Research Project: Genetic Improvement of Wheat and Barley for Environmental Resilience, Disease Resistance, and End-use Quality

Location: Wheat Health, Genetics, and Quality Research

2023 Annual Report

Objectives
The long-term objective of this project is to improve the resilience of wheat plants under environmental stress. Specifically, during the next five years we will focus on the following objectives. Objective 1. Genetically improve soft white winter and club wheat for environmental resilience, disease resistance, and end-use quality. Subobjective 1A: Develop and release club (Triticum aestivum ssp. compactum) wheat cultivars with resistance to major regional diseases and adaptation to diverse environments in the western U.S. Subobjective 1B: Select breeding lines with better end-use quality and high Falling Numbers (FN) due to preharvest sprouting (PHS) and late maturity alpha-amylase (LMA) resistance. Subobjective 1C: Select soft white wheat breeding lines using indirect selection based on high throughput phenotyping (HTP) targeted to specific combinations of climate variables. Objective 2. Identify genetic resources and introgress multiple genes for resistance to stripe rust and to soil borne diseases into wheat germplasm. Subobjective 2A: Identify novel genetic resources with resistance to stripe rust and soil borne disease and identify loci controlling this resistance. Subobjective 2B: Introgress novel sources of resistance to stripe rust and soil borne disease from landraces into adapted wheat germplasm. Subobjective 2C: Conduct collaborative pre-breeding to introgress disease resistance from multiple germplasm accessions into adapted germplasm. Objective 3. Develop, evaluate, and use genotyping technologies and sequence information to increase knowledge of basic genetic processes controlling environmental resilience, disease resistance, and end-use quality in wheat and barley. Subobjective 3A: Identify genetic and molecular mechanisms that regulate response to low temperatures. Subobjective 3B: Identify genetic and molecular mechanisms controlling seed dormancy, germination, and resistance to preharvest sprouting. Subobjective 3C: Identify genetic and molecular mechanisms causing late-maturity alpha amylase expression during grain development. Subobjective 3D: Identify genetic mechanisms for resistance to disease. Objective 4. Incorporate genomic data in wheat and barley selection strategies by collaborating with regional breeding programs. Subobjective 4A: Develop molecular methods for use in genome wide association (GWAS), genomic selection, and transcriptomic strategies to evaluate wheat and barley germplasm. Subobjective 4B: Develop bioinformatic pipelines to facilitate use of genomic data in wheat and barley improvement. Subobjective 4C: Provide genomic and phenotypic data to Western Regional and U.S. Wheat and Barley improvement programs.

Approach
Subobjective 1A: Doubled haploids, genomic selection, and high throughput phenotying are used to increase gains from selection targeted to dry or high rainfall environments in the USDA-ARS club wheat breeding program. Subobjective 1B: Selection for preharvest sprouting and late maturity alpha-amylase resistance based on phenotypic and genotypic data identifes wheat breeding lines with stable high falling number. Tools and tests are developed to detect low falling number wheat, and to distinguish between late maturity alpha amylase and preharvest sprouting. Controlled environment and field-based screening systems are optimized. Plant genetic, biochemical and physiological components associated with low falling numbers are investigated, including the protein biochemistry of alpha amylase, and hydrolytic enzymes expressed during wheat grain development and gation. Subobjective 1C: Genomic selection, high throughput phenotyping and meta-environmental analylsis are used to increase the accuracy breeding program data. Genome estimated breeding values are calculated for soft white and club wheat. Subobjectives 2A and 2B: Dominant male sterility, marker-assisted selection and phenotypic selection are used to incorporate new sources of resistance to stripe rust and to soil borne disease into adapted backcross populations of wheat.Subobjective 2C: F4 bulk populations are developed and selected for adult plant resistance to stripe rust in collaboration with U.S. wheat breeders, followed by selection for agronomic traits and re-evaluation for resistance. Subobjective 3A: Genes, identified from expression studies that contribute to low temperature tolerance, are combined to increase the level of low temperature tolerance in wheat. Subobjective 3B: Preharvest sprouting resistance is increased when mutant alleles associated with altered hormone sensitivity are combined to provide increased seed dormancy. Markers linked to emergence traits are developed. Subobjective 3C: A genome wide association study for resistance to late maturity alpha amylase is conducted, near isogenic lines differing for susceptibility loci are developed and breeding populations are screened in collaboration with wheat breeders. Subobjective 3D: The functional gene for stripe rust resistance is identified using a knock out of that resistance in an EMS-mutagenized population. Subobjective 4A: Targeted amplicon sequencing of at least 1500 known informative markers that are important for selection in western U.S. breeding programs is used to genotype breeding lines. Subobjective 4B: Software tools are developed to apply genomic data to crop improvement. Subobjective 4C: Genomic and phenomic data are provided to public and private sector participants in the Western Regional Cooperative Nurseries and the Western Regional Small Grains Genotyping Laboratory.

