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ARS Home » Southeast Area » Raleigh, North Carolina » Plant Science Research » Research » Research Project #434206

Research Project: Genetic Improvement of Small Grains and Characterization of Pathogen Populations

Location: Plant Science Research

2018 Annual Report

Objective 1. Identify and develop improved small grain germplasm with resistance to rusts, powdery mildew, Fusarium head blight, necrotrophic pathogens, and tolerance to freezing conditions during winter and spring. Sub-objective 1a. Develop wheat germplasm with resistance to stripe rust, leaf rust, stem rust, and powdery mildew. Sub-objective 1b. Develop wheat germplasm with resistance to Fusarium head blight (FHB). Sub-objective 1c. Develop wheat germplasm with resistance to Stagonospora nodorum blight (SNB). Sub-objective 1d. Identify oat, wheat and barley germplasm with tolerance to freezing. Objective 2. Develop improved methods of marker-assisted selection and genomic prediction, and apply markers in development of small grains cultivars. Sub-objective 2a. Identify and characterize new QTL for important traits in eastern winter wheat germplasm. Sub-objective 2b. Evaluate important traits in eastern winter wheat using molecular markers. Sub-objective 2c. Develop new eastern winter wheat germplasm using marker-assisted breeding and genomic selection. Objective 3. Develop new wheat and barley germplasm and cultivars having enhanced end-use characteristics for the eastern United States. Objective 4. Target resistance breeding efforts accurately by determining the relevant geographic variation in pathogen virulence profiles and the range of mycotoxin potential in pathogen populations. Sub-objective 4a. Determine the virulence frequencies and population structure in the wheat powdery mildew pathogen, Blumeria graminis f. sp. tritici, from different regions in the U.S. Sub-objective 4b. Identify and determine toxicological importance of minority Fusarium species causing FHB of wheat in North Carolina.

1a. Cross elite, adapted lines with sources of seedling and adult plant resistance to stripe rust, leaf rust, stem rust, and powdery mildew. Coordinate efforts to identify resistant lines in field breeding nurseries evaluated throughout the southeastern United States and in Njoro, Kenya (for Ug99). Evaluation with reliable molecular markers for known resistance genes. 1b. Continue use of inoculated, misted screening nurseries to evaluate regional and in-house breeding materials. Develop, evaluate and refine genomic selection models for scab resistance traits. 1c. Conduct appropriate phenotyping of regional and in-house breeding materials, including mapping populations, in inoculated Stagonospora blight nurseries to assist in locating the genes and associated markers to allow for marker-assisted selection. 1d. Select wheat and oat germplasm with superior resistance to freezing first by identifying genotypic differences in freezing patterns using IR technology. Crosses will be made with adapted cultivars to develop germplasm with improved resistance to freezing conditions. We will continue coordinating an oat and barley uniform nursery. 2a. Use sequencing based genotyping techniques to develop high-density genetic linkage maps of bi-parental mapping populations and association mapping populations as they are developed. Populations are phenotyped in conjunction with other unit scientists to identify regions of the genome involved in resistance to LR, YR, SR, PM, and SNB. 2b. Evaluate diverse germplasm with molecular markers linked to genes for pest resistance, agronomic and end-use quality, determine the level of marker polymorphism and the presence of favorable alleles in breeding lines. 2c. Apply MAS to introgress and pyramid new fungal resistance genes into eastern winter wheat germplasm. Genotype three-way cross and backcross F1s for populations entering into a doubled-haploid (DH) production pipeline. 2c. Use different parameters based on genomic position and linkage disequilibrium to select SNP sets that can be tested via cross-validation to identify the optimum number and most informative markers for GS. 3. Each year, approximately 600 crosses will be made to combine superior quality, yield, agronomic, and disease and insect resistance using recurrent parents from the program, as well as new sources of diversity. Utilize combinations of molecular markers with phenotypic selection and screening to accumulate favorable agronomic traits. Phenotyping and selection for improved hard wheats lines; grow and select populations under organic and conventional conditions. 4a. Samples will be gathered in each of two years from two to five states per region and derive single-pustule isolates; The phenotyping will be done in growth chambers using standard detached-leaf methodology. Population structure will be evaluated using molecular markers. 4b. Scabby wheat spikes will be collected from fields across a broad geographic range of North Carolina. Sequencing of the transcription elongation factor will be used to determine species. Population genetic analyses will determine if the Fusarium species are geographically clustered, or evenly distributed.

Progress Report
Research to develop new genotyping protocols were pursued. A second round of optimization for an amplicon sequencing approach targeting trait related markers was performed. Collaborative regional nurseries were genotyped using KASP assays and by amplicon sequences. A large collaborative project with ARS researchers at Ithaca, New York, Pullman, Washington, Manhattan, Kansas, and Fargo, North Dakota aimed at development of a haplotype based genotyping approach was initiated. The branched-heading and high seed number per head traits continued to be incorporated in both soft and hard wheats. Several of the early-maturing breeding lines having these traits were caught by late freezes in March 2017. We are continuing to sort-through these breeding lines to advance those having the best combination of inherited traits. Over our whole program, this year we continued our practice to bring millers and bakers into our research, to supply us with quality evaluations on our most elite lines. Accurate and repeatable procedures for identifying genotypes with elite freezing tolerant mechanisms are crucial to accomplishing the objectives of this research. Both winter-freeze tolerance and tolerance to unexpected spring freeze events are crucial traits if breeders are to improve winter cereals grown in the U.S. A technique to quickly image 3D patterns of vessel arrangement in crown tissue was developed and used to make histological comparisons of xylem vessel arrangement and size between the very hardy winter cereal and selected oat cultivars suggests more hardy cultivars have smaller vessels which explains freezing patterns that were observed using infrared thermography.

