Location: Corn, Soybean and Wheat Quality Research
2025 Annual Report
Objectives
Objective 1: Develop accurate and efficient testing methods for processing and marketing quality of soft winter (SW) wheat.
Sub-objective 1a. Develop simple and fast methods for the estimation of wheat grain PHS.
Sub-objective 1b. Improve the existing cracker baking test to make it easier and more widely useable.
Objective 2: Identify SW wheat varieties with various quality characteristics for new food uses.
Sub-objective 2a. Determine the suitability of eastern SW wheat for making tortillas and identify the required quality characteristics.
Sub-objective 2b. Determine the suitability of eastern SW wheat for making white salted noodles and identify the required quality characteristics.
Sub-objective 2c. Develop and evaluate partial and full waxy wheat germplasms for new use.
Objective 3: Develop markers for pre-harvest sprouting using a diverse SW wheat population.
Sub-objective 3a. Find Eastern SW wheat varieties closely related genetically that differ in PHS resistance.
Sub-objective 3b. Locate regions for PHS resistance using a Genome-Wide Association Study (GWAS) on a diverse panel of SW wheat with genotype-by-sequencing (GBS) markers.
Sub-objective 3c. Uncover genes differentially expressed under conditions conducive to PHS versus non-conducive comparing results between lines that are resistant or susceptible to PHS.
Sub-objective 3d. Develop markers for resistance to PHS.
Objective 4: Evaluate and report the milling (processing and intrinsic end-use quality) parameters of SW wheat commercially viable cultivars.
Approach
The Soft Wheat Quality Laboratory (SWQL) aims to improve the end-use quality, uses and marketability of soft winter (SW) wheat in the eastern U.S. by contributing to the development of wheat varieties of improved end-use quality potential and developing new food uses. To attain this goal, the SWQL works to develop reliable and efficient quality testing methods, performs fundamental research on grain characteristics and genetics associated with quality traits, explores potentials of eastern soft wheat for extended uses and performs the comprehensive evaluation of breeding lines for end use quality. The project plan encompasses the effective evaluation of pre-harvest sprouting (PHS) damage and cracker baking quality potential, extended use potentials for tortillas and noodles, genetic factors controlling PHS, and milling and baking quality evaluation of SW wheat, which are crucial for the quality improvement and extended uses of eastern SW wheat.
The required quality characteristics and suitability of eastern SW wheat grain for making tortillas and soft-bite wheat salted noodles will be identified and demonstrated, respectively. Development of partial and full waxy wheat germplasms will be continued, and their potential uses including tortilla and noodles will be examined.
The identification of genetic factors controlling PHS and development of markers for PHS resistance will be conducted in four phases: 1) identify eastern SW wheat varieties closely related genetically that differ in PHS resistance; 2) locate regions for PHS resistance using a Genome-Wide Association Study (GWAS) on a diverse panel of SW wheat with genotype-by-sequencing markers; 3) identify genes differentially expressed under conditions conducive to PHS versus non-conducive comparing results between lines that are resistant or susceptible to PHS; and 4) develop markers for PHS resistance from GWAS and expression analysis.
To contribute to the development of wheat varieties of improved end-use quality potential, the annual evaluation of eastern SW wheat breeding lines for defined milling and baking quality characteristics wil be conducted in collaboration with eastern SW breeding programs.
Progress Report
This final report summarizes the progress of the project which terminated in May 2025 and will continue under the new project 5082-30600- 001-000D, “Biochemical and Genetic Control of Eastern U.S. Soft Winter Wheat for Improved End-use Quality and Marketability”.
This project aimed to improve the milling and baking quality and uses of eastern soft wheat by developing accurate and reliable quality testing methods, identifying the associated biochemical and genetic characteristics, and contributing to the development of wheat varieties by conducting end-use quality evaluation of wheat breeding lines.
Objective 1, develop accurate and efficient testing methods to determine the processing and marketing quality of soft winter (SW) wheat. The electrical resistance of grain soaking water and hot-paste flow distance of whole wheat meal tests were developed to meet the wheat industry’s need for simpler and more efficient alternatives to the currently used falling number (FN) test for estimating preharvest sprouting (PHS). Because PHS negatively affects the quality and marketability of wheat grain, its assessment is essential for mitigating the associated quality reduction and for developing resistant wheat varieties. The electrical resistance of grain soaking water approximated FN with 51% predictability, whereas the hot-paste flow distance of whole grain meal approximated FN with 84% predictability for grains from 198 wheat varieties subjected to field sprouting conditions. It was concluded that while the electrical conductivity of grain soaking water is easy and fast to run, it provides only a marginally acceptable estimation of FN, whereas the hot-paste flow distance of whole grain meal provides a reliable estimation and is simpler, easier, and faster to run than the FN test. The throughput of the hot-paste flow distance test was improved by using a grinder that requires minimal cleaning between samples.
