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United States Department of Agriculture

Agricultural Research Service


Location: Plant Science Research

2009 Annual Report

1a.Objectives (from AD-416)
Objective 1: Identify sources of resistance to foliar fungal pathogens and introgress resistance into adapted wheat. Objective 2: Develop improved methods of marker-assisted selection and apply markers in development of improved wheat and oat. Objective 3: Characterize frequencies of virulence in pathogen populations to resistance sources in wheat germplasm and evaluate the risk potential of virulence transfer through gene flow. Objective 4: Characterize genetic factors conferring winter-hardiness in oat.

1b.Approach (from AD-416)
Approach 1: Evaluation, identification, and incorporation of major gene resistance in wheat to powdery mildew and stripe rust using greenhouse, growth chamber and field facilities. Evaluation and identification of major gene resistance in progenitors of wheat to powdery mildew and stripe rust. Evaluation, identification, and incorporation of minor gene resistance in wheat to powdery mildew and stripe rust. Approach 2: Will apply marker-assisted selection to determine if we can rapidly introgress and pyramid new fungal resistance genes into soft winter wheat germplasm. Will apply marker technology to characterize the genetic factors for resistance by haplotyping, genetic linkage and QTL analyses. Phenotypic and marker analyses will be used to identify and develop germplasm having genes of interest for use in developing improved cultivars of small grains. Approach 3: Powdery mildew samples are obtained from collaborators in the U.S., U.K., and Middle East. Virulence frequencies are determined using powdery mildew resistance gene differentials on detached-leaf plates. In order to evaluate the extent of population subdivision, migration, and gene flow, nested cladistic analysis will be used because it may allow inferences about historical processes such as fragmentation and range expansion. Approach 4: Two oat cultivars differing in winter-hardiness that have been grown in the UOWHN for more than 40 years have been used to develop a mapping population for identification of genomic regions containing winter-hardiness genes. After cold acclimation, crowns will be prepared for freezing by trimming roots and leaves to approximately 3 cm. To identify markers suitable for high-throughput genotyping for this QTL and to identify new regions associated with winter-hardiness, SSR markers will be evaluated on the mapping population.

3.Progress Report
Approximately 1,400 wheat breeding lines, representing wheats from all states east of the Mississippi River were evaluated for resistance to powdery mildew (Pm genes) and yellow rust, also known as stripe rust (Yr genes). The genetic base for powdery mildew resistance in these wheat lines was fairly narrow, with only three highly effective genes (Pm1a, Pm34, and Pm35) being present in the germplasm. The widely-deployed major mildew gene, Pm17, was defeated in the 2009-09 growing season. Resistance to yellow rust was even narrower, with only two highly effective genes present (Yr9 and Yr17). However, adult-plant resistance to yellow rust was apparent in about 50% of the lines tested, indicating good resistance in those lines to epidemic build-up of the disease under field conditions. Approximately 900 F1s were made between all possible combinations of 13 minor gene germplasm lines for resistance to powdery mildew, yellow rust, leaf rust and stem rust. Segregating populations between wheat progenitor-based stem rust resistance and adapted wheat genotypes were screened for adult-plant resistance.

Molecular markers produced in the project are enabling breeders and geneticists to select for disease resistance more rapidly, thereby accelerating the production on new wheat varieties. More than 150,000 marker-assisted selection data points were produced and analyzed at the Eastern Regional Small Grains Genotyping Lab during Fiscal Year 2009. In collaboration with regional wheat breeders, thousands of breeding lines have been selected that carry genes conferring resistance to Fusarium head blight, powdery mildew, Barley yellow dwarf virus, leaf, stripe and stem rust. Molecular markers were also used to rapidly deploy genes for resistance to head scab into cultivars adapted to the Southeast by backcrossing. Seed of plants having the scab resistance gene pyramids are being provided to breeders for evaluation in field nurseries during Fall 2009. Lines with acceptable performance will be released as varieties.

Freeze-damaged regions reported in last years report in crowns of oats were followed over time. Developed a protocol to precisely quantify regions of damage using color recognition software. Initiated a metabolomics analysis of crown tissue to determine the cause of the visible damage. Continued SSR analysis of hardy by non-hardy oat recombinant inbred line (RIL) population. Included a single sequence repeat (SSR) marker analysis in the Uniform Oat Nursery for the first time. Performed a controlled freeze test on the Uniform Southern Soft Red Winter Wheat Nursery and the Uniform Eastern Soft Red Winter Wheat Nursery.

1. Identification of new sources of adult-plant resistance to wheat stripe rust. Wheat stripe rust has been a major yield-reducing factor in central and eastern parts of the U.S. since 2000. Forty wheat breeding lines from ARS and other public breeding programs were analyzed under controlled conditions, and in the field at 6 locations in the U.S. Resistance to stripe rust was found and confirmed to be highly effective. These germplasms will enable researchers to develop and release wheat varieties that have resistance to stripe rust.

2. Development and release of stem rust resistant specialty wheats. Wheat varieties having bread wheat, end-use quality are needed for production in the eastern U.S. in order to serve as a local source of high protein flour. Two hard red lines (ARS03-3805 and ARS03-4736) and three hard white lines (ARS05-1034, ARS05-1044, and ARS05-1234) were developed and tested throughout North Carolina for local production. In addition to high protein, bread quality flour, these lines also have resistance to the Ug99 race of wheat stem rust. These lines will serve as the basis for new markets for wheat producers in North Carolina.

3. New sources of stem rust (Ug99) resistance were identified in 30 breeding lines developed in Raleigh. These lines were increased and sent to the International Wheat and Maize Agricultural Research Center (CIMMYT) for distribution globally in the first winter wheat stem rust resistance nursery.

