Jared Crain, Steve Larson, Kevin Dorn, Lee DeHaan & Jesse Poland

Theoretical and Applied Genetics August 2022; vol. 135: 2769–2784

Key message

Analysis of multi-year breeding program data revealed that the genetic architecture of an intermediate wheatgrass population was highly polygenic for both domestication and agronomic traits, supporting the use of genomic selection for new crop domestication.

Abstract

Perennial grains have the potential to provide food for humans and decrease the negative impacts of annual agriculture. Intermediate wheatgrass (IWG, Thinopyrum intermedium, Kernza®) is a promising perennial grain candidate that The Land Institute has been breeding since 2003. We evaluated four consecutive breeding cycles of IWG from 2016 to 2020 with each cycle containing approximately 1100 unique genets. Using genotyping-by-sequencing markers, quantitative trait loci (QTL) were mapped for 34 different traits using genome-wide association analysis. Combining data across cycles and years, we found 93 marker-trait associations for 16 different traits, with each association explaining 0.8–5.2% of the observed phenotypic variance. Across the four cycles, only three QTL showed an F_ST differentiation > 0.15 with two corresponding to a decrease in floret shattering. Additionally, one marker associated with brittle rachis was 216 bp from an ortholog of the btr2 gene. Power analysis and quantitative genetic theory were used to estimate the effective number of QTL, which ranged from a minimum of 33 up to 558 QTL for individual traits. This study suggests that key agronomic and domestication traits are under polygenic control and that molecular methods like genomic selection are needed to accelerate domestication and improvement of this new crop.

See https://link.springer.com/article/10.1007/s00122-022-04148-2

Figure 2: Manhattan plots of a shattering, b brittle rachis, and c seed circularity in intermediate wheatgrass (Thinopyrum intermedium) with line indicating 0.05 false discovery rate. Panels d–f show quantile–quantile (QQ) plots for p values under the null hypothesis (no association) and observed p values for shattering (d), brittle rachis (e), and seed circularity (f), respectively