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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

2014 Annual Report

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.

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
The wheat breeding program evaluated 40 Elite lines, 110 Advanced lines, 300 Preliminary lines, 1,100 First-Year yield trial lines, 24,000 head rows, 1800 segregating populations, and 800 F1s in the field during 2013-14. This included nine locations in North Carolina, two locations in Virginia, and one location each in Georgia, Maryland, Kentucky, New York, Texas, Oklahoma, and Nebraska. All lines and populations were selected for improved grain quality (both hard and soft), disease and insect resistance, high yield, and good agronomics. We identified new sources of resistance in powdery mildew, stem rust (including Ug99), stripe rust, and Stagonospora nodorum (S. nodorum) blotch in the Texas-Turkey Cereal Collection, 300 synthetic wheat populations from CIMMYT, and diverse material from the Plant Genetic Resources Institute of the Pakistan Agricultural Research Council. We made 346 crosses of this material into elite ARS breeding lines. We developed wheat lines for potential release as new hard red winter wheats for Eastern U.S. production. The most promising line, ARS09-367 had yields equal to the best soft red winter wheats in North Carolina, has resistance to stem, stripe, and leaf rust, as well as powdery mildew and S. nodorum blotch. The milling and baking quality is equal to that of hard red winter wheats produced in the U.S. Great Plains. We are in the fourth year of development of a malting-quality, 2-row, winter barley adapted to North Carolina and Virginia. We selected 50 lines for First-Year yield trials from about 700 head rows. We established protocols for development and analysis of data for genotyping by sequencing (GBS) data for wheat and barley. Samples of 1824 barley lines and 1920 wheat breeding lines were sent for next-generation sequencing. These genotype data are essential for genomic selection in wheat and barley of multiple traits including nitrogen use efficiency, abiotic stress tolerance and yield. We isolated DNA from 19,200 barley lines developed from crosses with diverse accessions from the USDA National Small Grains Collection. DNA is being used for GBS library preparation and genotyping of this germplasm resource. A pipeline for data analysis was developed for mapping DNA sequences against the reference genome of barley and the survey sequence of wheat genome. We provided genotypic data for advanced wheat breeding lines in ten regional cooperative nurseries and two international nurseries to wheat breeders and other cooperators. New high-throughput molecular markers were developed for marker-assisted selection for resistance to powdery mildew and stripe rust, vernalization and photoperiod response in wheat. These new markers will increase the ability of breeders to develop adapted, disease resistant varieties. Virulence data were collected and DNA was extracted for genotyping from all isolates of powdery mildew. Next-generation sequencing techniques are being used to identify genetic polymorphism. Population subdivision and migration rates will be estimated, enhancing our understanding of gene flow and the potential for movement of novel virulences. Advanced experimental wheat lines in eastern and southern regional cooperative nurseries were screened under S. nodorum pressure, and data on resistance provided to breeding programs. The third year of a multi-location field experiment was carried out to gather data for development of a fungicide decision aid for S. nodorum management. An experiment was conducted to determine the impact of intermittent moisture on Fusarium head blight (scab) development in winter wheat cultivars. The multi-year, multi-environment experiment is being conducted with researchers in Ohio and Minnesota. It will expand our understanding of how the timing of moisture in the week prior to wheat flowering affects levels of disease and mycotoxins. This information is helpful for refining forecasts of scab risk. 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 spring-freeze tolerance are crucial traits if breeders are to improve winter cereals grown in the U.S. Significant differences in spring-freeze tolerant wheat and oat germplasm were identified but, it is unclear if this is due to super cooling of heads or if heads are actually capable of tolerating ice in their tissues. Infra-red imaging will be used to determine where ice formation is initiated in heads so that the means by which some genotypes are able to survive freezing temperatures can be determined. The lack of correlation of winter-freezing tolerance with spring-freeze tolerance in 98 genotypes indicates that winter hardiness of germplasm is a poor predictor of spring-freeze tolerance. Barley and oat germplasm was evaluated at 11 and 13 locations respectively, worldwide. Eight barley and 10 oat experimental lines were evaluated. Winter conditions were either not severe enough to differentiate experimental lines or were too severe and killed all the entries for both nurseries. Fourteen molecular markers were evaluated in the oat nursery and the two most freezing tolerant genotypes had 10 significant alleles.

1. New data on types of Fusarium mycotoxins produced in North Carolina small grain crops. The Fusarium fungal pathogen causes head blight or “scab” of small grains, lowering yield and contaminating grain with mycotoxins. In most of the U.S., deoxynivalenol (DON) is by far the most common of these toxins, but in some southern states, Fusarium strains produce nivalenol (NIV) instead. Although it is more toxic to mammals than DON, no testing for NIV is currently done in the U.S. small grain industry. A study of about 1,000 Fusarium strains from several Atlantic seaboard states showed that North Carolina was the only state with an appreciable percentage of NIV producers. In 2014, a survey of about 10 North Carolina counties determined the proportions of DON and NIV producers by field, showing in which regions NIV is a potential risk.

2. New wheat varieties for Pakistan farmers and advanced breeding technology transferred to Pakistani scientists. ARS scientists in Raleigh, North Carolina, co-developed new wheat varieties, having high yields and resistance to Ug99 stem rust with scientists in the Pakistan Agricultural Research Council (PARC). These new varieties, named ‘NARC 2011’ and ‘PAK 2013’ were increased and distributed in Pakistan following several years of evaluation by ARS and PARC scientists in the field in Pakistan. The ARS scientists further evaluated the PARC scientists’ material using molecular markers, and trained the PARC scientists how to organize their wheat breeding programs to better utilize and integrate molecular data with traditional field data.

