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

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, 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 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 (MTA) 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 FST 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 was 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.

Perennials as Future Grain Crops: Opportunities and Challenges

“…Meanwhile, in both L. perenne and rye (Secale cereale; 2n = 2x = 14), the Z locus was mapped to homoeologous group 2 and shown to encode another domain of unknown function gene, DUF247, alongside a closely linked ubiquitin-specific protease (USP) (Hackauf and Wehling, 2005;Shinozuka et al, 2010;Manzanares et al, 2016). In intermediate wheatgrass (T. intermedium; 2n = 6x = 42), similar SI mechanisms appear to be involved, whereby assessment of progeny combinations resulting from a polycross led to the identification of S and Z loci gene candidates (Crain et al, 2020b). Consequently, the knockout of these SI candidate loci could increase the fertility of intermediate wheatgrass, and other perennial grain species, stimulating development Sacks et al, 2008;Fan et al, 2020;Yuan et al, 2020 Rye (Secale cereale) In many cases, interspecific crosses have facilitated QTL mapping of perennial traits.…”

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“…On a similar note, not all neighboring paternal genets close to one of the 15 mother plants were identified as fathers of the progeny sampled from the closest mother plant. Mating incompatibility could be a reason why we did not observe a higher frequency of pairs among neighboring genets (Crain et al, 2020). Another reason could be from the progeny size we sampled per mother plant.…”

“…Additionally, this is indicative that randomization of the half-sibs during their establishment in the nursery might not be necessary. The self-incompatibility (SI) system in IWG is hypothesized to be gametophytic and controlled by two independent genes, S and Z (Lundqvist, 1954;Crain et al, 2020). While the effect and extent of SI in IWG half-sibs yet to be studied, successful mating among half-sibs could help accumulate favorable alleles and thus aid in trait improvement.…”

“…Initially, all 21,256 genomic markers were used which led to the program halting with a "floating-point overflow error. " The number of markers was then reduced to a randomly selected set of 2,500 in a similar approach to a recently published study in IWG (Crain et al, 2020). For paternity analysis, the number of offspring was set to 10,000 and number of potential fathers as 749.…”

“…The IWG cultivars released by UMN are population synthetics generated from open pollination of 7-10 parent plants in 5-7 replications (Bajgain et al, 2020b). Crain et al (2020) used genotyping by sequencing to successfully assign paternity to progeny obtained from multiple breeding cycles of IWG, suggesting that parentage analysis could be used to characterize pollen dispersal and its influence on population diversity in IWG.…”