Multi-allelic haplotype-based association analysis identifies genomic regions controlling domestication traits in intermediate wheatgrass

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Intermediate wheatgrass (IWG) is a perennial forage grass undergoing a rigorous domestication as a grain crop. As a young grain crop, several agronomic and domestication traits need improvement for IWG to be relevant in current agricultural landscapes. This study genetically maps six domestication traits in the fourth cycle IWG breeding population at the University of Minnesota: height, seed length, seed width, shattering, threshability, and seed mass. A weak population structure was observed and linkage disequilibrium (r2 ) declined rapidly: 0.23 mega base pairs at conventional r2 value of 0.2. Broad-sense heritabilities were overall high and ranged from 0.71–0.92. Association analysis was carried out using 25,909 single SNP markers and 5379 haplotype blocks. Thirty-one SNP markers and 17 haplotype blocks were significantly associated with the domestication traits. These associations were of moderate effect as they explained 4–6% of the observed phenotypic variation. Ten SNP markers were also detected by the haplotype association analysis. One SNP marker on Chromosome 8, also discovered in haplotype block analysis, was common between seed length and seed mass. Increasing the frequency of favorable alleles in IWG populations via marker-assisted selection and genomic selection is an effective approach to improve IWG’s domestication traits.

Original languageEnglish (US)
Article number667
JournalAgriculture (Switzerland)
Issue number7
StatePublished - Jul 15 2021

Bibliographical note

Funding Information:
Funding: This research was funded by the Forever Green Initiative at the University of Minnesota through the Minnesota Department of Agriculture, the Minnesota Department of Agriculture’s AGRI Crop Research Grant, and the General Mills Foundation.

Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.


  • Domestication
  • Genetic mapping
  • Haplotype
  • Intermediate wheatgrass
  • Perennial crop
  • Quantitative trait locus


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