Crop rotation with perennial grain crops, such as intermediate wheatgrass (IWG; Thinopyrum intermedium), marketed as Kernza, promotes agroecological intensification and environmental sustainability relative to annual cropping systems. To assess yield performance and adaptability of IWG breeding populations across diverse environments, multilocation field trials were conducted from 2018 to 2022 in Minnesota, Wisconsin, Kansas, Nebraska, North Dakota, and Utah. Eight populations, MN-Clearwater, TLI-C5, TLI-C3, TLI-C4, MN1501, MN1502, MN1503, and the forage cultivar Rush, were evaluated using a randomized complete block design with four replications. Analysis of variance showed that location (27%) and location & times; harvest year interactions (44%) explained most seed yield variation, while genotype effects were modest. Yield declined after the second harvest year at most sites, indicating challenges in stand longevity. The Finlay-Wilkinson regression classified populations as high-yielding and responsive (MN-Clearwater and TLI-C5), low-yielding and stable (Rush), or intermediate-yielding but unstable (remaining populations). MN-Clearwater and TLI-C5 exceeded Rush by 78%-85%, reflecting breeding progress by the University of Minnesota and The Land Institute. Nonparametric analyses (Lin and Binns superiority index and Huehn's rank difference) consistently identified MN-Clearwater and TLI-C5 as the top-performing populations across favorable and stressed environments. Although yields declined by 82% and 74% under stress, these populations maintained competitive rankings with minimal rank crossover, indicating broad adaptability. Fall and summer rainfall were the primary environmental factors influencing yield across locations. These results highlight increases in grain yield that regional breeding programs have achieved across a broad geographical range, while also demonstrating the possibility to select for location-specific performance in the future.

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.

The USDA‐ARS and Utah Division of Wildlife Resources announce the release of bluebunch wheatgrass [ Pseudoroegneria spicata (Pursh.) A. Löve.] cultivars ‘USDA‐Basin’ (Reg. no. CV‐35, PI 708099) and ‘USDA‐Wasatch’ (Reg. no. CV‐36, PI 708100) (experimental designations: Basin/Basin‐STZ4 and Wasatch/Basin‐STZ3a, respectively) for their seedling drought tolerance and establishment, and as the first bluebunch wheatgrass cultivars that geographically and genetically originate from the Great Basin region of the United States. Though regionally sourced materials are desired, most bluebunch wheatgrass used for re‐seeding this region originate in the Columbia Plateau and Blue Mountains of eastern Washington state. Therefore, bluebunch wheatgrass was collected from the Great Basin and evaluated for relative fitness. Four collections from within each of two phylogeographic groups were selected and crossed to form USDA‐Basin and USDA‐Wasatch. Genotyping and morphological measurements demonstrated that USDA‐Basin and USDA‐Wasatch are significantly ( P < 0.05) different from each other and four check cultivars. In response to drought, seedling root growth for both was greater ( P < 0.05) than ‘Columbia’ and ‘P‐7’, but similar to ( P > 0.05) ‘Anatone’, whereas they had lesser ( P < 0.05) specific leaf area than checks, indicative of enhanced seedling drought tolerance. USDA‐Basin and USDA‐Wasatch were similar ( P > 0.05) to each other and Anatone for stand establishment (mean of 38%), and both had greater ( P < 0.05) establishment at two of three sites than Columbia and ‘Goldar’. USDA‐Basin and USDA‐Wasatch originate from two seed transfer zones that compose 65% of reseeding efforts within the Central Great Basin and thus contribute important regional components to restoration projects in this region.

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.

Forage yield estimates provide relevant information to manage and quantify ecosystem services in grasslands. We fitted and validated prediction models of forage yield for several prominent grasses used in restoration projects in semiarid areas. We used field forage harvests from three different sites in Northern Utah and Southern California, USA, in conjunction with multispectral, high-resolution UAV imagery. Different model structures were tested with simple models using a unique predictor, the forage volumetric 3D space, and more complex models, where RGB, red edge, and near-infrared spectral bands and associated vegetation indices were used as predictors. We found that for most dense canopy grasses, using a simple linear model structure could explain most (R2 0.7) of the variability of the response variable. This was not the case for sparse canopy grasses, where a full multispectral dataset and a non-parametric model approach (random forest) were required to obtain a maximum R2 of 0.53. We developed transparent protocols to model forage yield where, in most circumstances, acceptable results could be obtained with affordable RGB sensors and UAV platforms. This is important as users can obtain rapid estimates with inexpensive sensors for most of the grasses included in this study.

