Theoretical and Applied Genetics

, Volume 130, Issue 1, pp 137–150 | Cite as

Development of the first consensus genetic map of intermediate wheatgrass (Thinopyrum intermedium) using genotyping-by-sequencing

  • Traci Kantarski
  • Steve Larson
  • Xiaofei Zhang
  • Lee DeHaan
  • Justin Borevitz
  • James Anderson
  • Jesse PolandEmail author
Original Article


Key message

Development of the first consensus genetic map of intermediate wheatgrass gives insight into the genome and tools for molecular breeding.


Intermediate wheatgrass (Thinopyrum intermedium) has been identified as a candidate for domestication and improvement as a perennial grain, forage, and biofuel crop and is actively being improved by several breeding programs. To accelerate this process using genomics-assisted breeding, efficient genotyping methods and genetic marker reference maps are needed. We present here the first consensus genetic map for intermediate wheatgrass (IWG), which confirms the species’ allohexaploid nature (2n = 6x = 42) and homology to Triticeae genomes. Genotyping-by-sequencing was used to identify markers that fit expected segregation ratios and construct genetic maps for 13 heterogeneous parents of seven full-sib families. These maps were then integrated using a linear programming method to produce a consensus map with 21 linkage groups containing 10,029 markers, 3601 of which were present in at least two populations. Each of the 21 linkage groups contained between 237 and 683 markers, cumulatively covering 5061 cM (2891 cM––Kosambi) with an average distance of 0.5 cM between each pair of markers. Through mapping the sequence tags to the diploid (2n = 2x = 14) barley reference genome, we observed high colinearity and synteny between these genomes, with three homoeologous IWG chromosomes corresponding to each of the seven barley chromosomes, and mapped translocations that are known in the Triticeae. The consensus map is a valuable tool for wheat breeders to map important disease-resistance genes within intermediate wheatgrass. These genomic tools can help lead to rapid improvement of IWG and development of high-yielding cultivars of this perennial grain that would facilitate the sustainable intensification of agricultural systems.


Linkage Group Segregation Distortion Barley Chromosome Allele Count Sustainable Intensification 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This work was supported by the Malone Family Land Preservation Foundation and The Land Institute through The Perennial Agriculture Project, The Initiative of Renewable Energy & The Environment, University of Minnesota, grant number RL_0015-12, and The Forever Green Initiative, University of Minnesota. The work at Kansas State University was done under the auspices of the Wheat Genetics Resource Center (WGRC) Industry/University Collaborative Research Center (I/UCRC) supported by NSF grant contract (IIP-1338897) and industry partners. Trevor Rife (Kansas State University) provided great assistance with combining the Ion and Illumina data and Jonathan Mitchell (University of Michigan/The Field Museum) provided assistance with early versions of the R scripts for custom genotype calling.

Compliance with ethical standards

Ethical standard

The authors declare that the experiments comply with the current laws in the United States of America.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Department of Plant PathologyKansas State UniversityManhattanUSA
  2. 2.USDA-ARS, Forage and Range ResearchUtah State UniversityLoganUSA
  3. 3.Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulUSA
  4. 4.The Land InstituteSalinaUSA
  5. 5.Research School of BiologyAustralian National UniversityCanberraAustralia

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