Location: Hard Winter Wheat Genetics Research
2024 Annual Report
Objectives
OBJECTIVE 1: Characterize wheat genetic resources for priority traits including resistance to damaging fungal pathogens (stripe rust, leaf rust, stem rust, Fusarium head scab), resistance to viruses, resistance to Hessian fly and wheat stem sawfly, tolerance to heat stress, and nutritional quality.
Sub-Objective 1A: Characterize wheat genetic resources for resistance to stripe rust, leaf rust, and stem rust.
Sub-Objective 1B: Characterize wheat genetic resources for resistance to Fusarium head blight.
Sub-Objective 1C: Characterize wheat genetic resources for resistance to vectored viruses.
Sub-Objective 1D: Characterize wheat genetic resources for resistance to Hessian Fly and wheat stem sawfly.
Sub-Objective 1E: Characterize wheat genetic resources for tolerance to heat stress.
Sub-Objective 1F: Characterize wheat genetic resources for improved nutritional quality traits.
OBJECTIVE 2: Incorporate genetic traits into high yielding winter wheat germplasm and distribute germplasm to the breeding community.
Sub-Objective 2A: Incorporate resistance to stripe rust, leaf rust, and stem rust.
Sub-Objective 2B: Incorporate resistance to Fusarium head blight.
Sub-Objective 2C: Develop hard winter wheat germplasm with resistance to arthropod-vectored viruses.
Sub-Objective 2D: Incorporate new sources of genetic resistance to Hessian Fly and wheat stem sawfly.
Sub-Objective 2E: Incorporate tolerance to heat stress during grain development.
Sub-Objective 2F: Incorporate improved nutritional quality traits.
OBJECTIVE 3: Develop resource-efficient molecular marker technologies and bioinformatic tools for priority genetic traits and deploy these technologies for cultivar development.
Sub-Objective 3A: Develop new or improved trait-specific SNP-based markers for important genes.
Sub-Objective 3B: Develop and optimize new genome-wide multiplexed amplicon sequencing assay(s) and imputation protocols for gene postulation and genomic selection.
Sub-Objective 3C: Transfer genotyping data and information to the breeding community.
OBJECTIVE4: Characterize molecular foundations of critical plant-microbe and plant-insect interactions toward development of effective, durable host plant resistance in wheat.
Sub-Objective 4A: Identify Hessian fly effectors and their interacting targets in wheat.
Sub-Objective 4B: Characterize molecular foundations of virulence and resistance for leaf rust.
Sub-Objective 4C: Create new sources of resistance to Fusarium head blight.
Approach
Production of hard winter wheat on the Great Plains is constrained by recurring and intractable problems including diseases, insect pests, and heat stress. Nutrient deficiencies in grain affect nutritional quality of wheat food products. Our first objective is to identify germplasm with improved resistance to leaf rust, stripe rust, stem rust, Hessian fly, wheat stem sawfly, Fusarium head blight, and viruses; improved tolerance to heat stress; and increased grain protein, iron, and zinc concentrations. The second objective is to transfer these traits into adapted backgrounds and release new germplasm for use as parents in cultivar development. Our work will include a focused evaluation of the effects of new disease resistance traits on crop productivity. We will launch a novel application of a male-sterile recurrent selection population and our speed-breeding platform for a bulk selection project to improve grain filling and yield under heat stress. The third objective is to develop more efficient wheat breeding techniques using high-throughput genotyping technologies and large-scale data mining tools. New allele-specific PCR assays, multiplexed amplicon sequencing assays, and genomic databases will be developed and used to characterize breeding material for the presence of genes of interest. Phenotype and genotype data will be distributed to the breeding community through USDA-supported databases. The fourth objective is to characterize the molecular basis for interaction between wheat plants and the leaf rust and Fusarium head blight pathogens, and between wheat plants and the Hessian fly. Greater understanding of molecular foundations of host-pest interactions may lead to better strategies for durable resistance. This project directly supports and collaborates with public (CO, KS, MT, ND, NE, OK, SD, TX, USDA-ARS) and private hard winter wheat breeding programs. The ultimate beneficiaries of this project are wheat producers, grain handlers and the grain export industry, flour millers, bakers, and all who consume wheat.