Progress Report
This is the final report for project 2090-21000-033-000D, entitled “Genetic Improvement of Wheat and Barley for Environmental Resilience, Disease Resistance, and End-use Quality”, which expired started in March 2023, and has been replaced by new Project 2090-21000-039-000D, titled “Wheat and Barley Adaptation to a Changing Climate - Discovery of Genetic and Physiological Processes for Improved Crop Productivity and Quality". Progress was made on all four objectives. For Objective 1, ARS researchers in Pullman, Washington, developed and released the club wheat cultivar, 'Castella' for the intermediate rainfall production region and the club cultivar 'Cameo' was developed and released for the high rainfall production region and crop registration articles were published. Club wheat cultivars from the USDA-ARS breeding program are grown on over 85% of all club wheat acreage and Pritchett club wheat (released in 2017) was the no. 1 club wheat grown. Additionally, climate change effects on crop performance were investigated using historical variety trial data and an analysis pipeline was developed and used to characterize crop performance for spring wheat in southern Idaho. As well, carbon isotope discrimination and Root traits were characterized in spring wheat populations in response to drought in the Pacific Northwest (PNW). These traits showed inconsistent responses related to the timing and severity of drought. Genetic loci affecting preharvest sprouting were identified in soft white winter wheat. The following research was also accomplished by ARS researchers under Objective 1. A method of evaluating late maturity alpha amylase (LMA) in the field was developed to facilitate breeding for reduced LMA and genetic loci affecting late maturity alpha amylase were identified in hard red spring wheat. New statistical methodology identified wheat cultivars with stable high falling numbers and cultivars with stable high resistance to low falling number were identified in northwestern U.S. winter and spring wheat cultivars. Falling numbers data was analyzed from Washington Wheat Variety Trials and posted on the Falling Numbers web site and used by elevators and growers for cultivar choice and risk management. Data is available from 2013 at http://steberlab.org/project7599.php. For Objective 2, ARS researchers accomplished the following. A novel source of Cereal Cyst nematode (Heterodera avenae and H. filipjevi) resistance on the D-genome was identified in the DNAM population. Molecular markers for adult plant resistance to stripe rust were identified in winter and in spring wheat adapted to the PNW, and germplasm with novel combinations of multiple stripe rust resistance genes was developed. Additionally, in order to better manage stripe rust resistance, genetic variation within the causal pathogen, Puccinia striiformis, was studied via sequencing and genotyping, resulting in the identification of three major population subgroups and indication of dynamic and rapid ability to change to overcome resistance genes. Also, multiple new loci for resistance to barley net blotch, caused by Pyrenophora teres f. teres and P. teres f. maculatam, were identified in a barley landrace collection. Over 1,800 wheat breeding lines per year have been evaluated for 19 public and private sector wheat breeding programs in the United States, since 2015. Collaborators in Louisiana, Indiana and Oklahoma discovered a high degree of correlation between rankings of breeding lines rated in Eastern Washington and in the rest of the United States. Data was summarized each year, returned to individual breeding programs, and incorporated into breeder selection strategies for improved wheat varieties. In support of Objective 3, ARS researchers developed a perfect marker for the enhanced response to ABA-8 (ERA8) allele, a new source of resistance to preharvest sprouting in wheat. The marker is being used to introgress this gene into soft white winter wheat. As well, two bi-parental populations were evaluated for late-maturity alpha-amylase and molecular markers were identified for resistance. Additionally, the falling number method was improved and alternative methods to detect alpha amylase were developed. Also in support of Objective 3, ARS researchers determined that the plant hormone, gibberellin (GA), stimulates developmental transitions including seed germination, flowering, and the transition from juvenile to adult growth stage. Interactions between GA and the GA receptor GID1 (GA-INSENSITIVE DWARF1) have been determined to regulate embryo-to-seedling transition prior to emergence from the seed coat in Arabidopsis. Exogenous GA was applied as a seed treatment on multiple wheat genotypes with differential emergence revealing that GA interacted with the wheat sub-crown internode elongation even when the GA insensitive reduced height alleles, Rht-B1b and Rht-D1b, were present. For Objective 4, ARS researchers incorporated genomic data into wheat and barley selection strategies by collaborating with regional breeding programs. A new genotyping technology, GMS, was developed and used to identify multiple known genes in barley. Changes in genetic diversity in wheat were also examined over time to determine if diversity remained for major economic traits. As well, under Objective 4, four western regional cooperative nurseries were organized, and materials were evaluated for resistance to multiple diseases and agronomic characteristics. The results have been posted to the following website: https://www.ars.usda.gov/pacific-west-area/pullman-wa/whgq/research/western-regional-nurseries/. Finally, exome capture was performed on sets of breeding lines and cultivars contributed by regional breeders. The results were distributed to breeders and incorporated into selection strategies.

