Comparison of single-trait and multi-trait genomic predictions on agronomic and disease resistance traits in spring wheat

This study performed comprehensive analyses on the predictive abilities of single-trait and two multi-trait models in three populations. Our results demonstrated the superiority of multi-traits over single-trait models across seven agronomic and four to seven disease resistance traits of different genetic architecture. The predictive ability of multi-trait and single-trait prediction models has not been investigated on diverse traits evaluated under organic and conventional management systems. Here, we compared the predictive abilities of 25% of a testing set that has not been evaluated for a single trait (ST), not evaluated for multi-traits (MT1), and evaluated for some traits but not others (MT2) in three spring wheat populations genotyped either with the wheat 90K single nucleotide polymorphisms array or DArTseq. Analyses were performed on seven agronomic traits evaluated under conventional and organic management systems, four to seven disease resistance traits, and all agronomic and disease resistance traits simultaneously. The average prediction accuracies of the ST, MT1, and MT2 models varied from 0.03 to 0.78 (mean 0.41), from 0.05 to 0.82 (mean 0.47), and from 0.05 to 0.92 (mean 0.67), respectively. The predictive ability of the MT2 model was significantly greater than the ST model in all traits and populations except common bunt with the MT1 model being intermediate between them. The MT2 model increased prediction accuracies over the ST and MT1 models in all traits by 9.0-82.4% (mean 37.3%) and 2.9-82.5% (mean 25.7%), respectively, except common bunt that showed up to 7.7% smaller accuracies in two populations. A joint analysis of all agronomic and disease resistance traits further improved accuracies within the MT1 and MT2 models on average by 21.4% and 17.4%, respectively, as compared to either the agronomic or disease resistance traits, demonstrating the high potential of the multi-traits models in improving prediction accuracies.

Genome-based prediction of agronomic traits in spring wheat under conventional and organic management systems

Using phenotype data of three spring wheat populations evaluated at 6-15 environments under two management systems, we found moderate to very high prediction accuracies across seven traits. The phenotype data collected under an organic management system effectively predicted the performance of lines in the conventional management and vice versa. There is growing interest in developing wheat cultivars specifically for organic agriculture, but we are not aware of the effect of organic management on the predictive ability of genomic selection (GS). Here, we evaluated within populations prediction accuracies of four GS models, four combinations of training and testing sets, three reaction norm models, and three random cross-validations (CV) schemes in three populations phenotyped under organic and conventional management systems. Our study was based on a total of 578 recombinant inbred lines and varieties from three spring wheat populations, which were evaluated for seven traits at 3-9 conventionally and 3-6 organically managed field environments and genotyped either with the wheat 90 K SNP array or DArTseq. We predicted the management systems (CV0_M) or environments (CV0), a subset of lines that have been evaluated in either management (CV2_M) or some environments (CV2), and the performance of newly developed lines in either management (CV1_M) or environments (CV1). The average prediction accuracies of the model that incorporated genotype × environment interactions with CV0 and CV2 schemes varied from 0.69 to 0.97. In the CV1 and CV1M schemes, prediction accuracies ranged from - 0.12 to 0.77 depending on the reaction norm models, the traits, and populations. In most cases, grain protein showed the highest prediction accuracies. The phenotype data collected under the organic management effectively predicted the performance of lines under conventional management and vice versa. This is the first comprehensive GS study that investigated the effect of the organic management system in wheat.

Physical mapping of QTL associated with agronomic and end-use quality traits in spring wheat under conventional and organic management systems

Using phenotypic data of four biparental spring wheat populations evaluated at multiple environments under two management systems, we discovered 152 QTL and 22 QTL hotspots, of which two QTL accounted for up to 37% and 58% of the phenotypic variance, consistently detected in all environments, and fell within genomic regions harboring known genes. Identification of the physical positions of quantitative trait loci (QTL) would be highly useful for developing functional markers and comparing QTL results across multiple independent studies. The objectives of the present study were to map and characterize QTL associated with nine agronomic and end-use quality traits (tillering ability, plant height, lodging, grain yield, grain protein content, thousand kernel weight, test weight, sedimentation volume, and falling number) in hard red spring wheat recombinant inbred lines (RILs) using the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 physical map. We evaluated a total of 698 RILs from four populations derived from crosses involving seven parents at 3-8 conventionally (high N) and organically (low N) managed field environments. Using the phenotypic data combined across all environments per management, and the physical map between 1058 and 6526 markers per population, we identified 152 QTL associated with the nine traits, of which 29 had moderate and 2 with major effects. Forty-nine of the 152 QTL mapped across 22 QTL hotspot regions with each region coincident to 2-6 traits. Some of the QTL hotspots were physically located close to known genes. QSv.dms-1A and QPht.dms-4B.1 individually explained up to 37% and 58% of the variation in sedimentation volume and plant height, respectively, and had very large LOD scores that varied from 19.0 to 35.7 and from 16.7 to 55.9, respectively. We consistently detected both QTL in the combined and all individual environments, laying solid ground for further characterization and possibly for cloning.

