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Aims Perennial crops with more extensive and deep root systems could access deep stored water and build resilience to water shortage. In the context of human nutrition, perennial grain crops are very interesting. However, it is still questionable whether they are effective in using subsoil water. We compared intermediate wheatgrass (Kernza®) Thinopyrum intermedium , a perennial grain crop, to alfalfa Medicago sativa , a forage crop, for subsoil root growth and water uptake. Alfalfa was chosen because of its deep root system and agronomical interest as a companion crop. Methods Using TDR sensors, deuterium tracer labelling, minirhizotrons and the Hydrus-1D model we characterised the root distribution and water uptake patterns of these two perennial crops during two cropping seasons under field conditions down to 2.5 m soil depth. Results Both crops grew roots down to 2.0 m depth that were active in water uptake but alfalfa was deeper rooted than intermediate wheatgrass. All experimental methods concluded that alfalfa used more water from below 1.0 m depth than intermediate wheatgrass. However, simulations predicted that intermediate wheatgrass used more than 20 mm of water after anthesis from below 1 m soil depth. Simulations confirmed the advantage of deep roots in accessing deep soil water under drought. Conclusions In regions with high groundwater recharge, growing deep-rooted perennial crops have great potential to exploit deep soil water that is often left unused. However, the road to a profitable perennial grain crop is still long and breeding intermediate wheatgrass (Kernza®) cultivars for increased root growth at depth seems to be a worthy investment for the development of more drought tolerant cultivars.

Purpose Perennial crops have been suggested as a more sustainable alternative to the currently most common cropping systems. Compared with annual plants, perennial plants produce more biomass and have deeper roots, and are expected to lead to higher soil organic carbon (SOC). This hypothesis, however, has not been well tested for grain crops. Methods Using perennial intermediate wheatgrass (IWG, Thinopyrum intermedium ) and annual winter wheat ( Triticum aestivum ) as focal species, and native grassland as reference, we quantified the SOC accumulation via a process-based model, describing water and heat exchanges and carbon-nitrogen cycling in the canopy and soil to a depth of 2 m. The model includes C fixation via photosynthesis, plant biomass growth and litter production, physical protection of SOC, depolymerisation, C mineralisation, nitrification, denitrification, microbial growth, and necromass turnover in the soil. While of general applicability, we considered a sandy loam under warm-summer humid continental climate. Results Following a conversion from native grassland, IWG reduced SOC losses by at least 38%, especially in the particulate organic carbon (POC) pool, within the top 2 m of soil, compared with annual wheat. Soil microbial biomass and soil respiration were higher in IWG than annual wheat. Shifting from annual wheat to high photosynthetic capacity IWG increased SOC by about 33 g C m −2 y −1 (averaged over a 4-year continuous IWG cropping), with a large fraction of SOC gain stemming from restoring POC. Conclusion Compared with annual grains, perennial grains can increase soil carbon sequestration and maintain SOC at levels nearer to that of native grasslands.

Key messageAnalysis 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 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 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.

Allohexaploid (2n = 6x = 42) intermediate wheatgrass (Thinopyrum intermedium), abbreviated IWG, is an outcrossing perennial grass belonging to the tertiary gene pool of wheat. Perenniality would be valuable option for grain production, but attempts to introgress this complex trait from wheat-Thinopyrum hybrids have not been commercially successful. Efforts to breed IWG itself as a dual-purpose forage and grain crop have demonstrated useful progress and applications, but grain yields are significantly less than wheat. Therefore, genetic and physical maps have been developed to accelerate domestication of IWG. Herein, these maps were used to identify quantitative trait loci (QTLs) and candidate genes associated with IWG grain production traits in a family of 266 full-sib progenies derived from two heterozygous parents, M26 and M35. Transgressive segregation was observed for 17 traits related to seed size, shattering, threshing, inflorescence capacity, fertility, stem size, and flowering time. A total of 111 QTLs were detected in 36 different regions using 3826 genotype-by-sequence markers in 21 linkage groups. The most prominent QTL had a LOD score of 15 with synergistic effects of 29% and 22% over the family means for seed retention and percentage of naked seeds, respectively. Many QTLs aligned with one or more IWG gene models corresponding to 42 possible domestication orthogenes including the wheat Q and RHT genes. A cluster of seed-size and fertility QTLs showed possible alignment to a putative Z self-incompatibility gene, which could have detrimental grain-yield effects when genetic variability is low. These findings elucidate pathways and possible hurdles in the domestication of IWG.