Accomplishments
1. BRIDGE-cereal web app developed. A pan-genome with high quality gene assemblies from diverse crop varieties is shifting the biology research paradigm. Although the pan-genomes have been made publicly available after publication, leveraging these pan-genome remains challenging for most of scientists. ARS researchers in Pullman, Washington, developed two novo unsupervised machine learning algorithms, CHOICE and CLIPS, to overcome these challenges. Based on these two algorithms, ARS researchers further constructed a publicly accessible webapp, BRIDGEcereal (https://bridgecereal.scinet.usda.gov/) to provide a one-stop gateway to mine pan-genomes from five major cereal crops (approximately 120 assemblies). With this webapp, the only requirement for mining pan-genomes is the gene model ID to determine patterns of variants for a gene of interest. The BRIDGEcereal app is routinely accessed by worldwide users. Several major cereal genome databases hosted and maintained by USDA, ARS, including GrainGenes, MaizeGDB, and Sorghumbase, have added the link pointing to BRIDGEcereal. Scientists from MaizeGDB requested an in-depth collaboration to further incorporate CHOICE and CLIPS algorithms into MaizeGDB architecture.

2. Vivipary occurring in wheat grains contributes to low falling number. Farmers are assessed severe discounts for grain with low falling number (FN), an indicator that grain contains sufficiently elevated levels of the starch-digesting enzyme alpha-amylase which poses a risk to end-product quality and occurs due to preharvest sprouting and to late maturity alpha amylase. ARS researchers in Pullman, Washington, identified an additional cause, vivipary, which is visible sprouting occurring on immature grain. Experiments under controlled environmental conditions revealed that vivipary was more strongly induced under the cooler conditions (18°C day/7.5°C night) than warmer conditions (25°C day/18°C night). Investigation of the genetic causes of vivipary need to be considered when selecting wheat varieties for higher falling numbers. This knowledge is used by plant breeders and the grain industry to select for genetic resistance to low falling number, to schedule irrigation and manage grain for export customers.

3. Confirmation that TAMFT-3A and TAMFT-3B2 homeologs are associated with wheat preharvest sprouting. Farmers receive severe discounts for grain with low falling number caused by preharvest sprouting. ARS scientists in Pullman, Washington, collaborated with ARS researchers in Montana, to investigate the genetic control of preharvest sprouting in winter wheat doubled haploid population under controlled rain conditions. The researchers confirmed that the ‘mother of flowering time’ (MFT) genes on the group 3 chromosomes of wheat are major controllers of preharvest sprouting and that other loci that have been important in the literature were not detected. Molecular markers were developed that wheat breeders in the Great Plains use to select for this resistance in their breeding programs. These markers are critical to selection because the trait is difficult to phenotype.

