Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana

Abstract

BackgroundSimple sequence repeats (SSRs) are tandem repeats of DNA that have been used to develop robust genetic markers. These molecular markers are powerful tools for basic and applied studies such as molecular breeding. In the model plants in Nicotiana genus e.g. N. benthamiana, a comprehensive assessment of SSR content has become possible now because several Nicotiana genomes have been sequenced. We conducted a genome-wide SSR characterization and marker development across seven Nicotiana genomes.ResultsHere, we initially characterized 2,483,032 SSRs (repeat units of 1–10 bp) from seven genomic sequences of Nicotiana and developed SSR markers using the GMATA® software package. Of investigated repeat units, mono-, di- and tri-nucleotide SSRs account for 98% of all SSRs in Nicotiana. More complex SSR motifs, although rare, are highly variable between Nicotiana genomes. A total of 1,224,048 non-redundant Nicotiana (NIX) markers were developed, of which 99.98% are novel. An efficient and uniform genotyping protocol for NIX markers was developed and validated. We created a web-based database of NIX marker information including amplicon sizes of alleles in each genome for downloading and online analysis.ConclusionsThe present work constitutes the first deep characterization of SSRs in seven genomes of Nicotiana, and the development of NIX markers for these SSRs. Our online marker database and an efficient genotyping protocol facilitate the application of these markers. The NIX markers greatly expand Nicotiana marker resources, thus providing a useful tool for future research and breeding. We demonstrate a novel protocol for SSR marker development and utilization at the whole genome scale that can be applied to any lineage of organisms.The Tobacco Markers & Primers Database (TMPD) is available at http://biodb.sdau.edu.cn/tmpd/index.htmlElectronic supplementary materialThe online version of this article (10.1186/s12864-018-4878-4) contains supplementary material, which is available to authorized users.

High-throughput SSR marker development and its application in a centipedegrass (Eremochloa ophiuroides (Munro) Hack.) genetic diversity analysis

“…These SSRs were mined from the transcriptomes, meaning in the gene coding regions only. However, the gene-coding regions should have fewer SSRs than those of the intergenic regions [ 48 ]. Therefore, the SSRs developed here are only part of the SSRs in the genome of centipedegrass.…”

High-throughput simple sequence repeat (SSR) mining saturates the carrot (Daucus carota L.) genome with chromosome-anchored markers

“…Consequently, in silico high-throughput marker development approaches have almost totally replaced microsatellite-enriched library based methods. Accordingly, high-throughput development of SSR markers via mining publicly available genome assemblies has recently been reported for diverse crop plant taxa, including wheat [17], chickpea [18], cucumber [14], peach [19], melon [20], bitter melon [21], sesame [22], hazelnut [15], seven different Nicotiana species [23] and 16 different tree species [24].…”

“…Cui et al[21] designed 138,727 SSR markers using the bitter melon genome sequence and verified the amplification efficiency of 71 primer pairs on two accessions. Wang et al[23] designed 1,224,048 primer pairs that amplify SSR loci from seven Nicotiana genomes and experimentally evaluated 120 SSR markers on five Nicotiana accessions. All tested primers produced amplicons from at least four out of the five accessions.…”

Genome Wide Characterization and Comparative Analysis of Simple Sequence Repeats in Cucurbita Genomes

“…With the development of the sequencing technology, the discovery and mining of genomic SSR loci had successful applications in many plant species such as cotton [35,36], foxtail millet [37], cucumber [38], watermelon [39], tobacco [40] and melon [23]. Nevertheless, little effort has been paid on Cucurbita species.…”

“…GC, TC or GA types have relatively stable structures. Most of the AT types distribute in non-genic regions and TC/GA types in coding sequences [40]. It has been reported that many bacteria SSRs in intergenic regions have regulating functions [47].…”