known as microsatellite has become the molecular marker of choice because of its versatility, operational flexibility, and low-cost This has provided the foundation for its successful application in a wide range of fundamental and applicable fields, such as, genetic diversity, linkage/association mapping of gene/QTL, marker-assisted selection (MAS), variety identification, and evolution analysis (Jiao et al, 2012; Zhang Q. et al, 2012; Li et al, 2014; Shi et al, 2014; Dossa et al, 2016c). SSRs are relatively short tandem repeats (STRs) of DNA that are widely distributed throughout whole genomic sequences (Sharma, 2007) They are present in coding regions but are more abundant in non-coding regions (Hancock, 1995). SSRs have been demonstrated to have several important biological functions including the regulation of chromatin organization, DNA metabolic processes, gene activity, and RNA structure (Li et al, 2002, 2004)

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Discussion

Conclusion