4. Cameo club wheat is available for farmers to grow in Fall 2023. Club wheat is a major export commodity, grown commercially only in the Pacific Northwest of the United States, and growers need new competitive cultivars with improved disease resistance and end use quality. ARS scientists in Pullman, Washington, in collaboration with scientists at Washington State University, used classical and molecular breeding techniques to develop Cameo club wheat. As compared to other club wheat cultivars grown in the high rainfall region, Cameo has better agronomic performance than other club wheat cultivars, better stripe rust resistance, tolerance to soil borne mosaic virus and acid soils and similar excellent club wheat quality. Cameo is available as registered seed to seed companies and farmers in the region in the fall of 2023.

Review Publications
Shrestha, S.L., Garland-Campbell, K.A., Steber, C.M., Pan, W.L., Hulbert, S.H. 2022. Association of canopy temperature with agronomic traits in spring wheat inbred populations. Euphytica. 219. Article 7. https://doi.org/10.1007/s10681-022-03135-4.
Hauvermale, A.L., Parveen, R.S., Harris, T., Tuttle, K.M., Mikhaylenko, G.G., Nair, S., McCubbin, A.G., Pumphrey, M.O., Steber, C.M. 2023. Streamlined alpha-amylase assays for wheat preharvest sprouting and late maturity alpha-amylase detection. Agrosystems, Geosciences & Environment. 6(1). Article e20327. https://doi.org/10.1002/agg2.20327.
Tibbs-Cortes, L.E., Guo, T., Li, X., Tanaka, R., Vanous, A.E., Peters, D.W., Gardner, C.A., Magallanes-Lundback, M., Deason, N.T., DellaPenna, D., Gore, M.A., Yu, J. 2022. Genomic prediction of tocochromanols in exotic-derived maize. The Plant Genome. Article e20286. https://doi.org/10.1002/tpg2.20286.
Tanaka, R., Wu, D., Li, X., Tibbs-Cortes, L.E., Wood, J., Magallanes-Lundback, M., Bornowski, N., Hamilton, J.P., Vaillancourt, B., Li, X., Deason, N.T., Schoenbaum, G.R., Buell, C.R., DellaPenna, D., Yu, J., Gore, M.A. 2022. Leveraging prior biological knowledge improves prediction of tocochromanols in maize grain. The Plant Genome. Article e20276. https://doi.org/10.1002/tpg2.20276.
Guo, T., Li, X. 2023. Machine learning for predicting phenotype from genotype and environment. Current Opinion in Biotechnology. 79. Article 102853. https://doi.org/10.1016/j.copbio.2022.102853.
Garland-Campbell, K.A., Bellinger, B.S., Carter, A.H., Chen, X., DeMacon, P., Engle, D., Hagerty, C., Kiszonas, A., Klarquist, E.F., Murray, T., Morris, C.F., Neely, C., Odubiyi, S., Rashad, A., See, D., Steber, C., Wen, N. 2022. Registration of 'Cameo' soft white club wheat. Journal of Plant Registrations. 16(3):585-596. https://doi.org/10.1002/plr2.20234.
Elshikha, D.M., Wang, G., Waller, P.M., Hunsaker, D.J., Dierig, D., Thorp, K.R., Thompson, A.L., Katterman, M.E., Herritt, M.T., Bautista, E., Ray, D.T., Wall, G.W. 2022. Guayule growth and yield responses to deficit irrigation strategies in the U.S. desert. Agricultural Water Management. 277. Article 108093. https://doi.org/10.1016/j.agwat.2022.108093.
Ayankojo, I.T., Thorp, K.R., Thompson, A.L. 2023. Advances in the application of small unoccupied aircraft systems (sUAS) for high-throughput plant phenotyping. Remote Sensing. 15(10). Article 2623. https://doi.org/10.3390/rs15102623.
Conley, M.M., Thompson, A.L., Hejl, R.W. 2023. Proximal active optical sensing operational improvement for research using the CropCircle ACS-470, implications for measurement of normalized difference vegetation index (NDVI). Sensors. 23(11). Article 5044. https://doi.org/10.3390/s23115044.