Genetic architecture and QTL selection response for Kernza perennial grain domestication traits

Authors: CRAIN, JARED - Kansas State University; Larson, Steven; Dorn, Kevin; DEHAAN, LEE - The Land Institute; POLAND, JESSE - Kansas State University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/21/2022
Publication Date: 6/28/2022
Citation: Crain, J., Larson, S.R., Dorn, K.M., DeHaan, L., Poland, J. 2022. Genetic architecture and QTL selection response for Kernza perennial grain domestication traits. Theoretical and Applied Genetics. 135:2769-2784. https://doi.org/10.1007/s00122-022-04148-2.
DOI: https://doi.org/10.1007/s00122-022-04148-2

Interpretive Summary: Perennial grains have the potential to provide food for humans from plants that live and produce seeds for multiple years, unlike annual field crops that produce seed only once and must be replanted every year. Compared to annual field crops that are commonly used in agriculture, perennial plants have potential to reduce soil erosion, increase water infiltration, reduce water and nutrient run off, reduce nutrient leaching in the ground water, increase carbon sequestration in the soil, and provide enhanced ecosystem services. Some perennial plants could also be used for other purposes such as livestock forage or biofuels. Intermediate wheatgrass (IWG, Thinopyrum intermedium, trade name Kernza) has been widely used for soil conservation and forage production throughout large regions of the United States, and other countries, and it is also promising perennial grain crop that The Land Institute has been breeding since 2001. In this study, we evaluated the seed size, seed yield, seed threshing, and other critical traits from more than four thousand plants over four consecutive breeding cycles. These plants were screened using over twenty-thousand DNA markers to evaluate the inherent genetic variability and the potential for improvement through applied plant breeding. Combining data across cycles and years, we found 65 DNA markers with significant associations for seven different traits, with each association explaining between 0.8-3.5% of the observed trait variability. Only three markers showed significant allele frequency changes across breeding cycles, with one corresponding to a decrease in floret shattering. Power analysis was used to estimate the minimum number of genes controlling each trait, which ranged from a minimum of 33 up to 3281. This study suggest that key agronomic and domestication traits are controlled by hundreds genes, and that modern DNA-based breeding approaches, like genomic selection, are essential to rapidly domesticating this new crop.

Technical Abstract: Perennial grains have the potential to provide food for humans as well as decrease the negative impacts of annual agriculture. Intermediate wheatgrass (IWG, Thinopyrum intermedium, trade name Kernza) is a promising perennial grain candidate, that The Land Institute has been breeding since 2001. We evaluated four consecutive breeding cycles of IWG from 2016-2020 with each cycle containing c. 1100 unique genets. Using genotyping-by-sequencing markers quantitative trait loci (QTL) were evaluated for 34 different traits using genome-wide association analysis. Combining data across cycles and years, we found 65 marker trait associations (MTA) for seven different traits, with each association explaining between 0.8-3.5% of the observed phenotypic variance. Across the four cycles, only three markers showed an FST differentiation > 0.15 with one MTA corresponding to a decrease in floret shattering. Additionally, one marker was related to brittle rachis and was 216 bp from the known btr2 gene. Power analysis was used to estimate the effective number of QTL which ranged from a minimum of 33 up to 3281 QTL for individual traits. This study suggest that key agronomic and domestication traits are under polygenic control, and that molecular methods like genomic selection are essential to rapidly domesticating this new crop.