Development of simple sequence repeat markers in the halophytic turf grass Sporobolus virginicus and transferable genotyping across multiple grass genera/species/genotypes
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Simple sequence repeat (SSR) markers are highly informative and widely used in genetic studies and plant breeding. Sporobolus virginicus is a halophytic turf grass that shows a high tolerance to salinity of up to 1.5 M NaCl. In the present study, we developed 148,411 SSR markers on 48,512 transcriptome contigs derived from RNA sequencing data. Of 33 randomly selected SSR markers, 23 (69.7%) produced clean amplification products, and an average of 1.25 alleles per marker was detected in S. virginicus genotypes. These markers were also examined by detecting polymorphisms across 19 different genera/species/genotypes in Poaceae, resulting in a high percentage (40%) of transferability. The sequencing of amplified products from these genera/species/genotypes revealed a high level of sequence similarity; however, substitutions, deletions, and insertions were detected not only in the objective SSRs but also in their flanking sequences. This is the first study on SSR marker development from S. virginicus. These SSR markers are useful for mapping the genes in and the breeding of S. virginicus and also for comparative genomics across genera/species/genotypes in Poaceae.
KeywordsGenotyping Halophyte Sporobolus virginicus Simple sequence repeat (SSR) marker Transferability Turf grass
This work was partially supported by the New Technology Development Foundation to Y. T. This work was partially supported by MEXT-Supported Program for the Strategic Research Foundation at Private Universities (2014-2018), and Research Funding for Computational Software Supporting Program from Meiji University to K. Y. Computations were partially performed on the NIG (National Institute of Genetics) SuperComputer Facilities hosted at NIG/ROIS (Research Organization of Information and Systems).
Compliance with ethical standards
Conflict of interest
No conflict of interest exits in the submission of this manuscript, and the manuscript has been approved by all of the authors for publication.
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