1. 3D reconstruction of water conducting vessels. To understand freezing in plants it is important to understand the anatomy of water conducting vessels and how ice formation is initiated within them. Using infrared analysis of winter cereals under natural conditions an ARS researcher at Raleigh, North Carolina, determined that ice formation always began in roots and proceeded upwards into leaves. This was a counter-intuitive observation since leaves are colder than roots during freezing weather and it has always been assumed that freezing is initiated in leaves. In addition, leaves were found to freeze in an age-dependant sequence with older leaves freezing first; many times the youngest leaves never froze. Since freezing propagates in xylem vessels the three winter cereals were pulsed with dye and their xylem vessels were reconstructed in 3 dimensions with a procedure developed by an ARS researcher at Raleigh, North Carolina. Preliminary observations indicated that less hardy genotypes have larger vessels and that vessel diameter may be a valuable tool for screening freezing tolerant genotypes in a juvenile stage of growth.

Review Publications
Graybosch, R.A., Baenziger, S.P., Bowden, R.L., Dowell, F.E., Dykes, L., Jin, Y., Marshall, D.S., Ohm, J., Caffe-Treml, M. 2017. Release of 19 waxy winter wheat germplasm, with observations on their grain yield stability. Journal of Plant Registrations. 12(1):152-156.
Sallam, A.H., Tyagi, P., Brown Guedira, G.L., Muehlbauer, G.J., Hulse, A., Steffenson, B.J. 2017. Genome-wide association mapping of stem rust resistance in Hordeum vulgare subsp. spontaneum. G3, Genes/Genomes/Genetics. 7(10):3491-2507.
Ficke, A., Cowger, C., Bergstrom, G., Brodal, G. 2018. Understanding yield loss and pathogen biology to improve disease management: Stagonospora nodorum blotch - a case study in wheat. Plant Disease. 102:696-707.
Johnson, J.W., Chen, Z., Buck, J.W., Buntin, G.D., Babar, M.A., Mason, R.E., Harrison, S.A., Murphy, J.P., Ibrahim, A.H., Sutton, R.L., Simoneaux, B.E., Bockelman, H.E., Baik, B.-K., Marshall, D.S., Cowger, C., Brown Guedira, G.L., Kolmer, J.A., Jin, Y., Chen, X., Cambron, S.E., Mergoum, M. 2017. ‘GA 03564-12E6’: A high-yielding soft red winter wheat cultivar adapted to Georgia and the southeastern regions of the United States. Journal of Plant Registrations. 11:159-164.
Cowger, C., Mehra, L., Arellano, C., Meyers, E., Murphy, J.P. 2018. Virulence differences in blumeria graminis f. sp. tritici from the central and eastern United States. Phytopathology. 108:402-411.
Abdelrhim, A., Abd-Alla, H.M., Abdou, E., Ismail, M.E., Cowger, C. 2018. Virulence of Egyptian blumeria graminis f. sp. tritici population and powdery mildew response of Egyptian wheat cultivars. Plant Disease. 102:391-397.
McNally, K., Menardo, F., Luthi, L., Praz, C., Mueller, M., Kunz, L., Ben-David, R., Chandrasekhar, K., Dinoor, A., Cowger, C., Myers, E., Xue, M., Zeng, F., Gong, S., Yu, D., Bourras, S., Keller, B. 2018. Distinct domains of the AVRPM3A2/F2 avirulence protein from wheat powdery mildew are involved in immune receptor recognition and putative effector function. New Phytologist. 218:681-695.
Livingston, D.P., Tuong, T.D., Murphy, J.P., Gustal, L., Willick, I., Wisniewski, M.E. 2017. High-definition infrared thermography of ice nucleation and propagation in wheat under natural frost conditions and controlled freezing. Planta. 247:791-806.
Johnson, J.W., Chen, Z., Buck, J.W., Buntin, G.D., Babar, M.A., Mason, R.E., Harrison, S.A., Murphy, J.P., Ibrahim, A.M., Sutton, R.L., Simoneaux, B.E., Bockelman, H.E., Baik, B-K., Marshall, D.S., Cowger, C., Brown Guedira, G.L., Kolmer, J.A., Jin, Y., Chen, X., Cambron, S.E., Mergoum, M. 2018. ‘Savoy’: An adapted soft red winter wheat cultivar for Georgia and the South East regions of the USA. Journal of Plant Registrations. 12:85-89.
Ceron-Bustamante, M., Ward, T.J., Kelly, A.C., Vaughan, M.M., McCormick, S.P., Cowger, C., Leyva-Mir, S.G., Villasenor-Mir, H.E., Ayala-Escobar, V., Nava-Diaz, C. 2018. Regional differences in the composition of Fusarium head blight pathogens and mycotoxins associated with wheat in Mexico. International Journal of Food Microbiology. 273:11-19.
Tan, C., Yu, H., Yang, Y., Xu, X., Chen, M., Rudd, J.C., Xue, Q., Ibrahim, A., Garza, L., Wang, S., Sorrells, M.E., Liu, S. 2017. Development and validation of KASP markers for the greenbug resistance gene Gb7 and the Hessian fly resistance gene H32 in wheat. Theoretical and Applied Genetics. 130(9):1867-1884.