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ARS Home » Southeast Area » Raleigh, North Carolina » Plant Science Research » Research » Research Project #424645

Research Project: Genetic Improvement of Small Grains for Biotic and Abiotic Stress Tolerance and Characterization of Pathogen Populations

Location: Plant Science Research

2016 Annual Report


Objectives
1. Identify and develop improved small grain germplasm with resistance to rusts, powdery mildew, Fusarium head blight, necrotrophic pathogens, and freeze tolerance. 1a: Develop wheat germplasm with resistance to stripe rust, leaf rust, stem rust, and powdery mildew. 1b: Develop wheat germplasm with resistance to Fusarium head blight (FHB). 1c: Develop wheat germplasm with resistance to Stagonospora nodorum blight (SNB). 1d: Identify oat, wheat and barley germplasm with tolerance to freezing. 2. Develop improved methods of marker-assisted selection, and apply markers in development of small grains cultivars. 2a: Identify new markers for important traits in eastern winter wheat germplasm. 2b: Evaluate important traits in eastern winter wheat using molecular markers. 2c: Develop new eastern winter wheat germplasm using marker-assisted breeding. 3. Develop new wheat germplasm and cultivars having enhanced end-use characteristics for the eastern U.S. 4. Determine the virulence structure of small grain pathogen populations and evaluate the risk potential of virulence transfer through gene flow. 4a: Determine the virulence frequencies in the wheat powdery mildew pathogen, Blumeria graminis f. sp. tritici, from different regions in the U.S.


Approach
1. Develop wheat germplasm with resistance to stripe rust, leaf rust, stem rust, and powdery mildew. Develop wheat germplasm with resistance to Fusarium head blight (FHB). Develop wheat germplasm with resistance to Stagonospora nodorum blight (SNB). Identify oat, wheat and barley germplasm with tolerance to freezing. 2. Identify new markers for important traits in eastern winter wheat germplasm. Evaluate important traits in eastern winter wheat using molecular markers. 3. Make new crosses, marker-assisted selection for key traits; phenotyping and selection for improved hard wheats lines; introduce resistance to common bunt; grow and select populations under organic and conventional conditions. 4. Obtain infected plant samples from all states; make single-pustuled isolates, and begin phenotyping and genotyping.