An improved benchtop cracker baking method, which is essential for wheat flour quality control in commercial cracker production and for screening breeding lines in variety development, was developed using inexpensive, readily available equipment: a pasta dough sheeter attached to a tabletop dough mixer. The method was further improved by adopting the optimal water amount for cracker dough preparation and by incorporating a mechanical press that enables the efficient, even, and clean cutting and docking of the cracker dough sheet for baking. The cracker baking test, which uses a portable pasta dough sheeter, optimal water absorption, and a press device, effectively differentiated 20 wheat flours with varying quality characteristics and produced dough and crackers comparable to those made using a pilot-scale dough sheeter. Both the hot-paste flow distance test and the improved benchtop cracker baking test were presented to the Cereals and Grains Association Technical Committee to obtain approved method status.
Objective 2: Identify SW wheat varieties with various quality characteristics for new food uses. Seven of the 39 eastern U.S. soft wheat (ESW) varieties, which carry strong protein and form cohesive and elastic dough despite having a lower protein content, were found to produce tortillas of comparable quality to those prepared from commercial tortilla flours (CTFs) in terms of diameter, opacity score, and rollability score. With lower damaged starch content and polyphenol oxidase activity, which reduce the amount of water required for dough preparation and decrease dark-gray color development, respectively, ESW flours produced tortillas with a larger diameter and brighter color than CTFs. Lactic acid solvent retention capacity, a measure of protein strength, and high molecular weight glutenin subunits (HMW-GSs), which strongly influence gluten strength and product quality, effectively estimated the tortilla-making quality of ESW wheat flour. ESW wheat varieties carrying HMW-GS profiles associated with strong gluten produced tortillas most comparable to those prepared from CTFs in terms of diameter, opacity, and rollability scores.
Eight of the 25 ESW wheat varieties, characterized by relatively high protein content and strength, produced white salted noodles (WSN) of comparable quality to those prepared from commercial noodle flours, with low cooking loss and desirable tensile force and strength. ESW wheat varieties carrying one of three HMW-GS profiles associated with strong gluten produced WSN with relatively low cooking loss and adhesiveness, intermediate hardness, and relatively high tensile force and strength, and were most comparable to noodles prepared from commercial WSN flours. HMW-GS profiles and other protein strength tests can be effectively used to identify ESW wheat breeding lines and varieties suitable for making WSN. These results provide valuable guidelines and tools for screening wheat breeding lines in the development of tortilla and noodle wheat varieties, as well as for identifying wheat grains and flours suitable for making tortillas and WSN.
Ten full waxy and twelve partial waxy ESW wheat genotypes with reduced starch amylose content, which confers novel starch properties such as increased water affinity, higher hot-paste viscosity, and reduced cooking time, were developed by introducing null amylose synthesis genes into two parent varieties and were released with registration and publication in the Journal of Plant Registrations. The amylose content was lowest in full waxy genotypes, followed by double-null and single-null partial waxy genotypes and parents. One of the single-null and most of the double-null partial waxy wheat genotypes produced WSN that were closely comparable to those made from commercial noodle flours in terms of cooking time and textural properties of cooked noodles. Double-null partial waxy ESW wheat genotypes were found to be desirable for tortilla production, with increased extensibility when fresh and improved rollability scores at 12-day storage. These results provide valuable guidance to ESW wheat breeders and food processors for developing varieties suitable for noodle and tortilla production and for producing noodles and tortillas with improved quality, respectively.
Objective 3, Find genes and develop genetic markers, which are the chromosome locations of genes that control pre-harvest sprouting (PHS) resistance. PHS, the germination of grain before harvest in the field, reduces wheat quality and marketability and can lower prices paid to U.S. farmers by up to 30%. A population of 188 soft winter wheat cultivars with wide variation in PHS resistance was evaluated over three years under natural weather events, field rain simulations, and artificial growth chamber conditions, generating PHS data for analysis. Genome-wide association of 1,978 loci across all wheat chromosomes identified 11 chromosome locations significantly associated with PHS. The chromosome locations for agronomic and flour quality traits were distinct from those for PHS, indicating that breeding for PHS resistance is possible without disrupting other important crop traits. Using the chromosome and PHS data, two pairs of wheat cultivars, Scotty/Doublecrop and Cardinal/Logan, that exhibit high genetic similarity but differ in PHS resistance were selected for further testing. These cultivars were used to identify genes and develop specific genetic markers that wheat breeders can use to increase PHS resistance in widely grown wheat varieties. Two genes involved in the initiation of PHS were identified as targets for developing PHS resistance. A genetic marker was developed to enable wheat breeders to detect a cultivar-specific PHS resistance gene. A recently published expression study uncovered a gene with a novel PHS resistance mechanism in the wheat cultivar Logan. The gene is located at one of the eleven chromosome locations described herein. The PHS genes discovered thus far only account for a subset of soft winter wheat cultivars, as PHS is controlled by many genes.