Progress Report
Objective 1: Characterize wheat genetic resources for priority traits including resistance to damaging fungal pathogens including stripe rust (YR), leaf rust (LR), stem rust (SR), Fusarium head scab (FHB), resistance to viruses, resistance to Hessian fly (HF) and wheat stem sawfly, tolerance to heat stress, and nutritional quality. ARS researchers at Manhattan, Kansas, screened over 12,000 breeding lines for field resistance to YR in Rossville, Kansas. Trials included entries from regional nurseries, mapping populations, elite breeding lines from 14 public and private breeding programs and ARS germplasm in development. Over 2,200 breeding lines were screened for SR resistance in Manhattan, Kansas. Early natural SR infection near Castroville, Texas, enabled the evaluation of over 2,900 public and private breeding lines for stem rust resistance. In an inoculated nursery near Manhattan, Kansas, over 3,100 ARS breeding lines and breeding lines from public and private programs were evaluated for LR resistance. Over 5,000 lines were screened for HF resistance with the Kansas “Great Plains” biotype, and over 1,000 of these also were screened with a new biotype from Texas. Greenhouse testing of a set of durum landraces from the USDA-ARS National Small Grains Collection confirmed the value of CItr 17647 for resistance to both the Great Plains biotype and the new Texas biotype. A new source of HF resistance was identified Parvaz-94. Two genomic regions were identified in mapping, on the short arms of chromosomes 1A and 6B. Breeder-friendly DNA markers were developed for the two genes and can be used for marker-assisted selection in wheat breeding programs. Over 3,700 public and private breeding lines were evaluated for wheat streak mosaic virus resistance near Dighton, Kansas. Barley yellow dwarf virus (BYDV) resistance was evaluated in over 300 ARS breeding lines and in over 300 lines of a nested association mapping panel in early planted field trials near Manhattan, Kansas. ARS scientists in Manhattan, Kansas identified a genomic region associated with BYDV resistance (QByd.hwwg-2DL) from the U.S. hard winter wheat cultivar Jagger. This resistance gene consistently showed a major effect on BYDV resistance in three experiments and overlaps with the genes for thousand kernel weight, kernel area, kernel width, and kernel length in the same chromosome region. Tightly linked markers to the BYDV resistance were developed and breeders can use them for improvement of wheat BYDV resistance in wheat. Work continued to map the stripe rust resistance in cultivars Joe, Gallagher, Wesley, and SY Touchstone with resistance evaluation conducted both at Rossville, Kansas, and in Pullman and Mt. Vernon, Washington. Seed production was completed on two recombinant inbred populations developed to map the leaf rust and stripe rust resistance in the cultivar ‘SY Monument.’ And seed production was completed for a new association mapping panel of regional germplasm. FHB resistance was evaluated in over 500 ARS breeding lines and 300 breeding lines/cultivars in an association mapping panel in the field near Manhattan, Kansas. Wheat stem sawfly resistance was evaluated in over 600 ARS breeding lines in preliminary evaluation and 81 ARS breeding lines in replicated evaluation. Stem solidness evaluation was conducted in over 200 lines during the growing season. One family was identified from which five highly solid selections were identified. High throughput evaluation of wheat flour quality for breadmaking applications is critically needed. ARS scientists evaluated application of a machine learning algorithm to raw data from a new instrument, the GlutoPeak, for prediction of low-throughput Farinograph performance of flours from ARS wild emmer introgression germplasm. The 2.5-min GlutoPeak test can accurately classify flours into unacceptable/acceptable/excellent categories for Farinograph performance.
Objective 2: Incorporate resistance to stripe rust, leaf rust, and stem rust. Four breeding lines with the combination of two highly effective stripe rust resistance genes, Yr5 and Yr15, were entered in the Southern Regional Performance Nursery. These lines had excellent YR resistance and good to excellent yield performance in field trials. Lines also were tested in statewide yield trials in Oklahoma, Kansas, and Nebraska, in cooperation with public breeding programs. Breeding lines with YR resistance genes Yr47, Yr57, Yr63 and LR resistance genes Lr42 and Lr19 in combination with Bdv2 were evaluated in yield testing and distributed for regional breeder evaluation. Second backcrosses of adapted hard winter wheat cultivars TAM 114 and Skydance to recombinant hard winter wheat lines with a cassette of the stem rust resistance gene Sr2 in combination with the Fusarium head blight resistance gene Fhb1 were generated, and F2 seed produced. The first backcrosses of TAM 114 and Skydance to the Sr2-Fhb1 cassette lines were advanced to F3 with marker selection. This Sr2-Fhb1 cassette also was crossed with ARS germplasm carrying the new stripe rust gene Yr57 to initiate a project to couple Yr57 with the Sr2-Fhb1 cassette. Wheat germplasm with pyramids of three major Ug99 race complex effective SR genes, Sr22, Sr26 and Sr35, in genetic backgrounds adapted to southern Texas was evaluated in yield trials in Texas. The pyramid has expanded by backcrossing resistance genes Sr50 and SrTA10187 into Sr22+Sr26+Sr35 lines, and inbreeding with marker selection has continued through the F3 generation. Breeding germplasm in development was selected for wheat streak mosaic virus resistance in field trials near Dighton, Kansas. Sources of resistance included synthetic hexaploids, the Rec213 translocation for Wsm1, Wsm2, and Wsm3. Sib-pair selections with and without Wsm3 were multiplied in Arizona for yield trial evaluation in 2025. Yield evaluation of ARS germplasm in trial sites with wheat streak mosaic virus alone and in a mixed infection with Triticum mosaic virus confirmed the utility of ARS breeding line KS20U111616R3, which will be proposed for release in 2024. The dominant male sterile-facilitated recurrent selection populations for FHB resistance and heat stress tolerance were multiplied to prepare for germplasm release, and marker evaluations were initiated. High-temperature Hessian fly resistant breeding lines derived from crosses to durum landraces were evaluated in yield trials, and crosses were made to other sources of resistance present in elite lines from regional breeding programs. In cooperation with Colorado State University (CSU), three cycles of field selection under severe sawfly pressure were applied to breeding germplasm from wild emmer introgressions. Lines with very limited stem cutting and acceptable agronomic characteristics were evaluated in a replicated test at Akron, Colorado. Backcrosses and top-crosses of CSU germplasm to ARS sources of sawfly resistance were made and F2 seed produced, toward field selection for sawfly resistance. A dominant male sterile recurrent selection population incorporating both solid stem and non-solid stem sawfly resistance sources was initiated.