Progress Report
Significant differences in spring-freeze tolerant wheat and oat germplasm were identified and infra-red thermography was used to determine that differences in seed counts were due to damage in heads during a supercooled (below freezing but no ice present) state. This is important information because it confirms that sterility in the head will not initially be apparent and could account for unexplained reductions in yield during harvest. Seventeen barley and 13 oat experimental lines were evaluated at 9 and 14 locations, respectively, worldwide. In most locations winter conditions were either not severe enough to differentiate experimental lines or were too severe and killed all the entries for both nurseries. Differential survival in several international locations indicated that lines developed in the North Carolina oat breeding program were at least as hardy as the winter-hardy check cultivar. 14 simple sequence repeat (SSR) markers were evaluated in the oat nursery and the 2 most freezing tolerant genotypes had 10 significant alleles. Over 10,000 single nucleotide polumorphism (SNP) markers were recently tested on over 653 diverse spring and winter oat lines by members of the North American Collaborative Oat Research Enterprise. A subset of these, consisting of 247 diverse winter oats, are currently being evaluated for their response to crown freezing using controlled environment growth chambers. Three replications of response data have been completed for the entire set of lines, and a fourth replication is currently under way. Population structure will be accounted for using a Q-matrix generated through principle component analysis, as well as a kinship matrix. The phenotypic and genotypic data will be analyzed in concert through an association analysis. Wheat powdery mildew strains were collected from commercial wheat fields in 15 states and were evaluated for virulence, aggressiveness, and fungicide sensitivity. We determined virulence frequencies. We identified which resistance genes remain effective, including in some cases where genes are effective in one region and not in another. We are now genotyping by sequencing in order to vastly enhance the use of neutral markers to validate findings on population sub-division and gene flow. This work allows us to predict whether novel virulences in the pathogen population may spread, and in which directions. Results to date indicate the U.S. wheat powdery mildew population undergoes migration and gene flow from west to east across the Appalachians, but not in the opposite direction. In a large-scale study of fungicide sensitivity in the wheat powdery mildew population, we have identified regional differences in sensitivity to two widely-used triazole fungicides. On the other hand, there was neither genotypic nor phenotypic evidence of significant evolution to reduced mildew sensitivity to two strobilurins nor to a new active ingredient, fluxapyroxad. By associating genotypes with the fungicide sensitivity phenotypes of particular isolates, we will contribute genomics knowledge to aid in the identification of new targets in the fungal genome. This research is directly related to objective 4 of the project. ARS scientists analyzed and published data showing that partial profits from Fusarium head blight (FHB) management techniques depend on the wheat market targeted and on FHB severity. Our data showed that, across a range of FHB severities, a group of moderately FHB-resistant cultivars always generated equivalent or greater profits than a group of FHB-susceptible varieties after factoring in the economics of mycotoxin dockage, yield and test weight losses, and fungicide application costs. Fungicides were generally profitable only when epidemics were severe. These data will benefit producers who face complex cost-benefit decisions regarding scab-targeted fungicide use. The genotyping lab purchased and installed new instrumentation for more automated DNA isolation and quantification. This allowed for improved sample throughput and the number of samples analyzed with KASP markers increased substantially. New KASP assays associated with quantitative trait locus (QTL) for resistance to Fusarium head blight (FHB), powdery mildew, stem rust and stripe rust were developed. A pipeline for targeted identification of variants of flowering time genes was developed and used to identify new alleles in germplasm from the USDA National Small Grains Collection. KASP assays for flowering time genes were developed and used to select 144 diverse lines from the USDA winter wheat core collection that were evaluated for heading date in the field, greenhouse and phytotron. In addition, the ARS developed KASP markers were utilized in the development of near-isogenic lines that were grown at locations in NC, KY, GA and AR during harvest year 2016. These data will contribute to our understanding of the effect of different allele combinations on heading date across environments having varying duration of cold temperature and day-length exposure. ARS scientists utilized pipelines established for identifying variants from sequence data in wheat and barley to develop a database of tens of thousands of dispersed variants mapped to the respective draft reference genomes. Genotypes of lines in regional cooperative nurseries were combined with phenotypic data to develop genomic selection models for wheat grain yield, test weight and scab resistance. Preliminary testing of models using lines from different breeding cycles indicate that genomic selection will be powerful tool for selection of high yielding disease resistant wheat cultivars. The wheat breeding program evaluated 105 elite lines, 460 advanced and preliminary yield trial lines, 830 first year yield trial lines, 2367 segregating populations, 723 F1s, and 21,484 head-row selections during the 2015-16 growing season. Replicated trials of the elite, advanced, and preliminary lines were grown at 7 North Carolina locations, spanning the State. Two of these locations followed certified organic cropping. Early generation and head row material were grown at two locations. Two of the locations were not harvested due to flooding following planting. Taken together, we identified resistance to 8 diseases, one insect problem, 2 physiological stresses, and 6 growth characteristics on the material. Grain yields were below average and grain quality was average. The barley breeding program increased in size and scope, putting emphasis on the breeding of barley having malting quality. Forty elite, winter 2-row lines were evaluated at 4 locations in NC, along with 105 advanced and preliminary lines, 152 segregating populations, 5,432 head-rows, and 111 F1s. ARS scientists identified resistance to 3 diseases, one insect problem, 2 physiological stresses and 4 growth characteristics. Grain yields were below average and grain quality was average. Resistance to globally virulent races of the wheat stem rust pathogen was evaluated on 13,560 varieties and breeding lines in Kenya and Ethiopia. New combinations of resistance genes were shown to provide near-immunity to all races of the stem rust pathogen in east Africa. A greater number of resistant lines were found in material developed at ARS-Raleigh, North Carolina, than any other public or private breeding program. In cooperation with Pakistani researchers, the Wheat Production Enhancement Project (WPEP) has assisted in the identification and release to farmers, of 14 wheat varieties. They are ‘Bars 09’, ‘Dharabi 11’, ‘NARC 11’, ‘HB 11’, ‘Benazir 13’, ‘Hamal 13’, ‘Lalma 13’, ‘Pak 13’, ‘Shahkar 13’, ‘Borlaug 15’, ‘Insaf 15’, ‘Pakhtunkhwa 15’, ‘Pirsabak 15’, and ‘Ujala 15’. The final 5 varieties in this group were all released in FY 16.