The Integration of Spring and Winter Wheat Genetics With Agronomy for Ultra-Early Planting Into Cold Soils

Early seeding has been suggested as a method of increasing the grain yield and grain yield stability of wheat (Triticum aestivum L.) in the Northern Great Plains. The point at which early seeding results in a decrease in grain yield has not been clearly identified. Changes in climatic conditions have increased frost-free periods and increased temperatures during grain filling, which can either be taken advantage of or avoided by seeding earlier. Field trials were conducted in western Canada from 2015 to 2018 to evaluate an ultra-early wheat planting system based on soil temperature triggers as opposed to calendar dates. Planting began when soil temperatures at 5 cm depth reached 0°C and continued at 2°C intervals until 10°C, regardless of calendar date. Conventional commercial spring wheat genetics and newly identified cold tolerant spring wheat lines were evaluated to determine if ultra-early wheat seeding systems required further development of specialized varieties to maintain system stability. Ultra-early seeding resulted in no detrimental effect on grain yield. Grain yield increased at sites south of 51° latitude N, and was unaffected by ultra-early seeding at sites north of 51° latitude N. Grain protein content, kernel weight, and bulk density were not affected by ultra-early seeding. Optimal seeding time was identified between 2 and 6°C soil temperatures. A greater reduction in grain yield was observed from delaying planting until soils reached 10°C than from seeding into 0°C soils; this was despite extreme environmental conditions after initial seeding, including air temperatures as low as -10.2°C, and as many as 37 nights with air temperatures below 0°C. Wheat emergence ranged from 55 to 70%, and heads m^-2 decreased with delayed seeding while heads plant^-1 did not change. Cold tolerant wheat lines did not increase stability of the ultra-early wheat seeding system relative to the conventional spring wheat check, and are therefore not required for growers to adopt ultra-early seeding. The results of this study indicate that growers in western Canada can successfully begin seeding wheat earlier, with few changes to their current management practices, and endure less risk than delaying seeding until soil temperatures reach 10°C or greater.

A Systematic Review of Durum Wheat: Enhancing Production Systems by Exploring Genotype, Environment, and Management (G × E × M) Synergies

According to the UN-FAO, agricultural production must increase by 50% by 2050 to meet global demand for food. This goal can be accomplished, in part, by the development of improved cultivars coupled with modern best management practices. Overall, wheat production on farms will have to increase significantly to meet future demand, and in the face of a changing climate that poses risk to even current rates of production. Durum wheat [Triticum turgidum L. ssp. durum (Desf.)] is used largely for pasta, couscous and bulgur production. Durum producers face a range of factors spanning abiotic (frost damage, drought, and sprouting) and biotic (weed, disease, and insect pests) stresses that impact yields and quality specifications desired by export market end-users. Serious biotic threats include Fusarium head blight (FHB) and weed pest pressures, which have increased as a result of herbicide resistance. While genetic progress for yield and quality is on pace with common wheat (Triticum aestivum L.), development of resistant durum cultivars to FHB is still lagging. Thus, successful biotic and abiotic threat mitigation are ideal case studies in Genotype (G) × Environment (E) × Management (M) interactions where superior cultivars (G) are grown in at-risk regions (E) and require unique approaches to management (M) for sustainable durum production. Transformational approaches to research are needed in order for agronomists, breeders and durum producers to overcome production constraints. Designing robust agronomic systems for durum demands scientific creativity and foresight based on a deep understanding of constitutive components and their innumerable interactions with each other and the environment. This encompasses development of durum production systems that suit specific agro-ecozones and close the yield gap between genetic potential and on-farm achieved yield. Advances in individual technologies (e.g., genetic improvements, new pesticides, seeding technologies) are of little benefit until they are melded into resilient G × E × M systems that will flourish in the field under unpredictable conditions of prairie farmlands. We explore how recent genetic progress and selected management innovations can lead to a resilient and transformative durum production system.

