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Development and integration of EST–SSR markers into an established linkage map in switchgrass

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Abstract

Switchgrass (Panicum virgatum L.) is a model cellulosic biofuel crop in the United States. Simple sequence repeat (SSR) markers are valuable resources for genetic mapping and molecular breeding. A large number of expressed sequence tags (ESTs) of switchgrass are recently available in our sequencing project. The objectives of this study were to develop new SSR markers from the switchgrass EST sequences and to integrate them into an existing linkage map. More than 750 unique primer pairs (PPs) were designed from 243,600 EST contigs and tested for PCR amplifications, resulting in 538 PPs effectively producing amplicons of expected sizes. Of the effective PPs, 481 amplifying informative bands in NL94 were screened for polymorphisms in a panel consisting of NL94 and its seven first-generation selfed (S1) progeny. This led to the selection of 117 polymorphic EST–SSRs to genotype a mapping population encompassing 139 S1 individuals of NL94. Of 83 markers demonstrating clearly scorable alleles in the mapping population, 79 were integrated into a published linkage map, with three linked to accessory loci and one unlinked. The newly identified EST–SSR loci were distributed in 17 of 18 linkage groups with 27 (32.5 %) exhibiting distorted segregations. The integration of EST–SSRs aided in reducing the average marker interval (cM) to 3.7 from 4.2, and reduced the number of gaps (each >15 cM) to 10 from 23. Developing new EST–SSRs and constructing a higher density linkage map will facilitate quantitative trait locus mapping and provide a firm footing for marker-assisted breeding in switchgrass.

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Acknowledgments

The authors thank the following funding sources and individuals for sponsoring and helping in this research: National Science Foundation award EPS 0814361; Oklahoma Agricultural Experiment Station; Yiwen Xiang, Yunwen Wang and Pu Feng.

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Authors and Affiliations

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

    Linglong Liu, Yalin Huang, Somashekhar Punnuri, Tim Samuels & Yanqi Wu

  2. National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China

    Linglong Liu

  3. Nanjing Forest Police College, Nanjing, 210046, China

    Yalin Huang

  4. Agricultural Research Station, Fort Valley State University, Fort Valley, GA, 31030, USA

    Somashekhar Punnuri

  5. Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA

    Ramamurthy Mahalingam

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  1. Linglong Liu
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  2. Yalin Huang
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  3. Somashekhar Punnuri
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  4. Tim Samuels
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  5. Yanqi Wu
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  6. Ramamurthy Mahalingam
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Corresponding authors

Correspondence to Yanqi Wu or Ramamurthy Mahalingam.

Additional information

Linglong Liu and Yalin Huang have contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Information of 538 effective EST-SSR markers newly developed in switchgrass (XLSX 75 kb)

11032_2013_9921_MOESM2_ESM.xlsx

Genotyping data including 83 new EST-SSR loci (highlighted) and 506 previously mapped loci for the NL94 selfed population. The last column indicates significant levels of Chi square test for the expected Mendelian 1:2:1 ratio (XLSX 315 kb)

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Liu, L., Huang, Y., Punnuri, S. et al. Development and integration of EST–SSR markers into an established linkage map in switchgrass. Mol Breeding 32, 923–931 (2013). https://doi.org/10.1007/s11032-013-9921-1

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