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

Authors: Altendorf, Kayla; Larson, Steven; DEHAAN, LEE - The Land Institute; CRAIN, JARED - Kansas State University; NEYHART, JEFF - University Of Minnesota; Dorn, Kevin; ANDERSON, JAMES - University Of Minnesota

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/7/2021
Publication Date: 1/30/2021
Citation: Altendorf, K.R., Larson, S.R., Dehaan, L.R., Crain, J., Neyhart, J., Dorn, K.M., Anderson, J.A. 2021. Nested association mapping reveals the genetic architecture of spike emergence and anthesis timing in intermediate wheatgrass (Thinopyrum intermedium). G3, Genes/Genomes/Genetics. 11(3). Article jkab025. https://doi.org/10.1093/g3journal/jkab025.
DOI: https://doi.org/10.1093/g3journal/jkab025

Interpretive Summary: Understanding the genetic control of important traits can improve our ability to breed better performing crops. In the new perennial grain crop, Intermediate wheatgrass (IWG, Thinopyrum intermedium), the selection targets are numerous and the genetics of relatively few traits are known, presenting a barrier for breeding programs. Nested Association Mapping (NAM) is a proven method to identify the genetic control of complex traits in many crops. To test this approach in intermediate wheatgrass, we assessed the genetic control of an important adaptive trait, flowering time. The analysis revealed complex genetic control, involving many small effect genes whose importance in determining flowering time vary by environment, family, and analysis method. Four of the regions harboring genes align closely with known flowering time genes from barley, a related species, suggesting the two species share a similar control mechanism for flowering time. In addition to identifying these new significant regions that align with known genes, we also found similar regions to a previous study in IWG. This suggests that the NAM approach was effective and shows promise for uncovering the genetic control of additional traits critical to IWG improvement.

Technical Abstract: Intermediate wheatgrass (Thinopyrum intermedium) is an outcrossing, cool season grass species currently undergoing direct domestication as a perennial grain crop for human consumption. 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 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 characterize the genetic control of flowering time. In the analysis of two different measures of maturity across four separate environments, we detected as many as 65 significant QTL, many of which correspond to similar QTL regions on across 14 chromosomes. The results demonstrate a complex genetic control that is variable across years, locations, and traits, as well as within families. The population and 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, with the most evidence in support of Ppd-H1 and the Constans photoperiod genes. Our results demonstrate the utility of the NAM for understanding the genetic control of flowering time in IWG and its potential for application to other traits of interest.