Toward a Better Understanding of Genotype × Environment × Management Interactions-A Global Wheat Initiative Agronomic Research Strategy

The Wheat Initiative (WI) and the WI Expert Working Group (EWG) for Agronomy (www.wheatinitiative.org) were formed with a collective goal to "coordinate global wheat research efforts to increase wheat production, quality, and sustainability to advance food security and safety under changing climate conditions." The Agronomy EWG is responsive to the WI's research need, "A knowledge exchange strategy to ensure uptake of innovations on farm and to update scientists on changing field realities." The Agronomy EWG aims to consolidate global expertise for agronomy with a focus on wheat production systems. The overarching approach is to develop and adopt a systems-agronomy framework relevant to any wheat production system. It first establishes the scale of current yield gaps, identifies defensible benchmarks, and takes a holistic approach to understand and overcome exploitable yield gaps to complement genetic increases in potential yield. New opportunities to increase productivity will be sought by exploiting future Genotype × Environment × Management synergies in different wheat systems. To identify research gaps and opportunities for collaboration among different wheat producing regions, the EWG compiled a comprehensive database of currently funded wheat agronomy research (n = 782) in countries representing a large proportion of the wheat grown in the world. The yield gap analysis and research database positions the EWG to influence priorities for wheat agronomy research in member countries that would facilitate collaborations, minimize duplication, and maximize the global impact on wheat production systems. This paper outlines a vision for a global WI agronomic research strategy and discusses activities to date. The focus of the WI-EWG is to transform the agronomic research approach in wheat cropping systems, which will be applicable to other crop species.

Yield Gaps in Wheat: Path to Enhancing Productivity

Wheat production is required to supply food for the world's population, and increases in production will be necessary to feed the expanding population. Estimates show that production must increase by 1 billion metric tons to meet this demand. One method to meet future demand is to increase wheat yields by reducing the gap between actual and potential yields. Potential yields represent an optimum set of conditions, and a more realistic metric would be to compare actual yields with attainable yields, where these yields represent years in the record where there is no obvious limitation. This study was conducted to evaluate the yield trends, attainable yields, and yield gaps for the 10 largest wheat producing countries in the world and more localized yield statistics at the state or county level. These data were assembled from available government sources. Attainable yield was determined using an upper quantile analysis to define the upper frontier of yields over the period of record and yield gaps calculated as the difference between attainable yield and actual yield for each year and expressed as a percentage of the attainable yield. In all countries, attainable yield increase over time was larger than the yield trend indicating the technological advances in genetics and agronomic practices were increasing attainable yield. Yield gaps have not shown a decrease over time and reflect that weather during the growing season remains the primary limitation to production. Yield gap closure will require that local producers adopt practices that increase their climate resilience in wheat production systems.

Effect of Wheat Cultivars and Blends on the Oviposition and Larval Mortality of Cephus cinctus (Hymenoptera: Cephidae) and Parasitism by Bracon cephi (Hymenoptera: Braconidae)

The wheat stem sawfly (Cephus cinctus Norton) is a major historical pest of wheat in the northern Great Plains of North America. The insect spends most of its life as a larva protected inside grass stems so that its management has relied on strategies other than insecticides. We conducted a study in southern Alberta from 2006-2009 to assess the effects of wheat species, cultivar, seeding rate, and blending a resistant and a vulnerable cultivar, on oviposition, larval infestation, and cutting damage. The mortality caused by its primary parasitoid, Bracon cephi (Gahan), was also assessed to investigate the potential benefit of cultivar blends to enhance sawfly biological control. Sawfly laid fewer eggs on plants of the durum cultivar 'AC Avonlea' and on those of the solid-stemmed cultivar 'Lillian' compared to plants of the hollow-stemmed cultivar 'CDC Go.' Larval establishments (infestation) followed a similar pattern to that of oviposition. At these locations there was low cutting damage in most years and to a large extent this was due to mortality inflicted by the parasitoid Bracon cephi (40-60%). However, the remaining mortality was attributed to other factors and host, particularly the inclusion of the solid-stemmed cultivar. Direct and indirect factors likely affected the success of the parasitoid in the crop monocultures and blends, and these mechanisms require further research.

Solid-stemmed wheat does not affect overwintering mortality of the wheat stem sawfly, Cephus cinctus

The wheat stem sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae), is a key pest of wheat in the northern Great Plains of North America. Host plant resistance in the form of solid-stemmed wheat cultivars is the main control strategy for C. cinctus. This study investigated the effect of novel and traditional solid wheat hosts on the overwintering mortality and cold-hardiness of C. cinctus. Field conditions from 2003-2005 showed that overwintering mortality in various wheat cultivars averaged 8% and was not related to the type of wheat cultivar. Similarly, supercooling points (-22° C) were not influenced by wheat host type. C. cintus are cold-hardy; up to 80% survive 10 days at -20° C and 10% survive 40 days. Its overwintering microhabitat near the crown area of the plant is well insulated for temperatures above -10° C and remains ~ 20° C above ambient minima. These data suggest that winter mortality is a minor factor in the population dynamics of wheat stem sawfly, and despite clear detrimental effects on larval weight and adult fitness, solid-stemmed cultivars do not reduce the ability of larvae to survive winters.