Key message Development of the first consensus genetic map of intermediate wheatgrass gives insight into the genome and tools for molecular breeding. Intermediate wheatgrass ( Thinopyrum intermedium ) has been identified as a candidate for domestication and improvement as a perennial grain, forage, and biofuel crop and is actively being improved by several breeding programs. To accelerate this process using genomics-assisted breeding, efficient genotyping methods and genetic marker reference maps are needed. We present here the first consensus genetic map for intermediate wheatgrass (IWG), which confirms the species’ allohexaploid nature (2 n  = 6 x  = 42) and homology to Triticeae genomes. Genotyping-by-sequencing was used to identify markers that fit expected segregation ratios and construct genetic maps for 13 heterogeneous parents of seven full-sib families. These maps were then integrated using a linear programming method to produce a consensus map with 21 linkage groups containing 10,029 markers, 3601 of which were present in at least two populations. Each of the 21 linkage groups contained between 237 and 683 markers, cumulatively covering 5061 cM (2891 cM––Kosambi) with an average distance of 0.5 cM between each pair of markers. Through mapping the sequence tags to the diploid (2 n  = 2 x  = 14) barley reference genome, we observed high colinearity and synteny between these genomes, with three homoeologous IWG chromosomes corresponding to each of the seven barley chromosomes, and mapped translocations that are known in the Triticeae. The consensus map is a valuable tool for wheat breeders to map important disease-resistance genes within intermediate wheatgrass. These genomic tools can help lead to rapid improvement of IWG and development of high-yielding cultivars of this perennial grain that would facilitate the sustainable intensification of agricultural systems.

The perennial grain intermediate wheatgrass ( Thinopyrum intermedium , commercial name Kernza TM ) has been proposed as a diversification crop for producing forage and grain and providing ecosystem services to farmers. Although a few studies have addressed farmers’ interests in the crop, information is lacking about the links between farmers’ goals and crop management, i.e., how farmers aim at integrating this crop in their systems. Closing this gap, this paper analyzes for the first time the introduction of intermediate wheatgrass (IWG) from a farmer perspective, as a set of decision plans and goals. The overarching orientations of the farm and organization of the production system, referred as strategic decisions, interact with short-term crop management (i.e., tactical decisions) and farmers’ goals for IWG. In total, 17 individual semi-structured interviews and 2 collective crop management prototyping workshops in France were used to analyze farmers’ rationales as a function of their farm systems, agronomic constraints, and know-how. The study demonstrates that farmers’ interests in IWG revolved around multiple ecosystem services and financial returns. Three ideal-types of farms testing IWG emerged from the relationships between existing farming systems and goals for IWG. The strategic and tactical decisions regarding the integration and management of IWG were contingent on the farming systems, the goals for IWG, the farmers’ know-how, and their ability to mitigate risks. Implications for the future development of intermediate wheatgrass as a niche innovation are considered based on farmers’ points of view. This study provides insights into the ideas and concerns of French farmers regarding IWG and proposes a framework for discussing the introduction of a new crop in a farm system.

Intermediate wheatgrass (IWG, Thinopyrum intermedium [Host] Barkworth & D. R. Dewey) has been developed as a perennial grain crop for human consumption along with providing environmental benefits and ecosystem services. Grain and products derived from IWG cultivars improved for food production have been marketed under the registered trademark, Kernza. Development of IWG as a perennial grain crop began in 1980s with a phenotypic recurrent selection program as the Rodale Institute (RI) and the Big Flats Plant Material Center (BFPMC) used IWG plant introductions (PI) from the National Plant Germplasm System (NPGS) to improve populations of IWG. Initial selections were provided to The Land Institute (TLI) 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, and remnant seed and plant material from the initial RI selections 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.

The perennial forage grass Thinopyrum intermedium (Host) Barkworth & Dewey, commonly known as intermediate wheatgrass (IWG) or by the commercial name Kernza™, is being developed as a perennial grain crop, i.e. being bred for its improved agronomic performance and food qualities. Intercropping legumes and grasses is a strategy for improving resource use and sustainability in cropping systems. Here, we show for the first time the agronomic performance of IWG as a perennial cereal grown as a monocrop and as an intercrop (alternate row, 0.5:0.5) with Medicago sativa L. (alfalfa/lucerne) in southern Sweden. The seeds of cycle 3 IWG were accessed from The Land Institute (TLI) of Salinas, Kansas, USA, and used to establish a local seed production plot (in 2014) for the establishment of the perennial systems (in 2016) utilised in this study. Both the monocrop and intercrop were sown with 25 cm row spacing with alternate rows of IWG and alfalfa in the intercrop (i.e. replacement design) with unknown sowing density. Intercropping provided sustained IWG grain production under the dry conditions of 2018, but also in the following year. This was evidently associated with a higher nitrogen accumulation in intercropped practice. Thus, intercropping seems to have stabilised the IWG grain production in the dry conditions of 2018, when the grain production in the intercrop was similar to that of the monocrop in the same year. This result was further supported by the lower discrimination against 13 C (as an indicator of water use efficiency) in the intercrop components compared to the sole crop in 2018. The lower discrimination indicates high water use efficiency in the intercropped IWG in comparison to the IWG in monoculture, and we conclude that intercropping perennial cereal grain crops with legumes provides better growing conditions in terms of nitrogen acquisition, and water status, to cope with more extreme drought spells expected from climate change.