Basin wildrye [Leymus cinereus (Scribn. & Merr.) a. Love] is somewhat indeterminate and shatters its seed. To avoid shattering losses, growers tend to harvest basin wildrye seed prior to maximal physiological maturity. To resolve the intersecting problems of floral indeterminacy and seed shattering, USDA-ARS released the L-74X basin wildrye x creeping wildrye [L. triticoides (Buckl.) Pilger] germplasm (Reg. no. GP-106, PI 701909) on August 26, 2021. While L-74X has a narrow genetic base due to a biparental cross in its history, it can be used to introgress the nonshattering recessive sh6 allele of creeping wildrye (2n = 4x = 28) into 4x basin wildrye and closely related 4x Leymus species. L-74X originated with hybridization between 4x populations of basin wildrye and creeping wildrye, followed by eight generations of recombination and natural selection that restored fertility to the interspecific hybrid. Intentional selection led to fixation of the sh6 allele. Averaged across 2 years, shattering genotypes (Sh6/sh6) averaged 19.4% greater (P < 0.05) seed yield per spike 23 days after pollination (DAP), but by 95 DAP, nonshattering genotypes (sh6/sh6) averaged 167% greater (P < 0.05) seed yield per spike. Germination increased from 72.1% at 23 DAP to 86.4% at 95 DAP. The sh6 allele allows seed growers to delay seed harvest until seed is fully ripe, concomitantly reducing shattering losses and improving physiological seed quality.

Purpose The modification of clay minerals by exopolysaccharides (EPS) may significantly increase their adsorption capacity for heavy metals. Therefore, this study focused on the characterization of two typical clay minerals, montmorillonite, and kaolinite modified with EPS (produced by Rhizobium tropici ), their impact on the adsorption of uranium, U(VI), and the influence of pH, sulfate, and phosphate. Materials and methods The characterization of clays, EPS, and clay-EPS composites were carried out using X-ray power diffraction (XRD), fourier transform infrared spectroscopy (FTIR), atomic force microscope (AFM), and scanning electron microscopy (SEM)/energy dispersive X-ray (EDX) analysis. Results Results showed that EPS partially entered and dehydrated cations in the interlayers of montmorillonite, resulting in the decrease in interlayer d-spacing, which were confirmed by XRD and FTIR. Montmorillonite had better EPS adsorption capacity than kaolinite. The EPS-clay mineral composites significantly increased U(VI) adsorption capacity by 650% and 60% for montmorillonite and kaolinite, respectively. The adsorption capacity for U(VI) was ordered as montmorillonite-EPS > EPS > montmorillonite > kaolinite-EPS > kaolinite. Montmorillonite-EPS modification for U(VI) was maximized at pH 4, while the high pH such as pH 9 inhibited the U(VI) adsorption. Sulfate or phosphate has a negligible effect on the adsorption of UO 2 2+ on montmorillonite-EPS. Conclusion The current study provides a new insight for the application of biopolymers in remediation of U(VI) contaminated area.

The modification of clay minerals by exopolysaccharides (EPS) may significantly increase their adsorption capacity for heavy metals. This study focused on the adsorption of EPS (produced by Rhizobium tropici)-modified montmorillonite (MMT) and kaolinite (KLT) for Cs and Sr and the influence of external factors (pH, sulfate, and phosphate). The characterization of the composites was carried out using X-ray diffraction (XRD), Fourier transform infrared (FTIR), atomic force microscopy (AFM), and scanning electron microscopy/energy-dispersive X-ray analysis. With EPS modification, the adsorption capacity of MMT for Cs and Sr reached 256 and 90.9 mg/g, respectively, which were significantly improved by 53.8 and 54.5% compared to MMT alone, respectively. The adsorption capacity of KLT for Sr improved by 10.7%. KLT did not adsorb Cs either before or after EPS modification. The adsorption isotherms for Sr on MMT, EPS-MMT, KLT, and EPS-KLT as well as Cs on MMT and EPS-MMT were better described with the Freundlich adsorption models, indicating a heterogeneous layered adsorption process. XRD, FTIR, and AFM analysis confirmed the interlayer reaction of Sr/Cs with EPS-MMT. The Sr amounts adsorbed on EPS-MMT composites increased significantly with increasing pH, while the pH influence was not obvious on Cs adsorption but still slightly increased at pH 7 and then dropped at pH 9. In the presence of 50 and 500 mg/L sulfate, the Sr amount absorbed decreased by 12.5, and 29.3%, respectively. On the contrary, there was a significant increase in Cs adsorption by 12.2 and 33.9%, respectively. In the presence of phosphate, a significant increase (64.5%) was observed for Cs adsorption under 50 mg/L phosphate loading, but 500 mg/L phosphate inhibited (65.8%) the adsorption. In contrast, there was no significant change of Sr adsorption under different phosphate concentrations. The current study would provide a new insight for the application of biopolymers in remediation of Sr- and Cs-contaminated areas.