Objective 4: Evaluate and report the milling (processing and intrinsic end-use quality) parameters of SW wheat commercially viable cultivars. The milling and baking quality evaluation of 3,000 to 4,000 samples submitted each year by 9 to 12 public and private breeding programs developing eastern soft winter wheat was carried out annually. The test results were summarized and distributed to the breeding programs, directly contributing to the development of new wheat varieties possessing superior quality. Collaborative research projects with eastern soft winter wheat researchers at public universities were conducted to identify the genetic markers associated with milling and baking quality traits, using comprehensive milling and baking quality evaluations. The Soft Wheat Quality Council (SWQC) annual evaluation of new varieties and advanced breeding lines was coordinated and carried out by milling grain, distributing flour to collaborators, performing quality trait evaluations, and preparing a report that collates the results for presentation at the annual SWQC Meeting. We participated in the Pacific Northwest Wheat Quality Project and the Michigan State University Wheat Quality Testing Project and performed the comprehensive evaluation of advanced breeding lines and varieties for flour characteristics and baking quality.
Accomplishments
1. Development of a simple, fast, and reliable method for the estimation of wheat grain pre-harvest sprouting (PHS). PHS refers to the germination of grain in the head before harvest and is a major concern in wheat production, as it negatively affects grain quality, marketability, and price. The method currently used for assessing PHS in wheat grain is tedious and expensive, making it impractical for the rapid evaluation of large numbers of samples needed both to identify PHS-damaged grain at grain elevators for quality control and to screen breeding lines in the development of resistant varieties. ARS researchers in Wooster, Ohio, developed an improved method called hot-paste flow distance, which uses ground whole grain meal to predict the degree of PHS. Compared with the currently used test, this method achieved 84% predictive accuracy across 198 wheat varieties subjected to preharvest sprouting conditions in the field. The method was further improved by using a grinder that requires minimal cleaning between samples. The hot-paste flow distance test is expected to be readily adopted by wheat breeders to evaluate large numbers of breeding lines in the development of PHS-resistant wheat varieties and effectively used at grain elevators to rapidly screen and segregate grain based on the degree of PHS. This will reduce PHS incidence, improve grain quality, and benefit both wheat growers and the industry through enhanced quality and marketability.
2. A genetic marker, which is a chromosome location of a gene controlling pre-harvest sprouting (PHS) resistance, was developed. PHS reduces the quality and marketability of wheat grain and can lower prices paid to U.S. farmers by up to 30%, representing an estimated loss of ~800 million dollars for soft red winter wheat based on 2022/2023 reported data. The development of PHS-resistant wheat cultivars is the most effective way to reduce this loss. Among wheat cultivars, at least three to four duplicates of the Mother of Flowering Locus T (MFT) gene are known to affect PHS. One duplicate was identified as conferring increased PHS resistance in a group of older, lower yielding cultivars that are no longer grown by U.S. farmers. A genetic marker for this MFT gene was developed by ARS scientists in Wooster, Ohio. The genetic marker distinguishes the PHS-resistant gene from the susceptible gene. The developed genetic marker can be used by breeders to improve PHS resistance in wheat cultivars. Incorporating this PHS resistance gene into widely grown wheat cultivars through breeding programs will reduce losses to American farmers and increase the marketability of U.S. soft winter wheat. Multiple genes contribute to PHS resistance in different wheat cultivars, and the presence of additional resistance genes can provide greater PHS resistance.
3. Identification of a novel gene that confers pre-harvest sprouting (PHS) resistance by reducing alpha-amylase activity and PHS damage in wheat grain. PHS occurs when wheat grain sprouts before harvest in the field. PHS leads to the increased production of an enzyme called alpha-amylase which lowers grain quality and marketability in soft winter wheat varieties. Winter wheat crop values were estimated at $2.65 billion in 2022/2023. PHS-damaged grain can reduce the price paid to U.S. farmers by up to 30%. Using two genetically related winter wheat cultivars, one resistant and one susceptible to PHS, ARS scientists in Wooster, Ohio, identified a novel gene in the PHS-resistant cultivar that was associated with reduced alpha-amylase activity and decreased PHS grain damage. In contrast, the PHS-susceptible cultivar exhibited higher alpha-amylase activity. This discovery will enable wheat breeders to introduce the PHS-resistant gene into widely grown cultivars to reduce PHS. Reduced PHS damage will improve crop marketability and help provide price stability for U.S. farmers.