Intermediate wheatgrass (IWG; Thinopyrum intermedium), a nutritionally dense and sustainable crop, is a promising novel ingredient in bakery applications. The main aim of this study was to investigate the potential of IWG as a novel ingredient in breadmaking. The second aim was to investigate the characteristics of breads substituted with 15, 30, 45, and 60% IWG flour compared to control bread produced using wheat flour. The gluten content and quality, bread quality, bread staling, yellow pigment, and phenolic and antioxidant properties were determined. Enrichment with IWG flours significantly affected the gluten content and quality and bread characteristics. Increased levels of IWG flour substitution significantly decreased the Zeleny sedimentation and gluten index values and increased the dry and wet gluten contents. The bread yellow pigment content and crumb b* colour value increased with the increasing level of IWG supplementation. IWG addition also had a positive effect on the phenolic and antioxidant properties. Bread with 15% IWG substitution had the highest bread volume (485 mL) and lowest firmness values (654 g-force; g-f) compared to the other breads, including the control (i.e., wheat flour bread). The results indicated that IWG has great potential to be used in bread production as a novel, healthy, and sustainable ingredient.

Genomic selection (GS) can accelerate plant breeding gains by reducing breeding cycle times, reducing phenotyping costs, or improving selection accuracy. GS is especially promising for perennial crops such as intermediate wheatgrass (IWG, Thinopyrum intermedium) that may require multiple years of evaluation under phenotypic recurrent selection. A major obstacle in implementing GS is the need for an affordable, high‐density, genetic marker system that is scalable to thousands or tens‐of‐thousands of samples in breeding programs, especially in emerging or minor crop species. As sequencing costs continue to decrease, low‐coverage whole genome skim‐sequencing (skim‐seq) has become an attractive method for GS. Using commercial laboratory products and open‐source software, we implemented whole genome prediction at breeding program scale using ultra‐low coverage (0.01x– 0.05x, 100–125 million reads per sample) whole genome skim‐seq. Using STITCH (Sequencing to Imputation Through Constructing Haplotypes) imputation software, we evaluated optimization of imputation parameters including sequence coverage and number of assumed ancestral haplotypes. Finally, we evaluated whole genome prediction cross‐validation accuracies using reduced representation genotyping‐by‐sequencing (GBS) versus skim‐seq data for IWG, an outcrossing, heterozygous, large genome (12.7 Gb), polyploid perennial species. Our results indicate correlations between cross‐validation accuracies across five traits in IWG using skim‐seq data (r = 0.29–0.61) can be used as effectively as GBS (r = 0.29–0.55) while generating low‐coverage archival sequence data that will be robust to technological advances. These methods will be applicable to a wide range of crops and scale to breeding program size, allowing for more tractable implementation of GS within breeding programs. Core Ideas Skim‐sequencing, ultra‐low 0.05x genome coverage, was used to implement genomic prediction. Equivalent cross‐validation genomic prediction accuracies were achieved by skim‐seq and genotyping‐by‐sequencing. A bioinformatics pipeline from single nucleotide polymorphism discovery to imputation was developed, scalable to tens of thousands of samples. Skim‐seq leverages technological advances in sequencing, creating robust data resources for future applications. Skim‐seq alleviates barriers to entry for genomics‐assisted breeding in low‐resourced species. Plain Language Summary Plant breeding has been revolutionized by advances in genotyping technology. With the ability to genetically profile large populations, plant breeders can more effectively select plants that have greater agronomic performance based completely on their genetic makeup. However, few plant breeding programs have adopted these technological advances due to the challenges and cost associated with genotyping plants at a breeding scale (thousands) of plants. We investigated low‐cost sequencing techniques and computational methods to infer each plant's genetic makeup. Our results indicate that these methods can be used effectively, providing a road map for low‐resourced species and breeding programs to exploit the genomics revolution through open‐source, non‐proprietary methods. Furthermore, the data generated can be used for additional genetic studies.