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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

2015 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
The wheat breeding program evaluated 35 elite lines, 182 advanced and preliminary yield trial lines, 1100 first year yield trial lines, 1047 segregating populations, 250 F1s, and 23,500 head-row selections during the 2014-15 growing season. Replicated trials of the elite, advanced, and preliminary lines were grown at 8 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. Six of the 8 locations were not harvested due to poor fertilization at one, and a geographically-limited, but very severe freeze at a second location. Taken together, we identified resistance to 6 diseases, one insect problem, 2 physiological stresses, and 6 growth characteristics on the material. The grain yields were higher than previous years and grain quality was good. The best lines and selections will be planted in the fall of 2015. This research is directly related to objectives 1 and 3 of the project. The barley breeding program increased in size and scope, putting emphasis on the breeding of barley having malting quality. Advanced and preliminary lines numbered 56, along with 48 segregating populations, 630 head-rows, and 79 F1s. This material was evaluated at 5 locations in central and western North Carolina. One of these locations followed certified organic cropping. We identified resistance to 3 diseases, one insect problem, 2 physiological stresses and 4 growth characteristics. The grain yields were higher than previous years and grain quality was good. The best lines and selections will be planted in the fall of 2015. This research is directly related to objective 1 of the project. Resistance to globally virulent races of the wheat stem rust pathogen was evaluated on 7,500 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, than any other public or private breeding program. This research is directly related to objectives 1 and 3 of the project. Four new wheat stem rust resistant varieties were released for production in Pakistan as part of the ARS-Raleigh, Wheat Productivity Enhancement Project (WPEP). This research is directly related to objective 1 of the project. The 2014-15 milling and baking data, along with improved yield, agronomics, and disease resistance support the proposed release of a newly developed hard red winter wheat variety for eastern U.S. production. This new variety (experimentally designated as ARS10-0389) will be submitted for release in September 2015. This research is directly related to objective 3 of the project. The genetics of ozone damage was studied in a recombinant inbred line population of wheat. The data indicated that the genetic location of the ozone tolerance was highly correlated with a gene for resistance to African wheat stem rust. This research is directly related to objectives 1 and 3 of the project. DNA of wheat lines from Ethiopia (189 lines), Bangledesh and Nepal (150 lines) were genotyped for stem and leaf rust resistance genes. Wheat lines were genotyped for fourteen resistance genes including Sr2/Yr30/Lr27, Sr22, Sr24/Lr24, Sr25/Lr19, Sr26, Sr31/Yr9/Pm8/Lr26, SrAmigo/Pm17, Sr35, Sr36, Sr42, Lr34/Yr18/Sr57/Pm38, Lr37/Yr17/Sr38, Lr46/Yr29 and Lr67/Yr46/Sr55/Pm46. Data is used to assist breeders in selecting wheat lines with resistance to the stem rust pathogen race TTKSK (Ug99). This research is directly related to objectives 1 and 2 of the project. The genotyping lab evaluated 826 wheat landraces from the National Small Grains Collection, sixteen rust resistance genes and the Rht-B1 and Rht-D1 dwarfing genes. Lines with known resistance genes and are determined not to be landraces are excluded from further research. Lines with potentially new resistance to stem rust are further characterized and made available to wheat breeders to develop resistant cultivars. This research is directly related to objectives 1 and 2 of the project. New KASP assays were developed for stem rust resistance genes Sr22, Sr24/Lr24, Sr25/Lr19, Sr35, and Sr26. KASP assays are more efficient to use than sequencer-based markers. Using Kompetitive Allele-Specific PCR (KASP) assays to genotype domestic and international wheat lines also allows for validation of the assays and determination of their accuracy. Sequences and protocols for using the assays were provided to collaborators in the U.S., U.K., Mexico, Egypt and Turkey. This research is directly related to objective 2 of the project. A set of 7,586 taxa including 2-row and 6-row barley populations with their landrace parents and the common parent Rasmussen were analyzed using Genotype by Sequencing (GBS). The taxa represent 95 bi-parental nested association populations. 192-plex libraries prepared using two-enzyme method were sequenced and a total of 103 million reads were mapped to the reference genome of barley. The average number of mapped reads per individual was 1.57 million. A TASSEL pipeline was designed which identified 207,979 SNPs. After the dataset was divided into the 95 population subsets and filtered for 20% missing data, the number of SNPs per population ranged from 3900 to 10,300. Characterization of these genetic resources will allow for the localization of important traits in barley. This research is directly related to objective 2 of the project. 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, 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 one pattern of relative regional average sensitivities to triazoles, and other different patterns of regional average sensitivities to two strobilurins and 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. We screened 300 elite lines from major eastern U.S. wheat nurseries in replicated field nurseries under enhanced Stagonospora nodorum blotch (SNB) pressure, and provided data on resistance to breeding programs. Working in collaboration with researchers at NCSU, we completed a three-year field experiment on the effects of minimum tillage on SNB severity, yield and test-weight. We found a positive association between amount of wheat residue in the field and disease, but significant yield and test weight effects only in the most severe epidemics. We concluded that the economic threshold for fungicide applications targeting SNB should be re-examined. This research is directly related to objective 1 of the project. Continued to coordinate a winter oat and barley nursery by soliciting germplasm from breeders worldwide. Several barley and oat genotypes with superior winter hardiness were identified. Reports were submitted to breeders and interested personnel in 12 countries. This research is directly related to objective 1 of the project. Freezing that simulates winter freezing was monitored in wheat and oats using Infra Red (IR) Thermography. Unexpectedly, it was determined that the oldest leaves on a plant always freeze first and younger leaves/stems only freeze as the temperature is reduced. The significance of this finding has yet to be determined but may explain many of the anomalous results that are typical of freeze tests. Anatomical and chemical barriers within the overwintering tissue (Crown) that restrict ice growth are likely and may explain much of the difference in freezing tolerance between genotypes and species.


