Molecular Breeding

, Volume 32, Issue 4, pp 923–931 | Cite as

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

  • Linglong Liu
  • Yalin Huang
  • Somashekhar Punnuri
  • Tim Samuels
  • Yanqi Wu
  • Ramamurthy Mahalingam


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.


Simple sequence repeat (SSR) Expressed sequence tag (EST) Linkage map Switchgrass 



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.

Supplementary material

11032_2013_9921_MOESM1_ESM.xlsx (75 kb)
Information of 538 effective EST-SSR markers newly developed in switchgrass (XLSX 75 kb)
11032_2013_9921_MOESM2_ESM.xlsx (316 kb)
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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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Linglong Liu
    • 1
    • 2
  • Yalin Huang
    • 1
    • 3
  • Somashekhar Punnuri
    • 1
    • 4
  • Tim Samuels
    • 1
  • Yanqi Wu
    • 1
  • Ramamurthy Mahalingam
    • 5
  1. 1.Department of Plant and Soil SciencesOklahoma State UniversityStillwaterUSA
  2. 2.National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
  3. 3.Nanjing Forest Police CollegeNanjingChina
  4. 4.Agricultural Research StationFort Valley State UniversityFort ValleyUSA
  5. 5.Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterUSA

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