Objective 3: Develop resource-efficient molecular marker technologies and bioinformatic tools for priority genetic traits and deploy these technologies for cultivar development. We have analyzed over 10 short-read Illumina sequencing datasets of mapping populations and diversity populations, and 4 long-read genomic assemblies were generated. These data will be used to develop markers for breeders and targets for genomic editing projects to increase durability of resistance. We have also completed the third year of the diversity panel in the field for FHB phenotyping and will be analyzing the data for resistance and susceptibility regions. Once detected, we will develop markers for breeders to use to select for resistance. ARS scientists in Manhattan, Kansas, analyzed a total of 8,460 wheat samples for either singleplex or genome-wide multiplex markers. A total of 2784 samples were run with 981 single markers for different requests and generated 290,016 single marker datapoints for those requests. Genome-wide markers (genotyping-by-sequencing or multiplex restriction amplicon sequencing) was conducted on 4992 samples wheat samples that generated about 100 million datapoints. The commercial AgriSeq (ThermoFisher) genotyping platform was used to characterize 864 samples, generating about 4 million datapoints. Near-diagnostic KASP markers were developed and validated for Sr43, H13, Fhb9, the Jagger BYDV resistance, and the Parvaz-94 Hessian fly resistance.
Objective 4: Characterize molecular foundations of critical plant-microbe and plant-insect interactions toward development of effective, durable host plant resistance in wheat. Seven lines were identified as rust susceptibility mutants and RNA was isolated and exome sequenced (Sub Objective 4B.1). Lines were crossed to Kanmark and populations were moved through the F4 and F5 generation by single seed decent to develop near isogenic lines for genetic mapping. Once the chromosomal region is identified, mutant genes will be isolated. Transgenic and gene edited lines are being developed to verify one of these genes. A complete telomere to telomere, dikaryotic leaf rust genome was completed and annotated. A genetic map of virulence has been created which identified effector regions in the genome. These regions may contain virulent mutants, which have been identified for five leaf rust resistance genes. These have been sequenced and are being aligned to the new genome (Sub Objective 4B.2). Toward the development of new sources of FHB resistance (Sub-objective 4.C), one Jagger ethyl methanesulfonate mutant was sequenced, and genome assembly is in progress. Recombinant inbred lines from the Jagger mutant x Overley population were genotyped, and FHB resistance was evaluated under both field and greenhouse conditions.
Accomplishments
1. Validated effects of Fhb7 on Fusarium head blight resistance in wheat. ARS researchers in Manhattan, Kansas validated effects of Fhb7 is a gene for resistance to Fusarium head blight (FHB) that was transferred from a wheatgrass to wheat. A glutathione S-transferase (GST) gene was cloned as the candidate gene for Fhb7. ARS scientists in Manhattan, Kansas, evaluated Fhb7 near-isogenic lines and GST over-expressed transgenic lines for FHB resistance and confirmed that the lines with high GST expression had significantly higher FHB resistance. Knockout of GST in an Fhb7 resistant line using gene-editing significantly increased FHB susceptibility compared with the non-edited controls, confirming that GST is Fhb7 for FHB resistance. Breeders can pyramid Fhb7 with other major resistance sources to improve wheat FHB resistance.
2. Discovered that GH32 genes drive adaptation to diverse food sources in Hessian fly and other animals. ARS scientists in Manhattan, Kansas, discovered that some animal species including the Hessian fly have regained genes encoding glycoside hydrolase family 32 (GH32) enzymes via horizontal gene transfer. The regaining of the lost genes allows animals to use otherwise nutritially inaccessible fructans. The ability of animals like the Hessian fly to use fructans as nutrients from host plants results in rapid population expansion, which results in serious crop damage. The discovery of GH32 genes in Hessian fly and other animals may lead to novel strategies to control animal pests by incorporating GH32 enzyme inhibitors in crops.
