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Single-locus EST-SSR markers for characterization of population genetic diversity and structure across ploidy levels in switchgrass (Panicum virgatum L.)

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Abstract

Polyploidy, ploidal variation between populations, and aneuploidy within some populations complicate population genetic analyses in switchgrass. We report 21 genic-simple sequence repeat marker loci with single-locus disomic segregation in tetraploids and apparently tetrasomic inheritance in octoploids, thus allowing population genetic analyses across ploidy levels. Based on 472 individuals sampled over four tetraploid and eight octoploid cultivars, six to 55 alleles were detected per locus with an average of 24.1. Genetic diversity was greater in octoploids than tetraploids, as expected from polysomic inheritance. One tetraploid cultivar displayed comparable diversity to the least diverse octoploid cultivars, suggesting breeding history or population history in the native stands of origin may have also affected within-cultivar diversity. Amplicon number at each locus and population relationships suggest autopolyploid origin of octoploids within upland tetraploids with significant cultivar differentiation. However, model-based Bayesian clustering of individuals indicated that closely related octoploid cultivars are difficult to identify, possibly due to slowed differentiation by polysomic inheritance. The analysis of the sampling effect indicated addition of loci is more effective for cultivar identification than more individuals sampled per cultivar. Discriminating power of loci tended to correlate with their variability. The eight loci with greatest discriminatory power within tetraploids were equally successful as 20 loci at identifying the four tetraploid cultivars. The set of markers reported in this study are useful for characterization of switchgrass germplasm and identifying population structure for association studies.

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Acknowledgments

We thank Melanie Harrison-Dunn and Gautam Sarath for critical review of the manuscript. The US Department of Agriculture, Agricultural Research Service, is an equal opportunity/affirmative action employer and all agency services are available without discrimination. Mention of commercial products and organizations in this manuscript is solely to provide specific information. It does not constitute endorsement by USDA-ARS over other products and organizations not mentioned.

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  1. Miki Okada

    Present address: Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA

Authors and Affiliations

  1. USDA-ARS, Genomics and Gene Discovery Research Unit, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA

    Miki Okada, Christina Lanzatella & Christian M. Tobias

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  1. Miki Okada
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  2. Christina Lanzatella
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Correspondence to Christian M. Tobias.

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Okada, M., Lanzatella, C. & Tobias, C.M. Single-locus EST-SSR markers for characterization of population genetic diversity and structure across ploidy levels in switchgrass (Panicum virgatum L.). Genet Resour Crop Evol 58, 919–931 (2011). https://doi.org/10.1007/s10722-010-9631-z

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