4. Development of an easy-to-use, efficient experimental cracker baking method. A benchtop cracker baking test is essential for millers and bakers to verify wheat grain and flour quality for cracker production, as well as for selecting and developing varieties with superior quality for making crackers. The currently available experimental cracker baking methods require specialized, expensive sheeting equipment and employ manual dough-sheet cutting and docking. As a result, they have not been widely adopted or approved by scientific societies as official methods. ARS researchers in Wooster, Ohio, developed an experimental cracker baking method that is easily adoptable and efficient. The method uses a commonly available, inexpensive dough sheeting device, incorporates the optimal water level for dough preparation, and employs a mechanical press to produce cut cracker dough sheets for baking. A pasta dough sheeting attachment for a stand mixer produced cracker dough sheets comparable to those made using a pilot plant-scale sheeter in terms of dough weight and thickness, as well as in the thickness and break force of the baked crackers. Using an optimal amount of water to produce uniformly sized dough crumbs and a continuous, unbroken dough sheet provided better differentiation among wheat flours for cracker production than using a fixed water amount. This was reflected in quality parameters such as dough sheet weight and thickness, as well as the height and break force of the baked crackers. The new experimental cracker baking method offers an easily adoptable, efficient, and reliable approach for evaluating wheat flour quality for cracker production, making it well-suited for use by wheat quality testing laboratories, milling and baking companies, and researchers.
5. Identification of the protein composition of eastern U.S. soft winter (ESW) wheat appropriate for making tortillas. During dough mixing, wheat protein molecules interconnect to form gluten, a continuous, viscous, and elastic mass that is largely responsible for optimal handling and processing properties, as well as the production of quality baked goods. Gluten properties therefore largely depend on protein composition. Although high molecular weight glutenin subunits (HMW-GS) make up only a small portion of wheat protein, they have a critical influence on gluten development and dough properties. Thus, the composition of HMW-GS significantly influences gluten and dough characteristics and consequently affects tortilla quality, including pliability and rollability. HMW-GS profiles that are desirable for making tortillas have been identified in hard wheat, but not in soft wheat. To improve the tortilla-making quality and marketability of ESW wheat, ARS researchers in Wooster, Ohio, identified the HMW-GS profiles associated with the protein and dough characteristics required for tortilla production. ESW wheat with these profiles produced tortillas most comparable to those prepared from commercial tortilla flours, exhibiting relatively high opacity and rollability scores during storage. The identified HMW-GS profiles will serve as an effective tool for wheat breeders and food processors to efficiently screen ESW wheat breeding lines and varieties that possess the protein characteristics required for tortilla production.
Review Publications
Penning, B. 2025. Novel genetic control of alpha-amylase activity during pre-harvest sprouting indicated by RNA sequencing of soft winter wheat varieties Cardinal and Logan. Plant Gene. 42. Article 100495. https://doi.org/10.1016/j.plgene.2025.100495.
Penning, B. 2024. Mean normalization improved genome-wide association detection power of wheat (Triticum aestivum) grain and flour quality traits with year-to-year variation. Agriculture. 14(12) Article 2317. https://doi.org/10.3390/agriculture14122317.
Ma, F., Baik, B.V. 2024. High-molecular-weight glutenin subunit profiles of eastern U.S. soft winter wheat desirable for making soft-bite white salted noodles. Cereal Chemistry. 1-13. Article 10813. https://doi.org/10.1002/cche.10813.
Subedi, M., Bagwell, J.W., Lopez, B., Baik, B.V., Babar, M.A., Mergoum, M. 2024. A genome-wide association study approach to identify novel major-effect quantitative trait loci for end-use quality traits in soft red winter wheat. Genes. 15. Article 1177. https://doi.org/10.3390/genes15091177.
Mudiyanselage, P.S., Baik, B.V., Lindsey, L.E. 2025. Planting date and seeding rate effects on soft red winter wheat. Agronomy Journal. 117(3). Article e70099. https://doi.org/10.1002/plr2.20419.
Ma, F., Baik, B.V. 2025. High-molecular weight glutenin subunit profiles desirable for making tortillas in eastern US soft winter wheat. Journal of the Science of Food and Agriculture. 102:586-594. https://doi.org/10.1002/cche.10876.
Ma, F., Souza, E., Sturbaum, A., Baik, B.V. 2025. Registration of two extra-soft soft red winter wheat germplasms carrying the puroindoline genes on chromosome 5A. Journal of Plant Registrations. 19(1). Article e20419. https://doi.org/10.1002/plr2.20419.