Lead in yard soils has been recognized as the principal source of excess lead absorption among young children. The hazard imposed by soil lead is dependent on the geochemical forms of lead in soils. Soil properties such as pH, soil organic matter, clay, and carbonate content influence the geochemical forms of lead in soil. This study was conducted to investigate the correlation between soil properties and the geochemical speciation of lead in lead paint-contaminated residential soils from three major US cities. A comprehensive field survey was conducted, involving the collection of soils from ten houses in each of the cities: Baltimore, San Antonio, and Detroit. The influence of soil properties on geochemical speciation was analyzed to identify effective immobilization amendments for each soil type. Results showed that soils collected from San Antonio were slightly alkaline, whereas those from Baltimore were slightly acidic. Soils collected from Detroit were neutral to mildly alkaline in pH. San Antonio soils had relatively high soil salinity, high clay content, moderate to high soil organic matter (SOM), and high total carbon (TC). In contrast, soils collected from Baltimore had lower salinity and clay content, low SOM, and total carbon. Soils from Detroit exhibited relatively high salinity, clay, SOM, and TC contents. The average total soil lead concentrations were as follows; San Antonio 4,073 mg/kg, Baltimore 2,706 mg/kg, and Detroit 850 mg/kg. Geochemical speciation studies revealed significant differences in lead distribution among the studied soils. San Antonio soils exhibited high carbonate-bound and organic matter-bound fractions, while Baltimore soils had elevated soluble + exchangeable fractions. Detroit soils showed substantial lead in organic matter-bound fractions. Correlation analysis showed that the soil properties influencing exchangeable lead, were pH, total Al, and total Ca for San Antonio soils; pH and total P for Baltimore soils; and SOM and total Al for Detroit soils. Correlation analysis showed that there is a significant negative correlation (p < 0.05) between exchangeable lead and total Al (r = −0.653), and total Ca (r = −0.438) for San Antonio soils; pH (r = −0.286) and total p (r = −0.314) for Baltimore soils; and SOM (r = −0.628) and total Al (r = −0.408) for Detroit soils. Based on these results, the best potential immobilization amendments for each of these cities were predicted.

Perennial grains have potential to contribute to ecological intensification of food production by enabling the direct harvest of human-edible crops without requiring annual cycles of disturbance and replanting. Studies of prototype perennial grains and other herbaceous perennials point to the ability of agroecosystems including these crops to protect water quality, enhance wildlife habitat, build soil quality, and sequester soil carbon. However, genetic improvement of perennial grain candidates has been hindered by limited investment due to uncertainty about whether the approach is viable. As efforts to develop perennial grain crops have expanded in past decades, critiques of the approach have arisen. With a recent report of perennial rice producing yields equivalent to those of annual rice over eight consecutive harvests, many theoretical concerns have been alleviated. Some valid questions remain over the timeline for new crop development, but we argue these may be mitigated by implementation of recent technological advances in crop breeding and genetics such as low-cost genotyping, genomic selection, and genome editing. With aggressive research investment in the development of new perennial grain crops, they can be developed and deployed to provide atmospheric greenhouse gas reductions.

The National Plant Germplasm System (NPGS) is a vital resource for genetic diversity, yet utilization of this resource requires a thorough understanding of the germplasm and genetic diversity. Intermediate wheatgrass (IWG, Thinopyrum intermedium) is a perennial grass species that has been improved for forage production through breeding utilizing the NPGS collection and has also been targeted for domestication as a perennial grain crop. To better characterize the IWG collection, we combined previously published forage data with new agronomic and genomic data. A total of 331 NPGS accessions were genomically profiled with genotyping-by-sequencing (GBS) and a genome-wide association study (GWAS) was used to evaluate trait architecture. Along with the GWAS, in silico bulk samples were profiled by recoding GBS data to conduct association mapping through allele counting with extreme-phenotype (XP)-GWAS. Genomic analysis revealed two subpopulations, which were defined as European and Asian groups, and are differentiated around the Black Sea region. Phenotypic observations for forage and agronomic traits differed between the two groups (p < 0.05), even though greater than 70% of the genetic variance was partitioned within individual accessions. Finally, XP-GWAS revealed 303 marker-trait associations for five agronomic and four forage traits. These results suggest that genetic diversity within the NPGS collection should lead to genetic gains for both forage and grain breeding as well as opportunities for breeding programs to enhance genetic diversity. More broadly, the methods we applied could be applicable to low-resourced species, leveraging existing, and new data, to strengthen genetic characterization and breeding efficiency.

