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Development and characterization of genomic SSR markers in Cynodon transvaalensis Burtt-Davy

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Abstract

Simple sequence repeat (SSR) markers are a major molecular tool for genetic and genomic research that have been extensively developed and used in major crops. However, few are available in African bermudagrass (Cynodon transvaalensis Burtt-Davy), an economically important warm-season turfgrass species. African bermudagrass is mainly used for hybridizations with common bermudagrass [C. dactylon var. dactylon (L.) Pers.] in the development of superior interspecific hybrid turfgrass cultivars. Accordingly, the major objective of this study was to develop and characterize a large set of SSR markers. Genomic DNA of C. transvaalensis ‘4200TN 24-2’ from an Oklahoma State University (OSU) turf nursery was extracted for construction of four SSR genomic libraries enriched with [CA] n , [GA] n , [AAG] n , and [AAT] n as core repeat motifs. A total of 3,064 clones were sequenced at the OSU core facility. The sequences were categorized into singletons and contiguous sequences to exclude redundancy. From the two sequence categories, 1,795 SSR loci were identified. After excluding duplicate SSRs by comparison with previously developed SSR markers using a nucleotide basic local alignment tool, 1,426 unique primer pairs (PPs) were designed. Out of the 1,426 designed PPs, 981 (68.8 %) amplified alleles of the expected size in the donor DNA. Polymorphisms of the SSR PPs tested in eight C. transvaalensis plants were 93 % polymorphic with 544 markers effective in all genotypes. Inheritance of the SSRs was examined in six F1 progeny of African parents ‘T577’ × ‘Uganda’, indicating 917 markers amplified heritable alleles. The SSR markers developed in the study are the first large set of co-dominant markers in African bermudagrass and should be highly valuable for molecular and traditional breeding research.

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Acknowledgments

Authors would like to acknowledge Dr. Timmy Samuels for his help with lab techniques. The work has been supported, in part, by the United State Department of Agriculture Specialty Crop Research Initiative award 2010-51181-21064, the Oklahoma Agricultural Experiment Station, and the United States Golf Association.

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Authors and Affiliations

  1. Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74078, USA

    Chengcheng Tan, Yanqi Wu & Charles M. Taliaferro

  2. Department of Horticulture and Landscape Architecture, Oklahoma State University, Stillwater, OK, 74078, USA

    Greg E. Bell, Dennis L. Martin & Mike W. Smith

Authors
  1. Chengcheng Tan
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  2. Yanqi Wu
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  3. Charles M. Taliaferro
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  4. Greg E. Bell
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  5. Dennis L. Martin
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  6. Mike W. Smith
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Corresponding author

Correspondence to Yanqi Wu.

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Communicated by S. Hohmann.

The experiments comply with the current laws of the United States of America in which they were performed.

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Tan, C., Wu, Y., Taliaferro, C.M. et al. Development and characterization of genomic SSR markers in Cynodon transvaalensis Burtt-Davy. Mol Genet Genomics 289, 523–531 (2014). https://doi.org/10.1007/s00438-014-0829-1

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  • DOI: https://doi.org/10.1007/s00438-014-0829-1

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