Bearded or smooth? Awns improve yield when wheat experiences heat stress during grain fill in the southeastern United States.

The presence or absence of awns-whether wheat heads are 'bearded' or 'smooth' - is the most visible phenotype distinguishing wheat cultivars. Previous studies suggest that awns may improve yields in heat or water-stressed environments, but the exact contribution of awns to yield differences remains unclear. Here we leverage historical phenotypic, genotypic, and climate data for wheat (Triticum aestivum) to estimate the yield effects of awns under different environmental conditions over a 12-year period in the southeastern USA. Lines were classified as awned or awnless based on sequence data, and observed heading dates were used to associate grain fill periods of each line in each environment with climatic data and grain yield. In most environments, awn suppression was associated with higher yields, but awns were associated with better performance in heat-stressed environments more common at southern locations. Wheat breeders in environments where awns are only beneficial in some years may consider selection for awned lines to reduce year-to-year yield variability, and with an eye towards future climates.

Sustaining productivity gains in the face of climate change: A research agenda for US wheat.

Wheat is a globally important crop and one of the "big three" US field crops. But unlike the other two (maize and soybean), in the United States its development is commercially unattractive, and so its breeding takes place primarily in public universities. Troublingly, the incentive structures within these universities may be hindering genetic improvement just as climate change is complicating breeding efforts. "Business as usual" in the US public wheat-breeding infrastructure may not sustain productivity increases. To address this concern, we held a multidisciplinary conference in which researchers from 12 US (public) universities and one European university shared the current state of knowledge in their disciplines, aired concerns, and proposed initiatives that could facilitate maintaining genetic improvement of wheat in the face of climate change. We discovered that climate-change-oriented breeding efforts are currently considered too risky and/or costly for most university wheat breeders to undertake, leading to a relative lack of breeding efforts that focus on abiotic stressors such as drought and heat. We hypothesize that this risk/cost burden can be reduced through the development of appropriate germplasm, relevant screening mechanisms, consistent germplasm characterization, and innovative models predicting the performance of germplasm under projected future climate conditions. However, doing so will require coordinated, longer-term, inter-regional efforts to generate phenotype data, and the modification of incentive structures to consistently reward such efforts.

Genetic Trends in Fusarium Head Blight Resistance from 20 Years of Winter Wheat Breeding and Cooperative Testing in the Northern U.S.A.

Fusarium head blight (FHB) is a devastating disease of wheat and barley. In the U.S.A., a significant long-term investment in breeding FHB-resistant cultivars began after the 1990s. However, to this date, no study has been performed to understand and monitor the rate of genetic progress in FHB resistance as a result of this investment. Using 20 years of data (1998 to 2018) from the Northern Uniform and Preliminarily Northern Uniform winter wheat scab nurseries that consisted of 1,068 genotypes originating from nine different institutions, we studied the genetic trends in FHB resistance within the northern soft red winter wheat growing region using mixed model analyses. For the FHB resistance traits incidence, severity, Fusarium-damaged kernels, and deoxynivalenol content, the rate of genetic gain in disease resistance was estimated to be 0.30 ± 0.1, 0.60 ± 0.09, and 0.37 ± 0.11 points per year, and 0.11 ± 0.05 parts per million per year, respectively. Among the five FHB-resistance quantitative trait loci assayed for test entries from 2012 to 2018, the frequencies of favorable alleles from Fhb 2DL Wuhan1 W14, Fhb Ernie 3Bc, and Fhb 5A Ning7840 were close to zero across the years. The frequency of the favorable at Fhb1 and Fhb 5A Ernie ranged from 0.08 to 0.33 and 0.06 to 0.20, respectively, across years, and there was no trend in changes in allele frequencies over years. Overall, this study showed that substantial genetic progress has been made toward improving resistance to FHB. It is apparent that today's investment in public wheat breeding for FHB resistance is achieving results and will continue to play a vital role in reducing FHB levels in growers' fields.

Genomic selection for wheat traits and trait stability.

