Development of whole-genome prediction models to increase the rate of genetic gain in intermediate wheatgrass (Thinopyrum intermedium) breeding

Origin of current intermediate wheatgrass germplasm being developed for Kernza grain production

Intermediate wheatgrass (IWG, Thinopyrum intermedium [Host] Barkworth & D. R. Dewey) has been developed as a perennial grain crop to provide ecosystem services, environmental benefits, and human food. Grain and products derived from IWG varieties improved for food production have been marketed under the registered trademark, Kernza. In the 1980s, a joint breeding effort between the Rodale Institute (RI) and the Big Flats Plant Material Center used IWG plant introductions (PI) from the National Plant Germplasm System (NPGS) and recurrent phenotypic selection to improve populations of IWG with the goal of developing a perennial grain. Initial selections were provided to The Land Institute where they were subsequently improved for grain production, yet the identity of the founder material of improved, food-grade IWG has not been publicly documented. Recently recovered original documents have been used to reconstruct the early breeding program to identify the most likely 20 PIs that form the founders of modern food-grade IWG. Molecular data using genotyping-by-sequencing in current elite breeding material, remnant seed from the initial RI selections, and preserved sample material have provided supporting evidence for the historical records. The genetic origin for food-grade IWG is focused between the Black Sea and Caspian Sea in the Stavropol region of Russia, with smaller contributions likely from collections as distant as Kazakhstan in the east to Turkey in the west. This work connects the flow of germplasm and utility of NPGS PIs to present day IWG grain cultivars being developed in multiple breeding programs around the world.

Nitrate leaching losses and the fate of 15N fertilizer in perennial intermediate wheatgrass and annual wheat - A field study

Perennial grains, such as the intermediate wheatgrass (Thinopyrum intermedium) (IWG), may reduce negative environmental effects compared to annual grain crops. Their permanent, and generally larger, root systems are likely to retain nitrogen (N) better, decreasing harmful losses of N and improving fertilizer N use efficiency, but there have been no comprehensive N fertilizer recovery studies in IWG to date. We measured fertilizer N recovery with stable isotope tracers in crop biomass and soil, soil N mineralization and nitrification, and nitrate leaching in IWG and annual wheat in a replicated block field experiment. Nitrate leaching was drastically reduced in IWG (0.1 and 3.1 kg N ha^-1 yr^-1) in its third and fourth year since establishment, compared with 5.6 kg N ha^-1 yr^-1 in annual wheat and 41.0 kg N ha^-1 yr^-1 in fallow respectively. There were no differences in net N mineralization or nitrification between IWG and annual wheat, though there was generally more inorganic N in the soil profile of annual wheat. More ¹⁵N fertilizer was recovered in the straw and all depths of the roots and soils in IWG than annual wheat. However, annual wheat recovered much more ¹⁵N fertilizer in the seeds compared to IWG, which had lower grain yields. ¹⁵N-labeled fertilizer contributed little (<3 %) to nitrate-N in leachate, highlighting the role of soil microbes in regulating loss of current year fertilizer N. The large reduction in nitrate leaching demonstrates that perennial grains can reduce harmful nitrogen losses and offer a more sustainable alternative to annual grains.

