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Development of 1,030 genomic SSR markers in switchgrass

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Abstract

Switchgrass, Panicum virgatum L., a native to the tall grass prairies in North America, has been grown for soil conservation and herbage production in the USA and recently widely recognized as a promising dedicated cellulosic bioenergy crop. A large amount of codominant molecular markers including simple sequence repeats (SSRs) are required for the construction of linkage maps and implementation of molecular breeding strategies to develop superior switchgrass cultivars. The objectives of this study were (1) to identify SSR-containing clones and to design PCR primer pairs (PPs) in SSR-enriched genomic libraries, and (2) to validate and characterize the designed SSR PPs. Five genomic SSR enriched libraries were constructed using genomic DNA of ‘SL93 7 × 15’, a switchgrass genotype selected in an Oklahoma State University (OSU) southern lowland breeding population. A total of 3,046 clones from four libraries enriched in (CA/TG)n, (GA/TC)n, (CAG/CTG)n and (AAG/CTT)n SSR repeats were sequenced at the OSU Core Facility. From the sequences, we isolated 1,300 unique SSR-containing clones, from which we designed 1,398 PPs using SSR Locator V.1 software. Among the designed PPs, 1,030 (73.7%) amplified reproducible and strong bands with expected fragment size, and 802 detected polymorphic alleles, in SL93 7 × 15 and ‘NL94 16 × 13’, two parents of one mapping population. All of the four libraries contained a high rate of perfect SSR repeat types, ranging from 62.7 to 76.2%. Polymorphism of the effective SSR markers was also tested in two lowland and two upland switchgrass cultivars, encompassing ‘Alamo’ and ‘Kanlow’, and ‘Blackwell’ and ‘Dacotah’, respectively. The developed SSR markers should be useful in genetic and breeding research in switchgrass.

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Acknowledgments

We gratefully thank Sharon Williams, Pu Feng, and Gary Williams for maintenance of plant materials used in this study in greenhouse, Dr. Ming Su from Oklahoma State University for helping format the Electronic Supplementary Material, and Ms. Yan Song and Dr. Peter Hoyt of the OSU Microarray and Bioinformatics Core Facility for trimming the sequences. This work has been supported, in part, by the NSF EPSCoR award EPS 0814361. We are also grateful to the China Scholarship Council (No. [2006] 3142) and Quality Forage Products Promotion Program (2006-G38) funded by the Ministry of Agriculture of China for supporting a visiting research stay of Yunwen Wang at Oklahoma State University.

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Authors and Affiliations

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

    Y. W. Wang, T. D. Samuels & Y. Q. Wu

  2. Department of Grassland Science, China Agricultural University, Beijing, 100193, China

    Y. W. Wang

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  1. Y. W. Wang
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Correspondence to Y. Q. Wu.

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Communicated by A. Schulman.

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Wang, Y.W., Samuels, T.D. & Wu, Y.Q. Development of 1,030 genomic SSR markers in switchgrass. Theor Appl Genet 122, 677–686 (2011). https://doi.org/10.1007/s00122-010-1477-4

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