KEY MESSAGE: Based on the estimates of accuracy, genomic selection would be useful for selecting for improved trait values and trait stability for agronomic and quality traits in wheat. Trait values and trait stability estimated by two methods were generally independent indicating a breeder could select for both simultaneously. Genomic selection (GS) is a new marker-assisted selection tool for breeders to achieve higher genetic gain faster and cheaper. Breeders face challenges posed by genotype by environment interaction (GEI) pattern and selecting for trait stability. Obtaining trait stability is costly, as it requires data from multiple environments. There are few studies that evaluate the efficacy of GS for predicting trait stability. A soft winter wheat population of 273 lines was genotyped with 90 K single nucleotide polymorphism markers and phenotyped for four agronomic and seven quality traits. Additive main effect and multiplicative interaction (AMMI) model and  Eberhart and Russell regression (ERR) were used to estimate trait stability. Significant GEI variation was observed and stable lines were identified for all traits in this study. The accuracy of GS ranged from 0.33 to 0.67 for most traits and trait stability. Accuracy of trait stability was greater than trait itself for yield (0.44 using AMMI versus 0.33) and heading date (0.65 using ERR versus 0.56). The opposite trend was observed for the other traits. GS did not predict the stability of the quality traits except for flour protein, lactic acid and softness equivalent. Significant GS accuracy for some trait stability indicated that stability was under genetic control for these traits. The magnitude of GS accuracies for all the traits and most of the trait stability index suggests the possibility of rapid selection for these trait and trait stability in wheat breeding.

Identification of milling and baking quality QTL in multiple soft wheat mapping populations.

KEY MESSAGE: Two mapping approaches were use to identify and validate milling and baking quality QTL in soft wheat. Two LG were consistently found important for multiple traits and we recommend the use marker-assisted selection on specific markers reported here. Wheat-derived food products require a range of characteristics. Identification and understanding of the genetic components controlling end-use quality of wheat is important for crop improvement. We assessed the underlying genetics controlling specific milling and baking quality parameters of soft wheat including flour yield, softness equivalent, flour protein, sucrose, sodium carbonate, water absorption and lactic acid, solvent retention capacities in a diversity panel and five bi-parental mapping populations. The populations were genotyped with SSR and DArT markers, with markers specific for the 1BL.1RS translocation and sucrose synthase gene. Association analysis and composite interval mapping were performed to identify quantitative trait loci (QTL). High heritability was observed for each of the traits evaluated, trait correlations were consistent over populations, and transgressive segregants were common in all bi-parental populations. A total of 26 regions were identified as potential QTL in the diversity panel and 74 QTL were identified across all five bi-parental mapping populations. Collinearity of QTL from chromosomes 1B and 2B was observed across mapping populations and was consistent with results from the association analysis in the diversity panel. Multiple regression analysis showed the importance of the two 1B and 2B regions and marker-assisted selection for the favorable alleles at these regions should improve quality.

Molecular characterization of field resistance to Fusarium head blight in two US soft red winter wheat cultivars.

In the soft red winter wheat (Triticum aestivum L.) regions of the US, Fusarium head blight (FHB, caused by Fusarium spp.) resistance derived from locally adapted germplasm has been used predominantly. Two soft red winter wheat cultivars, Massey and Ernie, have moderate resistance to FHB. Mapping populations derived from Becker/Massey (B/M) and Ernie/MO 94-317 (E/MO) were evaluated for FHB resistance and other traits in multiple environments. Eight QTL in B/M and five QTL in E/MO were associated with FHB variables including incidence, severity (SEV), index (IND), Fusarium damaged kernels (FDK), deoxynivalenol (DON), and morphological traits flowering time and plant height. Four QTL were common to both populations. Three of them were located at or near known genes: Ppd-D1 on chromosome 2DS, Rht-B1 on 4BS, and Rht-D1 on 4DS. Alleles for dwarf plant height (Rht-B1b and Rht-D1b) and photoperiod insensitivity (Ppd-D1a) had pleiotropic effects in reducing height and increasing FHB susceptibility. The other QTL detected for FHB variables were on 3BL in both populations, 1AS, 1DS, 2BL, and 4DL in B/M, and 5AL (B1) and 6AL in E/MO. The additive effects of FHB variables ranged from 0.4 mg kg(-1) of DON to 6.2 % for greenhouse (GH) SEV in B/M and ranged from 0.3 mg kg(-1) of DON to 8.3 % for GH SEV in E/MO. The 4DS QTL had epistasis with Ppd-D1, Qdon.umc-6AL, and Qht.umc-4BS, and additive × additive × environment interactions with the 4BS QTL for SEV, IND, and FDK in E/MO. Marker-assisted selection might be used to enhance FHB resistance through selection of favorable alleles of significant QTL, taking into account genotypes at Rht-B1b, Rht-D1a and Ppd-D1a.

Genetic Variation and Heritability of Sensory and Artisan Bread Traits in a Set of SRW Wheat Breeding Lines.