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 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 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.

Sustainable agriculture in the future will depend on crops that are tolerant to biotic and abiotic stresses, require minimal input of water and nutrients and can be cultivated with a minimal carbon footprint. Wild plants that fulfill these requirements abound in nature but are typically low yielding. Thus, replacing current high-yielding crops with less productive but resilient species will require the intractable trade-off of increasing land area under cultivation to produce the same yield. Cultivating more land reduces natural resources, reduces biodiversity and increases our carbon footprint. Sustainable intensification can be achieved by increasing the yield of underutilized or wild plant species that are already resilient, but achieving this goal by conventional breeding programs may be a long-term prospect. De novo domestication of orphan or crop wild relatives using mutagenesis is an alternative and fast approach to achieve resilient crops with high yields. With new precise molecular techniques, it should be possible to reach economically sustainable yields in a much shorter period of time than ever before in the history of agriculture.

Perennial grain crops have the potential to improve agricultural sustainability but few existing species produce sufficient grain yield to be economically viable. The outcrossing, allohexaploid, and perennial forage species intermediate wheatgrass (IWG) [Thinopyrum intermedium (Host) Barkworth & D. R. Dewey] has shown promise in undergoing direct domestication as a perennial grain crop using phenotypic and genomic selection. However, decades of selection will be required to achieve yields on par with annual small-grain crops. Marker-aided selection could accelerate progress if important genomic regions associated with domestication were identified. Here we use the IWG nested association mapping (NAM) population, with 1,168 F1 progeny across 10 families to dissect the genetic control of brittle rachis, floret shattering, and threshability. We used a genome-wide association study (GWAS) with 8,003 single nucleotide polymorphism (SNP) markers and linkage mapping-both within-family and combined across families-with a robust phenotypic dataset collected from four unique year-by-location combinations. A total of 29 quantitative trait loci (QTL) using GWAS and 20 using the combined linkage analysis were detected, and most large-effect QTL were in common across the two analysis methods. We reveal that the genetic control of these traits in IWG is complex, with significant QTL across multiple chromosomes, sometimes within and across homoeologous groups and effects that vary depending on the family. In some cases, these QTL align within 216 bp to 31 Mbp of BLAST hits for known domestication genes in related species and may serve as precise targets of selection and directions for further study to advance the domestication of IWG.

The USDA announces the release of cultivar 'AlkarXL' (Reg. no. CV-286, PI 691611) tall wheatgrass [Thinopyrum ponticum (Podp.) Barkworth & D. R. Dewey] for use on semiarid rangelands and irrigated pastures that receive a minimum of 350 mm of average annual precipitation on alkali soils. AlkarXL is a 10-clone synthetic that originated from 56 plant introductions from the National Plant Germplasm System plus the cultivar Alkar. AlkarXL has undergone phenotypic recurrent selection for visual plant vigor (first cycle), seed yield (first cycle), dry-matter yield (DMY) (second cycle), and crude protein (second cycle). The 10 genotypes traced to PI 255146 (two genotypes; 30%, Turkey), PI 308592 (10%, Italy), PI 442631 (10%, Turkey), PI 109542 (10%, Turkey), PI 255443 (10%, llirkey), PI 383545 (10%, Turkey), PI 401006 (Turkey), PI 401009 (10%, Turkey), and W6 21870 (10%, Ukraine). Morphologically, AlkarXL has significantly wider lemmas and glumes and shorter glumes than cultivars Alkar, Greenstar, Jose, Largo, and Szarvasi-1. AlkarXL had narrower flag leaves than Largo. AlkarXL had more seedlings (P < .05) emerge than Alkar at Lages Junction, NV. AlkarXL had greater (P < .05) plant persistence (plant frequency) 3 (2017), 4 (2018), and 5 (2019) yr after seeding at Lages Junction than did Alkar. Dry-matter yield was less descriptive due to large variations in DMY among replications. AlkarXL had significantly (P < .10) more total DMY than Greenstar and Largo at Millville, UT, and similar DMY as Greenstar, Jose, and Savarsi-1 at Panguitch, UT.