3. New wheat germplasm for resistance to stem rust race Ug99 distributed. Stem rust race UG99 is capable of causing widespread, global crop losses. ARS researchers in Raleigh, North Carolina, developed 47 germplasm lines having Ug99-effective resistance genes Sr2, Sr1A:1R, Sr36, and Lr34 in hard red winter wheat backgrounds. The germplasm was developed by backcrossing unadapted spring wheat donor lines to elite breeding lines and varieties and selecting for the resistance genes using molecular markers and phenotypic selection in Kenya, the U.S., and Pakistan. These new germplasm broaden the diversity of stem rust resistance genes available to winter wheat breeders.

4. Spring-freeze tolerance in wheat and oat. A sudden spring-freeze can devastate winter cereal crops when they are in the reproductive phase of growth. Genotypic differences in wheat for spring-freeze tolerance have not been identified due to the inability to simulate a spring-freeze event for large numbers of genotypes while they are at the same morphological stage. We refined a screening procedure developed in FY 2013 that allowed us to confirm genotypic differences for spring-freeze tolerance in wheat and oat germplasm. We also determined that winterhardiness is a poor predictor of spring-freeze tolerance. The spring-freeze simulation procedure developed in Raleigh 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. Sustainable production of locally-produced wheat for small farms. ARS scientists in Raleigh, North Carolina, promoted local, sustainable farming in North Carolina by developing bread wheats which can be reliably produced on small farms, taken to local mills for grinding, and sold directly to small-scale bakeries. The North Carolina-produced bread wheats have also been sold in small quantities directly for home-milling and baking at Farmer’s Markets in Ashville, Salisbury, and Cary, North Carolina.

6. New process for screening winter wheat for resistance to soilborne mosaic virus. Wheat yields can be reduced by as much as 30% if plants are infected by wheat soilborne mosaic virus. Host plant resistance is the only effective method of control; no chemical management technique is feasible. Yet field screening of commercial varieties and advanced breeding materials is often hampered by spotty or absent virus epidemics. A test was developed to use virus-laden soil in pots to screen wheat seedlings. The procedure gives data in three months, and has allowed us to provide soilborne mosaic virus ratings on all entries in the 2013-14 North Carolina Wheat Official Variety Trial.

7. Introgressions from related species impact results of genetic association studies. Techniques developed in humans to associate traits with DNA markers commonly rely on estimates of the relatedness of individuals that are based on sharing of DNA markers types. ARS researchers at Raleigh, North Carolina, determined that when these gene mapping techniques are applied to crop plants, researchers should account for the presence of large segments of DNA that were transferred from the crop plants’ wild relatives or related species, often to provide resistance to disease or insect pests. The biasing effect of three DNA segments originating from wheat relatives on estimates of genetic diversity among lines was shown to have a negative impact on association mapping results. Researchers determined that excluding markers in the alien regions results in more accurate estimates of relatedness and more robust identification of markers that can be used to select for important agronomic traits.

8. Metabolic changes during recover from freezing in oat crowns. An important aspect of winterhardiness that has received very little attention is the mechanism(s) plants use to recover from being frozen during winter. In a collaborative effort with an ARS Laboratory in Madison WI, we demonstrated that a considerably different metabolic system is operative during recovery of plants from freezing than during any other growth phase. Differences between cultivars in genes for recovery from freezing could be a basis for improving freezing tolerance.

9. Visualizing ice formation in 3 dimensions. Being able to visualize the precise tissue where ice forms and to what extent tissue is disrupted when it is frozen can give considerable insight into how freezing tolerance genes prevent freeze damage. Using a procedure that we developed to image ice formation in 3 dimensions, we determined that a barrier may restrict ice growth from roots into the lower crown. This technique has even been used to visualize vessels in mammalian tissue in a collaborative project with the National Institute of Health and North Carolina State College of Veterinary Medicine. Being able to associate the precise anatomical position of ice formation with the expression of candidate genes for freezing tolerance will help explain much of the contradictory physiological explanations for freezing tolerance in plants. This will in turn provide a more accurate basis for identifying elite freezing tolerant mechanisms.

Review Publications
Bertucci, M., Brown Guedira, G.L., Murphy, P., Cowger, C. 2014. Genes conferring sensitivity to stagonospora nodorum necrotrophic effectors in stagonospora nodorum blotch-susceptible U.S. wheat cultivars. Plant Disease. 98:746-753.
Worthington, M., Lyerly, J., Petersen, S., Brown Guedira, G.L., Marshall, D.S., Cowger, C., Parks, W.R., Murphy, J.P. 2014. MlUM15: an Aegilops neglecta-derived powdery mildew resistance gene in common wheat. Crop Science. 54(4):1397-1406.
Del Blanco, I.A., Hegarty, J., Gallagher, L., Falk, B.W., Brown Guedira, G.L., Pellerin, E., Dubcovsky, J. 2014. Mapping of QTL for tolerance to cereal yellow dwarf virus in two-rowed spring barley. Crop Science. 54:1468-1475.
Guedira, M., Maloney, P., Murphy, J.P., Xiong, M., Marshall, D.S., Johnson, J., Harrison, S., Brown Guedira, G.L. 2014. Vernalization duration requirement in soft winter wheat is associated with variation at the vrn-B1 locus. Crop Science. 54:1960-1971.