Nested association mapping reveals the genetic architecture of spike emergence and anthesis timing in intermediate wheatgrass

Kayla R. Altendorf, Steven R. Larson, Lee R. DeHaan, Jared Crain, Jeff Neyhart, Kevin M. Dorn, James A. Anderson

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12 Scopus citations


Intermediate wheatgrass (Thinopyrum intermedium) is an outcrossing, cool season grass species currently undergoing direct domestication as a perennial grain crop. Though many traits are selection targets, understanding the genetic architecture of those important for local adaptation may accelerate the domestication process. Nested association mapping (NAM) has proven useful in dissecting the genetic control of agronomic traits many crop species, but its utility in primarily outcrossing, perennial species has yet to be demonstrated. Here, we introduce an intermediate wheatgrass NAM population developed by crossing ten phenotypically divergent donor parents to an adapted common parent in a reciprocal manner, yielding 1,168 F1 progeny from 10 families. Using genotyping by sequencing, we identified 8,003 SNP markers and developed a population-specific consensus genetic map with 3,144 markers across 21 linkage groups. Using both genomewide association mapping and linkage mapping combined across and within families, we characterized the genetic control of flowering time. In the analysis of two measures of maturity across four separate environments, we detected as many as 75 significant QTL, many of which correspond to the same regions in both analysis methods across 11 chromosomes. The results demonstrate a complex genetic control that is variable across years, locations, traits, and within families. The methods were effective at detecting previously identified QTL, as well as new QTL that align closely to the well-characterized flowering time orthologs from barley, including Ppd-H1 and Constans. Our results demonstrate the utility of the NAM population for understanding the genetic control of flowering time and its potential for application to other traits of interest.

Original languageEnglish (US)
Article numberjkab025
JournalG3: Genes, Genomes, Genetics
Issue number3
StatePublished - Apr 23 2021

Bibliographical note

Funding Information:
This work was supported by the Perennial Agriculture Project in conjunction with the Malone Family Land Preservation Foundation and The Land Institute. We thank Garett C. Heineck for assistance on phenotypic data analysis, line fitting methodology, and for providing emergency watering assistance after transplanting in STP. Thank you to Prabin Bajgain for instruction in developing genotyping by sequencing libraries, and Brett Heim and Marty Christians for technical assistance in processing and in the field. We also thank Xiaofei Zhang for his guidance and contributions in designing this population. Many thanks to the University of Minnesota undergraduate students Jennifer LaValley, Charlotte Bonner, Ellen Goedtke, and 2017 & 2018 Land Institute summer interns for assistance in data collection. We thank the Minnesota Agricultural Student Trainee Program (MAST), specifically, Andressa Spuri Azarias, Arthur Martins, Oswaldo Birungi, Caroline Elmer, Phoebe Wanjira and Mario Fagundes for assistance with harvesting and extensive postharvest processing procedures. Finally, we thank the IWG Genome Sequencing Consortium for access to the prepublication genome sequence.

Publisher Copyright:
© 2021 Genetics Society of America. All rights reserved.


  • Flowering time
  • Intermediate wheatgrass
  • Nested association mapping


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