Focus on local food production and supply chains has heightened in recent years, as evidenced and amplified by the COVID-19 pandemic. This study aimed to assess the suitability of soft red winter (SRW) wheat breeding lines for local artisan bakers interested in locally sourced, strong gluten wheat for bread. Seventy-six genotyped SRW wheat breeding lines were milled into whole wheat flour and baked into small loaves. Bread aroma, flavor, and texture were evaluated by a sensory panel, and bread quality traits, including sedimentation volume, dough extensibility, and loaf volume, were measured to estimate heritability. SE-HPLC was performed on white flour, and breeding lines were characterized for different protein fraction ratios. Heritability of loaf volume was moderately high (h2 = 0.68), while heritability of sedimentation volume, a much easier trait to measure, was slightly lower (h2 = 0.55). Certain protein fraction ratios strongly related to loaf volume had high heritability (h2 = 0.7). Even though only a moderate heritability estimate of dough extensibility was found in our study, high positive correlations were found between this parameter and sedimentation volume (r = 0.6) and loaf volume (r = 0.53). This low-input and highly repeatable parameter could be useful to estimate dough functionality characteristics. Flavor and texture heritability estimates ranged from 0.16 to 0.37, and the heritability estimate of aroma was not significantly different from zero. However, the sensorial characteristics were significantly correlated with each other, suggesting that we might be able to select indirectly for aroma by selecting for flavor or texture characteristics. From a genome-wide association study (GWAS), we identified six SNPs (single nucleotide polymorphisms) associated with loaf volume that could be useful in breeding for this trait. Producing high-quality strong gluten flour in our high rainfall environment is a challenge, but it provides local growers and end users with a value-added opportunity.

Integrating Management Practices to Decrease Deoxynivalenol Contamination in Soft Red Winter Wheat.

Fusarium graminearum, the major causal agent of Fusarium head blight (FHB) of wheat (Triticum aestivum) in the U.S., can produce mycotoxins, such as deoxynivalenol (DON), during infection. Contamination of wheat grain with DON is a major concern for wheat producers and millers, and the U.S. Food and Drug Administration (FDA) has set advisory levels for DON in finished wheat products for human and animal consumption. Practices utilized to manage FHB and DON contamination include planting wheat cultivars with moderate resistance to FHB and applying efficacious fungicides at the beginning of anthesis. Under severe epidemics, DON contamination can exceed FDA advisory levels despite implementation of these measures. Additionally, fungicide efficacy can be limited when anthesis is not uniform among plants in the field, which can occur when planting is delayed or if there is non-uniform seedling establishment. The objectives of this study were to evaluate the effect of (1) in-furrow phosphorus application at planting and seeding rate on heading and anthesis uniformity, FHB symptomology, DON contamination, grain yield, yield components, and test weight; and (2) harvesting at different grain moisture concentrations on FHB symptomology, DON contamination, grain yield and test weight. Field trials were established in Princeton, Kentucky, from 2017 to 2019, to evaluate in-furrow phosphorus application at planting (0 kg P2O5 ha-1 and 47 kg P2O5 ha-1); seeding rate (377 live seeds m-2 and 603 live seeds m-2); and grain moisture at harvest (20 to 22% and 13 to 15%). In-furrow phosphorus increased grain yield and spikes m-2, but had no effect on heading and anthesis uniformity or DON contamination. The 603 live seeds m-2 seeding rate decreased the number of days to Zadoks 60 for the November planted wheat, and decreased FHB incidence, but did not decrease DON contamination. Harvesting at 20 to 22% grain moisture decreased Fusarium damaged kernel ratings and percent kernel infection but increased DON contamination in the harvested grain. Although in-furrow phosphorus, seeding rate, and harvesting 20 to 22% grain moisture did not decrease DON contamination, there is potential for these treatments to alleviate negative effects of late planted wheat grown in stressful environments.

Optical Sorter-Based Selection Effectively Identifies Soft Red Winter Wheat Breeding Lines With Fhb1 and Enhances FHB Resistance in Lines With and Without Fhb1.