Accomplishments
1. New stem rust 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, NC into the Pakistani varieties ‘Benazir-12’, ‘Dharabi-12’, ‘Hamal-11’, and ‘Pirsabak-13’.

2. New DNA markers for disease resistance genes in wheat. Numerous pathogens can potentially cause significant yield losses in wheat. Working in collaboration with other ARS and university researchers, ARS researchers at Raleigh, NC identified DNA markers linked to three genes conferring resistance to powdery mildew (Pm1a, Pm53, and Pm54). New markers were also identified for genes conferring resistance to stem rust, stripe rust, and Fusarium head blight. Having DNA markers linked to resistance genes allows for selection of disease resistant plants in the absence of the pathogen and for selection of varieties having multiple resistances.

3. Improving breeding and deployment of powdery mildew resistance. Powdery mildew is an economic problem for wheat producers across the U.S. Mildew strains were collected from commercial wheat fields in 15 states and evaluated for virulence, aggressiveness, and fungicide sensitivity. ARS researchers at Raleigh, NC generated virulence data and used them to assess which mildew resistance genes remain effective and useful in wheat breeding programs. Researchers are using next-generation sequencing to identify genetic polymorphism. Population subdivision and migration rates have been calculated to show where the risk lies in the U.S. for migration and gene flow of novel wheat powdery mildew virulences.

4. Improving spray decisions on wheat foliar disease. Stagonospora nodorum blotch is a widespread wheat disease in the Mid-Atlantic USA, and severe epidemics can result in yield and test weight losses. 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. Working in collaboration with researchers at NCSU, ARS researchers at Raleigh, NC completed a three-year field experiment on the effects of minimum tillage on disease, yield and test-weight. They found significant yield and test weight effects only in the most severe epidemics, and concluded that the economic threshold for spraying fungicides should be re-examined.

