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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• 作者：Chisato Endo ; Naoki Yamamoto ; Masaaki Kobayashi ; Yukino Nakamura…
• 关键词：Genotyping ; Halophyte ; Sporobolus virginicus ; Simple sequence repeat (SSR) marker ; Transferability ; Turf grass
• 刊名：Euphytica
• 出版年：2017
• 出版时间：February 2017
• 年：2017
• 卷：213
• 期：2
• 全文大小：
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Plant Sciences; Plant Genetics & Genomics; Plant Pathology; Plant Physiology; Biotechnology;
• 出版者：Springer Netherlands
• ISSN：1573-5060
• 卷排序：213

文摘

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.