Theoretical and Applied Genetics

, Volume 132, Issue 8, pp 2325–2351 | Cite as

Genome mapping of quantitative trait loci (QTL) controlling domestication traits of intermediate wheatgrass (Thinopyrum intermedium)

  • Steve LarsonEmail author
  • Lee DeHaan
  • Jesse Poland
  • Xiaofei Zhang
  • Kevin Dorn
  • Traci Kantarski
  • James Anderson
  • Jeremy Schmutz
  • Jane Grimwood
  • Jerry Jenkins
  • Shengqiang Shu
  • Jared Crain
  • Matthew Robbins
  • Kevin Jensen
Original Article


Allohexaploid (2n = 6x = 42) intermediate wheatgrass (Thinopyrum intermedium), abbreviated IWG, is an outcrossing perennial grass belonging to the tertiary gene pool of wheat. Perenniality would be valuable option for grain production, but attempts to introgress this complex trait from wheat-Thinopyrum hybrids have not been commercially successful. Efforts to breed IWG itself as a dual-purpose forage and grain crop have demonstrated useful progress and applications, but grain yields are significantly less than wheat. Therefore, genetic and physical maps have been developed to accelerate domestication of IWG. Herein, these maps were used to identify quantitative trait loci (QTLs) and candidate genes associated with IWG grain production traits in a family of 266 full-sib progenies derived from two heterozygous parents, M26 and M35. Transgressive segregation was observed for 17 traits related to seed size, shattering, threshing, inflorescence capacity, fertility, stem size, and flowering time. A total of 111 QTLs were detected in 36 different regions using 3826 genotype-by-sequence markers in 21 linkage groups. The most prominent QTL had a LOD score of 15 with synergistic effects of 29% and 22% over the family means for seed retention and percentage of naked seeds, respectively. Many QTLs aligned with one or more IWG gene models corresponding to 42 possible domestication orthogenes including the wheat Q and RHT genes. A cluster of seed-size and fertility QTLs showed possible alignment to a putative Z self-incompatibility gene, which could have detrimental grain-yield effects when genetic variability is low. These findings elucidate pathways and possible hurdles in the domestication of IWG.



This research was supported by the Malone Family Land Preservation Foundation. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. KD is supported by USDA-NIFA Post-doctoral Fellowships Grant No. 2017-67012-26129/Project Accession No. 1011622 “Exploring the Genomic Landscape of Perenniality within the Triticeae.” The authors wish to thank Martin Mascher and LiangLiang Gao for advice and contributions to the continuing development of the Thinopyrum intermedium genome assembly.

Compliance with ethical standards

Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Supplementary material

122_2019_3357_MOESM1_ESM.xlsx (81 kb)
Supplementary material 1 (XLSX 81 kb)
122_2019_3357_MOESM2_ESM.xlsx (32 kb)
Supplementary material 2 (XLSX 31 kb)


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© This is a U.S. government work and its text is not subject to copyright protection in the United States; however, its text may be subject to foreign copyright protection 2019

Authors and Affiliations

  1. 1.United States Department of Agriculture, Agriculture Research Service, Forage and Range ResearchUtah State UniversityLoganUSA
  2. 2.The Land InstituteSalinaUSA
  3. 3.Department of Plant PathologyKansas State UniversityManhattanUSA
  4. 4.Department of Horticultural ScienceNorth Carolina State UniversityRaleighUSA
  5. 5.American Association for the Advancement of Science, Science and Technology Policy Fellow at the United States Department of AgricultureAnimal and Plant Health Inspection ServiceRiverdaleUSA
  6. 6.Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulUSA
  7. 7.Department of EnergyJoint Genome InstituteWalnut CreekUSA
  8. 8.Hudson Alpha Institute for BiotechnologyHuntsvilleUSA

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