5. New understanding of spring freeze tolerance in wheat. A sudden spring-freeze can devastate winter cereal crops when they are in the reproductive phase of growth. However, using new Infra Red (IR) Thermography equipment, ARS researchers at Raleigh, NC determined that most plants exposed to a sudden spring freeze do not freeze but supercool. Plants that do freeze are completely killed and unable to produce a head while those that super cool have a reduced seed set. A screening procedure was developed that allows testing for spring freeze tolerance of up to 90 varieties at a time. Using this procedure three wheat lines with superior spring freeze tolerance have been identified that are being used in an attempt to improve spring freeze tolerance in existing varieties.


Review Publications
Livingston, D.P., Tuong, T.D. 2014. Understanding the response of winter cereals to freezing stress through freeze-fixation and 3d reconstruction of ice formation in crowns. Environmental and Experimental Botany. 106:24-33.
Hao, Y., Parks, W.R., Cowger, C., Chen, Z., Wang, Y., Bland, D., Murphy, J.P., Guedira, M., Brown Guedira, G.L., Johnson, J. 2015. Molecular characterization of a new powdery mildew resistance gene Pm54 in soft red winter wheat. Theoretical and Applied Genetics. 128:465-476.
Petersen, S., Lyerly, J.H., Worthington, M.L., Marshall, D.S., Brown Guedira, G.L., Cowger, C., Parks, W.R., Murphy, J.P. 2014. Mapping of novel powdery mildew resistance gene Pm53 introgressed from Aegilops speltoides into soft red winter wheat. Theoretical and Applied Genetics. 128:303-312.
Bonman, J.M., Babiker, E.M., Cuesta-Marcos, A., Esvelt Klos, K.L., Brown Guedira, G.L., Chao, S., See, D.R., Chen, J., Akhunov, E., Zhang, J., Bockelman, H.E., Gordon, T.C. 2015. Genetic diversity among wheat accessions from the USDA National Small Grains Collection. Crop Science. 55(3):1243-1253.
Worthington, M., Regerg-Horton, S.C., Brown Guedira, G.L., Jordan, D., Weisz, R., Murphy, J.P. 2014. Morphological traits associated with weed-suppressive ability of winter wheat against Italian ryegrass. Crop Science. 55:50-56.
Clark, A., Costa, J., Griffey, C., Brown Guedira, G.L., Dong, Y., Souza, E.J., Murphy, J.P., Van Sanford, D. 2014. Registration of scab-resistant KY06C-11-3-10 soft red winter wheat germplasm. Journal of Plant Registrations. 8:211-216.
Worthington, M., Reberg-Horton, S.C., Brown Guedira, G.L., Jordan, D., Weisz, R., Murphy, J.P. 2015. Relative contributions of allelopathy and competitive traits to the weed suppressive ability of winter wheat lines against Italian ryegrass. Crop Science. 55:57-64.
Brooks, W.S., Vaughn, M.E., Berger, G.L., Griffey, C.A., Thomason, W.E., Pitman, R.M., Malla, S., Seago, J.E., Dunaway, D.W., Hokanson, E.G., Behl, H.D., Beahm, B.R., Schmale, D.G., Mcmaster, N., Hardiman, T., Custis, J.T., Starner, D.E., Gulick, S.A., Ashburn, S.R., Jones, E.H., Marshall, D.S., Fountain, M.O., Tuong, T.D., Kurantz, M.J., Moreau, R.A., Hicks, K.B. 2014. Registration of ‘Atlantic’ winter barley. Journal of Plant Registrations. 8:231-236.
Kumssa, T.T., Baenziger, P.S., Rouse, M.N., Guttieri, M., Dweikat, I., Brown Guedira, G.L., Williamson, S.M., Graybosch, R.A., Wegulo, S.N., Lorenz, A.J., Poland, J. 2015. Characterization of stem rust resistance in wheat cultivar 'Gage'. Crop Science. 55:229-239.