Genomic prediction enables rapid selection of high‐performing genets in an intermediate wheatgrass breeding program

Abstract

In an era of constrained and depleted natural resources, perennial grains could provide sustainable food production along with beneficial ecosystem services like reduced erosion and increased atmospheric carbon capture. Intermediate wheatgrass (IWG) [Thinopyrum intermedium (Host) Barkworth & D. R. Dewey subsp. intermedium] has been undergoing continuous breeding for domestication to develop a perennial grain crop since the 1980s. As a perennial, IWG has required 2-5 yr per selection generation, but starting in 2017, genomic selection (GS) was initiated in the breeding program at The Land Institute, Salina, KS (TLI), enabling one complete cycle per year. For each cycle, ∼4,000 seedlings were profiled using genotyping-by-sequencing (GBS) and genomic estimated breeding values (GEBVs) were calculated. Selection based on GEBVs identified ∼100 individuals to advance as parents each generation, while validation populations of 1,000-1,200 genets for GS model training were also selected using the genomic relationship matrix to represent genetic diversity in each cycle. The selected parents were randomly intermated in a greenhouse crossing block to form the subsequent cycle, while the validation populations were transplanted to irrigated and nonirrigated field sites for phenotypic evaluations in the following years. For priority breeding traits of seed mass, free threshing, and nonshattering, correlations between predicted values and observed data were >.5. The realized selection differential ranged from 11-23% for selected traits, and the expected genetic gains for these traits, including spike yield, ranged from 6 to 14% per year. Genomic selection is a powerful tool to speed the domestication and development of IWG and other perennial crops with extended breeding timelines.

Genetic Architecture and QTL Selection Response For Kernza Perennial Grain Domestication Traits

“…Each year phenotypic traits were measured to evaluate genet performance, with a total 34 unique traits (Crain et al 2021a). Within the breeding program the most important traits which are key selection targets include shattering, percent free-threshing seed, seed mass, and spike yield.…”

“…Interestingly, we identified that 2.3% (548 markers) had diverged between TLI-cycle 6 and 9, yet only four of the 217 MTAs showed high or very high FST. Since genomic selection has been exclusively used for the last four breeding cycles (Crain et al 2021a), we evaluated the genome-wide estimated marker effects for yield traits. Of the 72 highly diverged markers, 60% and 56% (43 and 40 markers respectively) had coefficients with higher spike yield and seed mass and the mean of all these markers indicated selection was in the favorable direction.…”

“…The estimated genetic gains have generally been favorable and at a more rapid rate than phenotypic selection alone, yet there has been some evidence of unanticipated results. Within the breeding program, increasing spike yield has been associated with increased seeds per spike, number of florets per spike, and florets per spikelet, yet the floret site utilization (FSU, referred to as percent seed set in Crain et al, 2021a) decreased, suggesting less efficient use of resources. While FSU has not been a direct target of selection in the TLI program, Altendorf et al (2021a) have found that FSU was the primary driver of yield for spaced plants grown on 1m centers (e.g.…”

“…While the initial cycles of selection relied on recurrent phenotypic selection (Zhang et al 2016;DeHaan et al 2018), advances in low cost, high-throughput DNA sequencing has permitted IWG breeding to harness the power of genomic selection (GS) (Zhang et al 2016;Bajgain et al 2020a;Crain et al 2020aCrain et al , 2021b. Within TLI's breeding program, GS has reduced the breeding cycle from three years 89 to one year per cycle (DeHaan et al 2018) and simultaneously maintained an estimated 8% year -1 increase in spike yield (Crain et al 2021a). Furthermore, decreased sequencing cost has resulted in a wealth of genomic information for crop improvement including genetic maps (Kantarski et al 2016), a draft genome sequence (https://phytozomenext.jgi.doe.gov/info/Tintermedium_v2_1).…”

“…While there are some arguments against perennial grains due to the ecological and physiological limitation of perennial plants (Smaje 2015), current work suggest that favorable gains can be made through artificial selection (DeHaan et al 2014;Zhang et al 2016;Crain et al 2021a). As breeding programs mature, they should assess whether the realized gains in perennial crops are matching the target gains for both agronomic yield and increased ecosystem services.…”