Previous results from our lab have shown that using an optical sorter to identify Fusarium head blight (FHB) resistant breeding lines was effective at reducing the toxin deoxynivalenol (DON) and FHB-associated kernel damage. In this paper we quantified the proportion of desirable genotypes at FHB resistance QTL in lines from three selection cycles of optical sorting. Breeding lines were genotyped at loci on chromosomes 3BS, 2DL, and 5A using the following DNA markers: TaHRC, CFD233, and GWM304. TaHRC is a KASP marker for Fhb1, a major FHB resistance QTL on chromosome 3BS. CFD233 is an SSR marker for Qfhs.nau-2DL on chromosome 2DL. GWM304 is an SSR marker for Qfhs.ifa-5A on chromosome 5A. Sorter selection was effective at identifying lines that had the resistant genotype at TaHRC; in other words, the sorter was able to identify lines with resistance alleles at Fhb1. The sorter was less effective at selecting for the resistant genotype at CFD233 and GWM304. However, the proportion of lines with resistant genotypes at GWM304 did increase with additional sorter selection, just not to the degree that was observed for the Fhb1-associated marker. The proportion of lines with resistant alleles at CFD233 did not show a consistent trend. In addition to increasing the proportion of lines with Fhb1 and Qfhs.ifa-5A each selection cycle, optical sorter-based mass selection enhanced FHB resistance in different marker genotype combinations evaluated in this study. For example, there were net reductions in DON and kernel damage after two cycles of sorter selection in 15X110601S07002, a line with Fhb1, with Qfhs.nau-2DL, and with Qfhs.ifa-5A; final C3 DON levels were 63% of the resistant check (KY02C-3005-25). Kernel damage was also reduced in 15X110601A08221 a line without Fhb1, without Qfhs.nau-2DL, and without Qfhs.ifa-5A. Our findings suggest the increased resistance observed in different marker genotype combinations was conferred by QTL other than Fhb1, QFhs.nau-2DL, and Qfhs.ifa-5, and validate our previous results that the optical sorter is effective at selecting FHB-resistant breeding material.

Training Population Design With the Use of Regional Fusarium Head Blight Nurseries to Predict Independent Breeding Lines for FHB Traits.

Fusarium head blight (FHB) is a devastating disease in cereals around the world. Because it is quantitatively inherited and technically difficult to reproduce, breeding to increase resistance in wheat germplasm is difficult and slow. Genomic selection (GS) is a form of marker-assisted selection (MAS) that simultaneously estimates all locus, haplotype, or marker effects across the entire genome to calculate genomic estimated breeding values (GEBVs). Since its inception, there have been many studies that demonstrate the utility of GS approaches to breeding for disease resistance in crops. In this study, the Uniform Northern (NUS) and Uniform Southern (SUS) soft red winter wheat scab nurseries (a total 452 lines) were evaluated as possible training populations (TP) to predict FHB traits in breeding lines of the UK (University of Kentucky) wheat breeding program. DON was best predicted by the SUS; Fusarium damaged kernels (FDK), FHB rating, and two indices, DSK index and DK index were best predicted by NUS. The highest prediction accuracies were obtained when the NUS and SUS were combined, reaching up to 0.5 for almost all traits except FHB rating. Highest prediction accuracies were obtained with bigger TP sizes (300-400) and there were not significant effects of TP optimization method for all traits, although at small TP size, the PEVmean algorithm worked better than other methods. To select for lines with tolerance to DON accumulation, a primary breeding target for many breeders, we compared selection based on DON BLUES with selection based on DON GEBVs, DSK GEBVs, and DK GEBVs. At selection intensities (SI) of 30-40%, DSK index showed the best performance with a 4-6% increase over direct selection for DON. Our results confirm the usefulness of regional nurseries as a source of lines to predict GEBVs for local breeding programs, and shows that an index that includes DON, together with FDK and FHB rating could be an excellent choice to identify lines with low DON content and an overall improved FHB resistance.

Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia.

Grain yield is a trait of paramount importance in the breeding of all cereals. In wheat (Triticum aestivum L.), yield has steadily increased since the Green Revolution, though the current rate of increase is not forecasted to keep pace with demand due to growing world population and increasing affluence. While several genome-wide association studies (GWAS) on yield and related component traits have been performed in wheat, the previous lack of a reference genome has made comparisons between studies difficult. In this study, a GWAS for yield and yield-related traits was carried out on a population of 322 soft red winter wheat lines across a total of four rain-fed environments in the state of Virginia using single-nucleotide polymorphism (SNP) marker data generated by a genotyping-by-sequencing (GBS) protocol. Two separate mixed linear models were used to identify significant marker-trait associations (MTAs). The first was a single-locus model utilizing a leave-one-chromosome-out approach to estimating kinship. The second was a sub-setting kinship estimation multi-locus method (FarmCPU). The single-locus model identified nine significant MTAs for various yield-related traits, while the FarmCPU model identified 74 significant MTAs. The availability of the wheat reference genome allowed for the description of MTAs in terms of both genetic and physical positions, and enabled more extensive post-GWAS characterization of significant MTAs. The results indicate a number of promising candidate genes contributing to grain yield, including an ortholog of the rice aberrant panicle organization (APO1) protein and a gibberellin oxidase protein (GA2ox-A1) affecting the trait grains per square meter, an ortholog of the Arabidopsis thaliana mother of flowering time and terminal flowering 1 (MFT) gene affecting the trait seeds per square meter, and a B2 heat stress response protein affecting the trait seeds per head.