Accomplishments
1. Improved understanding of winter wheat heading date. In wheat, genes controlling response to cold requirement (vernalization) and day-length (photoperiod) influence time from planting to head emergence. ARS researchers identified new alleles of major genes for winter wheat heading date in a population developed from a cross between two early flowering cultivars from the southeast. The Vernalization-A1 (VRN-A1) gene influenced heading time such that plants having three copies required longer cold exposure for flowering than those having two copies. Sequencing the Vernalization-B1 (VRN-B1) genes of the parents revealed differences associated with earlier heading date after warm winters. The genes interacted significantly and influenced time to heading in field experiments in Louisiana, Georgia and North Carolina. The Photoperiod1 (PPD1) genes were significant determinants of heading date in all field environments. The PPD-D1 locus was determined to have the largest genetic effect, followed by PPD-A1 and PPD-B1. Our results demonstrate that combinations of VRN1 and PPD1 alleles of varying strength can fine tune winter wheat flowering time to suit specific growing environments and changing climates.

2. Improved decision-making for Fusarium head blight (FHB) management. Fusarium head blight causes economic losses to small grain growers every year in at least some region of the eastern U.S. Variety resistance and fungicide applications each afford only partial control. ARS researchers in Raleigh, North Carolina were the first to use data on mycotoxin and test weight practices, as well as fungicide application costs, to evaluate partial profits from use of resistant varieties and fungicides. Using cultivars with varying FHB resistance levels in scab epidemics of varying intensity, researchers showed that the most profitable FHB management strategy depended on the wheat market (feed, flour, or feed/flour). Their results indicated that while fungicide profitability was market- and epidemic-dependent, the moderately scab-resistant cultivars were on average always at least as profitable as the susceptible cultivars when the economics of FHB management were factored in.

3. Improved understanding of wheat powdery mildew. The U.S. population of wheat powdery mildew is widespread, but the degree to which novel virulences in one region might spread to other wheat-growing regions was unknown. ARS researchers in Raleigh, North Carolina, surveyed the mildew population across 15 states and determined that new wheat powdery mildew epidemics likely come from mainly local sources, rather than blowing in from distant regions. The researchers also assessed gene flow and migration in the powdery mildew population stretching from Oklahoma to New York to Georgia. They determined that there is significant gene flow from west to east in that region, but not in the opposite direction. This helps account for observed virulence frequency differences, and suggests that Plains growers can effectively deploy mildew resistance genes that are have been defeated in soft-wheat regions farther east.

4. Tolerance of wheat to an unexpected spring-freeze during reproductive growth. A sudden spring-freeze can devastate winter cereal crops when they are in the reproductive phase of growth. A repeatable and accurate procedure developed in 2013 for evaluating large numbers of wheat genotype for spring freeze was modified by a field evaluation using infra-red (IR) thermography. These experiments determined that most spring freeze damage is not caused by ice formation in heads but by freezing temperatures where heads remain unfrozen. This is important information because it suggests that sterility in the head will not initially be apparent and could account for unexplained reductions in yield during harvest. We also determined that while temperatures at head level can remain as low as -10 degrees celsius, the soil always remains above freezing. IR analysis indicated that heat from the soil could provide protection from freezing to heads, and may explain how heads remain super-cooled. The laboratory spring-freeze simulation we developed will give wheat breeders the opportunity to incorporate this important trait in existing cultivars by allowing them to screen segregating germplasm in early generations.