Shifting the life cycle of grain crops from annual to perennial would usher in a new era of agriculture that is more environmentally friendly, resilient to climate change, and capable of soil carbon sequestration. Despite decades of work, transforming the annual grain crop wheat (Triticum aestivum) into a perennial has yet to be realized. Direct domestication of wild perennial grass relatives of wheat, such as Thinopyrum intermedium, is an alternative approach. Here we highlight protein coding sequences in the recently released T. intermedium genome sequence that may be orthologous to domestication genes identified in annual grain crops. Their presence suggests a roadmap for the accelerated domestication of this plant using new breeding technologies.

Bluebunch wheatgrass (referred to as BBWG) [Pseudoroegneria spicata (Pursh) Á. Löve] is an important rangeland Triticeae grass used for forage, conservation, and restoration. This diploid has the basic St genome that occurs also in many polyploid Triticeae species, which serve as a gene reservoir for wheat improvement. Until now, the St genome in diploid species of Pseudoroegneria has not been mapped. Using a double-cross mapping populations, we mapped 230 expressed sequence tag derived simple sequence repeat (EST-SSR) and 3468 genotyping-by-sequencing (GBS) markers to 14 linkage groups (LGs), two each for the seven homologous groups of the St genome. The 227 GBS markers of BBWG that matched those in a previous study helped identify the unclassified seven LGs of the St sub-genome among 21 LGs of Thinopyrum intermedium (Host) Barkworth & D.R. Dewey. Comparisons of GBS sequences in BBWG to whole-genome sequences in bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) revealed that the St genome shared a homology of 35% and 24%, a synteny of 86% and 84%, and a collinearity of 0.85 and 0.86, with ABD and H, respectively. This first-draft molecular map of the St genome will be useful in breeding cereal and forage crops.

Paternity assignment and genome-wide association analyses for fertility were applied to a Thinopyrum intermedium breeding program. A lack of progeny between combinations of parents was associated with loci near self-incompatibility genes. In outcrossing species such as intermediate wheatgrass (IWG, Thinopyrum intermedium), polycrossing is often used to generate novel recombinants through each cycle of selection, but it cannot track pollen-parent pedigrees and it is unknown how self-incompatibility (SI) genes may limit the number of unique crosses obtained. This study investigated the potential of using next-generation sequencing to assign paternity and identify putative SI loci in IWG. Using a reference population of 380 individuals made from controlled crosses of 64 parents, paternity was assigned with 92% agreement using Cervus software. Using this approach, 80% of 4158 progeny (n = 3342) from a polycross of 89 parents were assigned paternity. Of the 89 pollen parents, 82 (92%) were represented with 1633 unique full-sib families representing 42% of all potential crosses. The number of progeny per successful pollen parent ranged from 1 to 123, with number of inflorescences per pollen parent significantly correlated to the number of progeny (r = 0.54, p < 0.001). Shannon’s diversity index, assessing the total number and representation of families, was 7.33 compared to a theoretical maximum of 8.98. To test our hypothesis on the impact of SI genes, a genome-wide association study of the number of progeny observed from the 89 parents identified genetic effects related to non-random mating, including marker loci located near putative SI genes. Paternity testing of polycross progeny can impact future breeding gains by being incorporated in breeding programs to optimize polycross methodology, maintain genetic diversity, and reveal genetic architecture of mating patterns.

It has been hypothesized that the genetic control of forage traits, especially biomass, for grass plants growing as spaced-plants versus swards is different. Likewise, the genetic control of compatibility in grass–legume polyculture mixtures is assumed to be different than for forage production in a grass monoculture. However, these hypotheses are largely unvalidated, especially at the DNA level. This study used an intermediate wheatgrass mapping population to examine the effect of three competition environments (spaced-plants, polyculture, and monoculture) on classical quantitative genetic parameters and quantitative trait loci (QTL) identification for biomass, morphology, and forage nutritive value. Moderate to high heritable variation was observed for biomass, morphological traits, and nutritive value within all three environments (H ranged from 0.50 to 0.87). Genetic correlations (rG) among environments for morphology and nutritive value were predominantly high, however, were moderately-low (0.30 to 0.48) for biomass. Six biomass QTL were identified, including three on linkage groups (LG) 1, 6, and 15 that were only expressed in the monoculture environment. Moreover, three biomass QTL on LG 10, 14, and 15 exhibited significant QTL by environment interactions. This study verified that the genetic control of grass biomass in a monoculture versus a grass–legume mixture is only partially the same, with additional genes expressed in monoculture, and that biomass in widely spaced-plants versus swards is predominantly under different genetic control. These results indicate that selection for improved grass biomass will be most successful when conducted within the targeted monoculture or polyculture sward environment per se.

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.