The use of wheatgrass (<i>Thinopyrum intermedium</i>) in breeding

Wheatgrass (Th. intermedium) has been traditionally used in wheat breeding for obtaining wheat-wheatgrass hybrids and varieties with introgressions of new genes for economically valuable traits. However, in the 1980s in the United States wheatgrass was selected from among perennial plant species as having promise for domestication and the development of dual-purpose varieties for grain (as an alternative to perennial wheat) and hay. The result of this work was the creation of the wheatgrass varieties Kernza (The Land Institute, Kansas) and MN-Clearwater (University of Minnesota, Minnesota). In Omsk State Agrarian University, the variety Sova was developed by mass selection of the most winter-hardy biotypes with their subsequent combination from the population of wheatgrass obtained from The Land Institute. The average grain yield of the variety Sova is 9.2 dt/ha, green mass is 210.0 dt/ ha, and hay is 71.0 dt/ha. Wheatgrass is a crop with a large production potential, benef icial environmental properties, and valuable grain for functional food. Many publications show the advantages of growing the Kernza variety compared to annual crops in reducing groundwater nitrate contamination, increasing soil carbon sequestration, and reducing energy and economic costs. However, breeding programs for domestication of perennial crops are very limited in Russia. This paper presents an overview of main tasks faced by breeders, aimed at enhancing the yield and cultivating wheatgrass eff iciency as a perennial grain and fodder crop. To address them, both traditional and modern biotechnological and molecular cytogenetic approaches are used. The most important task is to transfer target genes of Th. intermedium to modern wheat varieties and decrease the level of chromatin carrying undesirable genes of the wild relative. The f irst consensus map of wheatgrass containing 10,029 markers was obtained, which is important for searching for genes and their introgressions to the wheat genome. The results of research on the nutritional and technological properties of wheatgrass grain for the development of food products as well as the differences in the quality of wheatgrass grain and wheat grain are presented.

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

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. 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.

Perennials as Future Grain Crops: Opportunities and Challenges

Perennial grain crops could make a valuable addition to sustainable agriculture, potentially even as an alternative to their annual counterparts. The ability of perennials to grow year after year significantly reduces the number of agricultural inputs required, in terms of both planting and weed control, while reduced tillage improves soil health and on-farm biodiversity. Presently, perennial grain crops are not grown at large scale, mainly due to their early stages of domestication and current low yields. Narrowing the yield gap between perennial and annual grain crops will depend on characterizing differences in their life cycles, resource allocation, and reproductive strategies and understanding the trade-offs between annualism, perennialism, and yield. The genetic and biochemical pathways controlling plant growth, physiology, and senescence should be analyzed in perennial crop plants. This information could then be used to facilitate tailored genetic improvement of selected perennial grain crops to improve agronomic traits and enhance yield, while maintaining the benefits associated with perennialism.

How the Nitrogen Economy of a Perennial Cereal-Legume Intercrop Affects Productivity: Can Synchrony Be Achieved?

The UN's Sustainable Development goal of Zero Hunger encompasses a holistic set of targets that range from ending hunger by 2030, to increasing environmental sustainability and resilience of food production. Securing and managing soil nutrients remains one of the most basic challenges to growing adequate food while simultaneously protecting biodiversity and the integrity of ecosystems. To achieve these objectives, it is increasingly clear that the management of ecological processes will need to supplant reliance on non-renewable and environmentally damaging inputs. In recent years, progress has been made in developing perennial grain crops that show promise to improve on a range of ecological functions such as efficient nitrogen cycling and soil carbon accretion that tend to be well-developed in natural ecosystems but become compromised following land conversion to row crop agriculture. Here we report on a multi-faceted, 5-year experiment in which intermediate wheatgrass (IWG) (Thinopyrum intermedium), a perennial relative of wheat that is bred to produce the grain Kernza®, was intercropped in alternating rows with the perennial legume alfalfa (Medicago sativa). The performance of the unfertilized intercrop was compared to monocropped IWG treatments, with and without urea-N applications, planted at two row densities such that the intercrop could be interpreted as either an addition or substitution design. Comparisons of relative IWG yields (RYs) in the intercrop with unfertilized monocrops suggest net competitive interactions between alfalfa and IWG in the establishment year, followed by increasing degrees of facilitation over the next 4 years. Evidence from N fertilizer responsiveness, SPAD readings, net N mineralization assays, and N balance calculations suggest that alfalfa contributed to an aggrading pool of soil organic nitrogen over the course of the experiment. Comparisons of grain RYs of intercropped IWG and fertilized IWG monocultures suggest N-limitation in the first half of the experiment, and N sufficiency in the second half. Grain yields in the intercrop did not decline significantly over 5 years in contrast to all IWG monocrop treatments that did significantly decline. This study contributes to a growing literature on approaches to ecological nutrient management that incorporate diversity and perenniality to increase food security and resilience.