Breeding for resilience to increasing temperatures: A field trial assessing genetic variation in soft red winter wheat.

Breeding for resilience to climate change is a daunting prospect. Crop and climate models tell us that global wheat yields are likely to decline as the climate warms, causing a significant risk to global food security. High temperatures are known to affect crop development yet breeding for tolerance to heat stress is difficult to achieve in field environments. We conducted an active warming study over two years to quantify the effects of heat stress on genetic variation of soft red winter (SRW) wheat (Triticum aestivum L.). Forty SRW cultivars and breeding lines were chosen based on marker genotypes at photoperiod sensitivity and reduced height loci. These genotypes were planted in a randomized complete block design replicated twice across two environments, ambient and artificially warmed. Average heading date occurred 5 days earlier in the warmed environment than in the ambient environment over both years (p ≤ 0.05). On average, grain yield was significantly reduced in the warmed environment by 211.41 kg/ha (p ≤ 0.05) or 4.84%, though we identified 13 genotypes with increased yield in response to warming in both years. Of these genotypes, eight had significantly increased N uptake while six showed significantly increased N utilization efficiency under warming. Under warming, genotypes with wild-type alleles at the Rht-D1 locus display significantly greater yields (p ≤ 0.01) and biomass (p ≤ 0.001) than genotypes with reduced height alleles. Of the 13 genotypes with higher (p ≤ 0.01) yields under warming, nine have the wild-type allele at the Rht-D1 locus in addition to being photoperiod insensitive. The next steps will be to validate these findings in other populations and to develop an efficient breeding/phenotyping scheme that will lead to more resilient cultivars.

Identifying Rare FHB-Resistant Segregants in Intransigent Backcross and F2 Winter Wheat Populations.

Fusarium head blight (FHB), caused mainly by Fusarium graminearum Schwabe [telomorph: Gibberella zeae Schwein.(Petch)] in the US, is one of the most destructive diseases of wheat (Triticum aestivum L. and T. durum L.). Infected grain is usually contaminated with deoxynivalenol (DON), a serious mycotoxin. The challenge in FHB resistance breeding is combining resistance with superior agronomic and quality characteristics. Exotic QTL are widely used to improve FHB resistance. Success depends on the genetic background into which the QTL are introgressed, whether through backcrossing or forward crossing; QTL expression is impossible to predict. In this study four high-yielding soft red winter wheat breeding lines with little or no scab resistance were each crossed to a donor parent (VA01W-476) with resistance alleles at two QTL: Fhb1 (chromosome 3BS) and QFhs.nau-2DL (chromosome 2DL) to generate backcross and F2 progeny. F2 individuals were genotyped and assigned to 4 groups according to presence/ absence of resistance alleles at one or both QTL. The effectiveness of these QTL in reducing FHB rating, incidence, index, severity, Fusarium-damaged kernels (FDK) and DON, in F2-derived lines was assessed over 2 years. Fhb1 showed an average reduction in DON of 17.5%, and conferred significant resistance in 3 of 4 populations. QFhs.nau-2DL reduced DON 6.7% on average and conferred significant resistance in 2 of 4 populations. The combination of Fhb1 and QFhs.nau-2DL resistance reduced DON 25.5% across all populations. Double resistant lines had significantly reduced DON compared to double susceptible lines in 3 populations. Backcross derived progeny were planted in replicated yield trials (2011 and 2012) and in a scab nursery in 2012. Several top yielding lines performed well in the scab nursery, with acceptable DON concentrations, even though the average effect of either QTL in this population was not significant. Population selection is often viewed as an "all or nothing" process: if the average resistance level is insufficient, the population is discarded. These results indicate that it may be possible to find rare segregants which combine scab resistance, superior agronomic performance and acceptable quality even in populations in which the average effect of the QTL is muted or negligible.