5. Using infra-red thermography to understand freezing patterns in plants. When water freezes it gives off heat which is visible in the infra-red spectrum. This wavelength can be visualized and recorded using an infra-red camera. Studies of freezing in winter cereals has revealed that counter to decades of published research on freezing tolerance, winter cereals freeze in sequence from oldest leaf to youngest rather than the entire plant freezing at once. In addition, counter intuitively, leaves freeze from the bottom up, rather than from top down. Our research suggests that winter cereals survive freezing by keeping critical tissues in a super-cooled state rather than by resisting stresses caused by ice. Numerous barriers exist within the crown that prevent freezing in some tissues. This concept explains much of the experimental variability experienced when studying freezing tolerance in winter cereals. The nature of the barriers is unknown but may be related to carbohydrate concentrations at the base of leaves.

6. New stem rust (Ug99) resistant wheat varieties released in Pakistan. The globally-virulent stem rust race, known as ‘Ug99’ can potentially cause significant yield loss and even crop death. The rust resistance in these varieties was identified and incorporated by ARS researchers in Raleigh, North Carolina into the Pakistani varieties ‘Borlaug 15’, ‘Insaf 15’, ‘Pakhtunkhwa 15’, ‘Pirsabak 15’, and ‘Ujala 15’.


None.


Review Publications
Mehra, L., Cowger, C., Weisz, R., Ojiambo, P. 2015. Quantifying the effects of wheat residue on severity of Stagonospora nodorum blotch and yield in winter wheat. Phytopathology. 105:1417-1426.
Cowger, C., Parks, W.R., Kosman, E. 2016. Structure and migration in U.S. Blumeria graminis f. sp. tritici populations. Phytopathology. 106:295-304.
Van Sanford, D.A., Clark, A.J., Hershman, D., Brown Guedira, G.L., Cowger, C., Dong, Y., Baik, B.V. 2016. Registration of ‘Pembroke 2014’ soft red winter wheat. Journal of Plant Registrations. 10:41-46.
Liu, L., Barnett, M., Griffey, C., Malla, S., Brooks, W., Seago, J.E., Butler, H., Thomason, W.E., Rucker, E., Behl, H.D., Pitman, R.M., Dunaway, D.W., Vaughn, M.E., Custis, J.T., Seabourn, B.W., Chen, Y.R., Fountain, M.O., Marshall, D.S., Graybosch, R.A., Divis, L.A., Hansen, L.E., Cowger, C., Cambron, S.E., Jin, Y., Beahm, B.R., Hardiman, T.H., Lin, C.J., Mennel, D.F., Mennel, D.L. 2016. Registration of 'LCS Wizard' wheat. Journal of Plant Registrations. 10:28-35.
Subramanian, N.K., Mason, R.E., Milus, E.A., Moon, D.E., Brown Guedira, G.L. 2015. Characterization of two adult-plant stripe rust resistance genes on chromosomes 3BS and 4BL in soft red winter wheat. Crop Science. 56(1):143-153.
Guedira, M., Xiong, M., Hao, Y.F., Johnson, J., Harrison, S., Marshall, D.S., Brown Guedira, G.L. 2016. Heading date QTL in winter wheat (Triticum aestivum L.) coincide with major developmental genes Vernalization-1 and Photoperiod-1. PLoS One. 11(5):e0154242.
Thapa, R., Brown Guedira, G.L., Ohm, H.W., Mateos-Hernandez, M., Wise, K.A., Goodwin, S.B. 2016. Determining the order of resistance genes against Stagonospora nodorum blotch, Fusarium head blight and stem rust on wheat chromosome 3BS. BMC Research Notes. 9:58. doi: 10.1186/s13104-016-1859-z.