4. Seventy new markers were added to a hardy by non-hardy recombinant inbred line (RIL) population. Of these markers 65 were single sequence repeat’s (SSR's) associated with trait that are components of winter hardiness: winter field survival, crown freeze tolerance, leaf survival score, root survival score, presence or absence of the translocation 7C-17P, photoperiod and vernalization. This enabled us to perform a quantitative trait loci (QTL) analysis of the uniform oat nursery for all these traits. Results need to be repeated since the field survival data was too variable to make any conclusive indicated that the complexity of winter hardiness makes this kind of analysis.

5. Southeastern Piedmont wheat growers often confront severe epidemics of barley yellow dwarf virus (BYDV) in wheat crops, which are normally seeded no-till into corn or soybean debris. BYDV is transmitted to the wheat by aphids, and the virus may cause severe stunting and discoloration if the aphids arrive in the fall. Severity of BYDV and yield were compared in wheat planted in large field plots that either had whole corn stalks, chopped corn debris, or corn debris removed. In two years when severe BYDV epidemics developed, disease severity was greater and wheat yield was lower in plots with corn debris, either chopped or unchopped, than in the plots where corn debris had been removed. A systematic survey using molecular detection techniques confirmed that the wheat plants were primarily infected with three strains of BYDV. The results suggest that BYDV-transmitting aphids are attracted to the light-colored corn debris, and that growers who plant BYDV-susceptible wheat with low or no tillage into heavy corn debris should consider treating either wheat seed or seedlings with an insecticide.

6. Septoria tritici blotch (STB) and Stagonospora nodorum blotch (SNB) take a variable but chronic toll on wheat yield and test weight in the eastern U.S., and breeding programs have lacked the capacity to screen for resistance. Over 280 advanced lines were tested in 2008, and 311 lines were screened in 2009. Among these lines were a majority of the soft red winter wheat (SRWW) varieties to be released in the next two years. A 50-line “Septoria Stars” nursery provides cooperators with the most resistant lines from the previous year for additional screening and crossing. Data on cultivar resistance level were supplied to 25 breeders in 15 states and coordinators of 6 regional nurseries. These data enable researchers to release wheat varieties that have a higher average level of resistance to STB and SNB.

7. Our work is leading to a better understanding of the epidemiology of Fusarium Head Blight (FHB) that will allow us to more accurately forecast deoxynivalenol (DON) risk, and give growers another tool (adjustment of harvest timing) in managing high-DON situations. We have shown that post-flowering moisture increases both scab and DON levels in winter wheat. Our research also indicates that the window of infection for FHB in North Carolina extends from mid-anthesis to approximately 10 days after mid-anthesis, but that environmental factors that extend the period of flowering can extend the window of scab vulnerability. Our findings lend support to the hypothesis that “late” (post-flowering) infections coupled with elevated moisture levels can lead to sound-appearing grain with excessive DON content. Finally, we are showing that DON declines during the growing season, and apparently continues to decline during and after harvest-ripeness.

8. Improved wheat germplasm having stem rust resistance was developed. The stem rust resistance gene Sr22 confers resistance to the Puccinia graminis f.sp. tritici race TTKS that developed in Africa (Ug99) and is an immediate threat to world wheat production. Sr22 was present on a large chromosomal translocation derived from wild einkorn wheat. Through crossing and selection with DNA markers, individuals with reduced alien segments were developed. These new lines having less genetic material from the wild species should provide a more agronomically desirable source of the resistance gene that can be readily deployed utilizing molecular markers.

5.Significant Activities that Support Special Target Populations
The development of wheat varieties having high protein, bread wheat end-use quality will enable small, niche farmers in North Carolina to produce high quality flour for on-farm or small bakery, local use.

6.Technology Transfer

Number of Web Sites Managed1
Number of Other Technology Transfer2

Review Publications
Costa, J.M., Griffey, C.A., Bockelman, H.E., Cambron, S.E., Cooper, A., Graybosch, R.A., Grybauskas, A., Kratochvil, R.J., Jin, Y., Marshall, D.S. 2007. Registration of 'Chesapeake' Wheat. Journal of Plant Registrations. 1:26-27.

Coram, T., Brown Guedira, G.L., Chen, X. 2008. Using Transcriptomics to Understand the Wheat Genome. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources.3:083.

Marshall, D.S. 2009. Diseases which challenge global wheat production - powdery mildew, leaf, and head blights. Wheat: Science and Trade. 7:155-170.

Wooten, D.R., Livingston, D.P., Lyerly, H.J., Holland, J.B., Jellen, E.N., Marshall, D.S., Murphy, J. 2009. Quantitative Trait Loci and Epistasis for Oat Winter Hardiness Component Traits. Crop Science. 48:149-157.

Parks, R., Carbone, I., Murphy, J., Cowger, C. 2009. Population Genetic Analysis of an Eastern U.S. Wheat Powdery Mildew Population Reveals Geographic and Recent Common Ancestry with U.K. and Israeli Populations. Phytopathology. 99:840-849.

Mundt, C.C., Sackett, K.E., Wallace, L.D., Cowger, C., Dudley, J.P. 2009. Long Distance Dispersal and Accelerating Waves of Disease: Empirical Relationships. The American Naturalist. 173:456-466.

Cowger, C., Patton Ozkurt, J.L., Brown Guedira, G.L., Perugini, L. 2009. Post-flowering moisture increased Fusarium head blight and deoxynivalenol levels in North Carolina field experiment with winter wheat. Phytopathology. 99:320-327.


Livingston, D.P., Hincha, D.K., Heyer, A.G. 2009. The relationship of fructan to abiotic stress tolerance in plants. Cellular and Molecular Life Sciences. 66:2007-2023.

Last Modified: 4/23/2014
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