Evaluation of alternative planting strategies to reduce wheat stem sawfly (Hymenoptera: Cephidae) damage to spring wheat in the northern Great Plains

Wheat, Triticum aestivum L., producers are often reluctant to use solid-stemmed wheat cultivars resistant to wheat stem sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae), due to concerns regarding yield, efficacy or market opportunities. We evaluated the impact of several planting strategies on wheat yield and quality and wheat stem sawfly infestation at two locations over a three-year period. Experimental units consisted of large plots (50 by 200 m) located on commercial farms adjacent to wheat stem sawfly-infested fields. Compared with a monoculture of a hollow-stemmed cultivar ('AC Barrie'), planting a monoculture of a solid-stemmed cultivar ('AC Eatonia') increased yield by an average of 16% (0.4 mg ha(-1)) and increased the grade of wheat by one unit at the two most heavily infested site-years. Planting a 1:1 blend of AC Eatonia and AC Barrie increased yield by an average of 11%, whereas planting 20- or 40-m plot margins to AC Eatonia increased yield by an average of 8%. High wheat stem sawfly pressure limited the effectiveness of using resistant cultivars in field margins because plants were often infested beyond the plot margin, with uniform infestation down the length of the plots at the two most heavily infested site-years. The effectiveness of AC Eatonia to reduce wheat stem sawfly survivorship was modest in this study, probably due to weather-related factors influencing pith expression and to the high abundance of wheat stem sawfly. Greater benefits from planting field margins to resistant cultivars or planting a blend of resistant and susceptible cultivars might be achievable under lower wheat stem sawfly pressure.

Evaluation of crossability between triticale (X Triticosecale Wittmack) and common wheat, durum wheat and rye

Development of transgenic triticale as a platform for novel bio-industrial products is predicated on an environmental biosafety assessment that quantifies the potential risks associated with its release. Pollen-mediated gene flow to related species and conventional triticale varieties is one pathway for transgene movement. A tier 1 quantification of triticale hybridization was conducted by emasculating and hand pollinating flowers under greenhouse conditions. Approximately 2000 manual pollinations were conducted for each cross and its reciprocal between two triticale genotypes: a modern triticale cultivar (AC Alta) and primary triticale (89TT108), and common wheat, durum wheat and rye. The frequency of outcrossing, hybrid seed appearance and weight, and F(1) emergence and fertility were recorded. Outcrossing, F(1) emergence and fertility rates were high from crosses between triticale genotypes. Outcrossing in inter-specific crosses was influenced by the species, and the genotype and gender of the triticale parent. In crosses to common and durum wheat where triticale was the male parent, outcrossing was > or =73.0% and > or =69.5%, respectively, but < or =23.9% and < or =3.0% when triticale was the female parent. Overall, outcrossing with rye was lower than with common and durum wheat. F(1) hybrid emergence was greater when triticale was the female parent. With the exception of a single seed, all wheat-triticale F(1) hybrid seeds were non-viable when triticale was the male parent in the cross. Only seven durum wheat-triticale F(1) hybrids emerged from 163 seeds sown, and all were produced with triticale 89TT108 as female parent. With rye, 8 F(1) hybrids emerged from 38 seeds sown, and all were produced from crosses to AC Alta; five with AC Alta as the female parent and three as the male. Interspecific F(1) hybrids were self-sterile, with the exception of those produced in crosses between common wheat and triticale where triticale was the female parent. Tier 2 hybridization quantification will be conducted under field conditions.

Effect of wheat stem sawfly damage on yield and quality of selected Canadian spring wheat

The wheat stem sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae), has reached outbreak status at most locations in the southern Canadian prairies. Solid-stemmed wheat, Triticum aestivum L., cultivars, which are less susceptible to damage, remain the primary management option. This article quantifies the effect of wheat stem sawfly damage on grain yield and quality at harvest and determines how cultivar selection affects harvest losses. Solid-stemmed cultivars were compared with hollow-stemmed cultivars and with blends of a 1:1 ratio of each. The hollow-stemmed cultivars with the exception of'McKenzie', which had intermediate levels of stem cutting, were all significantly more susceptible to stem cutting than solid-stemmed cultivars. Cultivar blends had lower damage but were still significantly higher than the solid-stemmed cultivars. The solid-stemmed 'AC Eatonia' and 'AC Abbey' had the lowest levels of stem cutting and ranked second and third overall for yield in 2001 and 2002. McKenzie ranked first, which reflects its yield potential in combination with its partial resistance to stem cutting. Lower cutting in AC Eatonia, AC Abbey, McKenzie, and the blend of AC Abbey/ McKenzie was significantly correlated with lower grain losses. Grain lost at harvest has major economic implications if sawfly pressure is moderate to high and susceptible cultivars predominate.