Clark, A., Sarti-Dvorjak, D., Brown Guedira, G.L., Dong, Y., Baik, B.V., Van Sanford, D. 2016. Identifying rare FHB-resistant transgressive segregants in intransigent backcross and F2 winter wheat populations. Frontiers in Microbiology. 7:277.
Arruda, M., Lipka, A., Brown, P.J., Krill, A.M., Thurber, C., Brown Guedira, G.L., Dong, Y., Foresman, B.J., Kolb, F. 2016. Comparing genomic selection and marker-assisted selection for Fusarium head blight resistance in wheat (Triticum aestivum L.). Molecular Breeding. 36(7):1-11.
Ben David, R., Cowger, C., Parks, W.R., Dinoor, A., Kosman, E., Wicker, T., Keller, B. 2016. Differentiation among Israeli Blumeria graminis f. sp. tritici isolates originating from wild vs. domesticated Triticum species. Phytopathology. http://dx.doi.org/10.1094/PHYTO-07-15-0177-R.
Peterson, S., Lyerly, J., Maloney, P., Brown Guedira, G.L., Cowger, C., Costa, J., Dong, Y., Murphy, J.P. 2016. Mapping of Fusarium Head Blight resistance QTL in winter wheat cultivar NC-Neuse. Crop Science. 56(4):1473-1483.
Liu, L., Barnett, M., Griffey, C., Malla, S., Brooks, W., Seago, J.E., Thomason, W.E., Rucker, E., Behl, H.D., Pitman, R.M., Dunaway, D.W., Vaughn, M.E., Custis, J.T., Seabourn, B.W., Chen, Y.R., Fountain, M.O., Marshall, D.S., Cowger, C., Cambron, S.E., Jin, Y., Beahm, B.R., Hardiman, T.H., Lin, C.J., Mennel, D.F., Mennel, D.L. Registration of Vision 45 Wheat. Journal of Plant Registrations. 9:338-344. 2015.
Cowger, C., Weisz, R., Arellano, C., Murphy, J.P. 2016. Profitability of integrated management of fusarium head blight in North Carolina winter wheat. Phytopathology. 106:814-823.
Mehra, L., Cowger, C., Gross, K., Ojiambo, P. 2016. Predicting pre-planting risk of Stagonospora nodorum blotch in winter wheat using machine learning models. Frontiers in Plant Science. http://dx.doi.org/10.3389/fpls.2016.00390.
Shu, X., Livingston, D.P., Franks, R.G., Boston, R., Woloshik, C., Payne, G.A. 2015. Aspergillus flavus and fusarium verticillioides induce tissue specific gene expression of PRms and UGT in maize kernels. Molecular Plant Pathology. 16:662-674.
Livingston, D.P., Tuong, T.D., Isleib, T., Murphy, J.P. 2016. Differences between wheat genotypes in damage from freezing temperatures during reproductive growth. European Journal of Agronomy. 74:164-172.
Swartley, O., Foley, J., Livingston, D.P., Sabio, D., Cullen, J., Elmore, S. 2016. Histology atlas of the developing mouse hepatobiliary hemolymphatic vascular system with emphasis on embryonic days 11.5-18.5 and early postnatal development. Toxicologic Pathology. 44:705-725.
Renolds, W.C., Miller, G., Livingston, D.P., Rufty, T. 2016. Athletic field paint color impacts transpiration and canopy temperature in bermudagrass. Crop Science. 56:2016-2025.
Li, K., Hegarty, J., Zhang, C., Wan, A., Wu, J., Brown Guedira, G.L., Chen, X., Munoz-Amatriain, M., Fu, D., Dubcovsky, J. 2016. Fine mapping of barley locus Rps6 conferring resistance to wheat stripe rust. Theoretical and Applied Genetics. 129(4):845-859.
Grogan, S., Brown Guedira, G.L., Haley, S., Mcmaster, G.S., Reid, S., Smith, J.H., Byrne, P. 2016. Allelic variation in developmental genes and effects on winter wheat heading date in the U.S. Great Plains. PLoS One. 11(4):e0152852.
Arruda, M., Brown, P., Krill, A., Brown Guedira, G.L., Thurber, C., Foresman, B., Kolb, F. 2016. Genome-wide association mapping of fusarium head blight resistance in wheat (Triticum aestivum L.) using genotyping by sequencing. The Plant Genome. 9(1):1-14.