3. Cloning a gene for wheat curl mite resistance in wheat. Wheat curl mite is a serious wheat pest that transmits wheat streak mosaic virus, thus causing significant wheat yield loss. Cmc4 is a highly effective wheat curl mite resistance gene. ARS Scientists in Manhattan, Kansas, cloned a Cmc4-associated gene that confers resistance by disrupting mite growth and causing mite death on wheat leaves. Diagnostic high-throughput genetic markers have been developed for selection of Cmc4 in wheat breeding programs developing commercial cultivars.
4. Developed and validated diagnostic markers for Rht8 in wheat. ARS researchers in Manhattan, Kansas, developed & validated Rht8, a reduced height (Rht) gene that does not reduce coleoptile length. This feature is critical for wheat emergence with deep planting with low soil moisture conditions. Rht8 recently was cloned by scientists working in China and it encodes a ribonuclease H-like (RNHL) superfamily protein. However, this gene has not been widely deployed in the United States due to a lack of diagnostic markers. ARS scientists in Manhattan, Kansas developed two breeder-friendly DNA markers based on the gene sequence and validated them to be diagnostic in a large hard winter wheat breeding panel. Wheat breeders can use these markers to accurately transfer Rht8 to the US wheat cultivars to breed semidwarf wheat cultivars.
5. Identified new genetic resources for Hessian fly resistance in wheat. Hessian fly can be a devastating pest of winter wheat production as it can result is substantial stand reduction and yield loss. Because the Hessian fly populations in the field rapidly evolve to overcome resistance genes, new sources of resistance continue to be needed. ARS Scientists in Manhattan, Kansas evaluated a global collection of wheat for resistance to the Kansas Hessian fly biotype, "Great Plains." New sources with resistance to Hessian fly were uncovered, which may be useful for future Hessian fly resistance breeding.
Review Publications
Xu, X., Mornhinweg, D.W., Bai, G., Li, G., Bian, R., Bernardo, A.E., Armstrong, J.S. 2023. Identification of a new Rsg1 allele conferring resistance to multiple greenbug biotypes from barley accessions PI 499276 and PI 566459. The Plant Genome. https://doi.org/10.1002/tpg2.20418.
Xu, X., Li, G., Bai, G., Bian, R., Bernardo, A.E., Kolmer, J.A., Carver, B.F., Wolabu, T.W., Wu, Y. 2024. Characterization of quantitative trait loci for leaf rust resistance in the Uzbekistani wheat landrace Teremai Bugdai. Phytopathology. 114:1373-1379. https://doi.org/10.1094/PHYTO-09-23-0320-R.
Xu, X., Li, G., Bai, G., Bian, R., Bernardo, A.E., Watira, T.W., Carver, B.F., Wu, Y., Elliott, N.C. 2024. Characterization of a new greenbug resistance gene Gb9 in a synthetic hexaploid wheat. Theoretical and Applied Genetics. 137. Article 140. https://doi.org/10.1007/s00122-024-04650-9.
Yulfo-Soto, G., McCormick, S., Hui, C., Bai, G., Trick, H.N., Hao, G. 2024. Reduction of Fusarium head blight and trichothecene contamination in transgenic wheat expressing Fusarium graminearum trichothecene 3-O-acetyltransferase. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2024.1389605.
Peirce, E.S., Evers, B., Raupp, J.W., Guttieri, M.J., Poland, J., Akhunov, E., Broeckling, C., Haley, S., Mason, E., Nachappa, P. 2024. Identifying novel sources of resistance to wheat stem sawfly in five wild wheat species. Pest Management Science. https://doi.org/10.1002/ps.8008.
Miner, G.L., Stewart, C.E., Delgado, J.A., Ippolito, J.A., Mason, R.E., Haley, S.D., Guttieri, M.J., Ainsworth, E.A., McGrath, J.M., Beebout, S.E. 2024. Global change impacts on mineral nutritional quality of cereal grains: Coordinated datasets and analyses to advance a systems-based understanding. Field Crops Research. 310. Article e109338. https://doi.org/10.1016/j.fcr.2024.109338.
Chahal, S.K., Hettiarachchi, G.M., Nelson, N., Guttieri, M.J. 2023. Fate and plant uptake of different zinc fertilizer sources upon their application to an alkaline calcareous soil. American Journal of Agricultural Science and Technology. 3:725-737. https://doi.org/10.1021/acsagscitech.2c00287.
Wang, H., Bernardo, A.E., St. Amand, P.C., Bai, G., Bowden, R.L., Guttieri, M.J., Jordan, K. 2023. Skim exome capture genotyping in wheat. The Plant Genome. 16(4). Article.e20381. https://doi.org/10.1002/tpg2.20381.