Genetic architecture of yield-component traits in the new perennial grain crop intermediate wheatgrass

Authors: Altendorf, Kayla; DEHAAN, LEE - The Land Institute; ANDERSON, JAMES - University Of Minnesota

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/19/2022
Publication Date: 2/2/2022
Citation: Altendorf, K.R., DeHaan, L.R., Anderson, J.A. 2022. Genetic architecture of yield-component traits in the new perennial grain crop intermediate wheatgrass. Crop Science. 62(2):880-892. https://doi.org/10.1002/csc2.20716.
DOI: https://doi.org/10.1002/csc2.20716

Interpretive Summary: Increasing perennial cover on the agricultural landscape may improve sustainability. Plant breeders are actively domesticating the perennial forage grass species Intermediate wheatgrass (Thinopyrum intermedium; IWG hereafter) as a grain crop. Grain yield is a primary target of selection and improvement in IWG breeding programs as grain size in this species is small, seed set or fertility is low, and yields decline as the plants age. Grain yield is a challenging trait to breed for because it is influenced of a series of component traits, including but not limited to the number of seed heads per unit area, the number of seeds a head produces, and the size and weight of the grain. We utilized a large mapping population to evaluate a series of yield and yield component traits using two different mapping approaches. We found several genetic regions that were consistently significant across mapping methodologies, environments, and traits. Yield and certain biomass traits such as the size of flag leaves and stems, and the number of stems a plant produces, have been shown to be highly correlated with yield. Here we found that many of these traits are controlled by the same genomic regions, suggesting they are either controlled by separate genes under tight linkage (frequently inherited together) or by the same gene. We also identified regions controlling the number of tillers a plant produces, and the fertility of the spikes, which are critical for determining yield in this species. These results improve our understanding of how these traits are controlled on a genetic level and will enable breeders to utilize genomics-assisted breeding to increase the efficiency and precision of selection for yield in IWG.

Technical Abstract: Intermediate wheatgrass (Thinopyrum intermedium; IWG hereafter) is a perennial, cool-season grass species currently undergoing direct domestication as the world’s first perennial grain crop. To domesticate and improve this obligately outcrossing allohexaploid (2n = 6x = 42), breeders are utilizing both phenotypic and genomic-assisted recurrent selection methodologies. Thus far, efforts have focused primarily on improving domestication traits and yield, but breeders are limited by the relatively limited understanding of the genetic control of these traits. An IWG nested association mapping population (NAM) with 1,168 F1 progeny from ten families was grown in four unique growing environments (St. Paul, MN and Salina, KS in 2017 and 2018) and evaluated for a series of 11 yield component traits. Using a population-specific genetic map and 8,003 SNP markers, we utilized both linkage mapping and GWAS to dissect the genetic control of a series of yield component traits. We identified 20 significant markers in GWAS and 28 in linkage mapping that were detected in at least two environments, several of which were shared across traits. QTL regions on chromosomes 5 and 9 were significant for 8 of 11 traits and many were detected across multiple analysis methods. The results described herein provide additional resources for incorporating QTL as fixed effects in routine genomic selection pipelines to expedite the gains from selection for yield in this new perennial grain crop.