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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

2018 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
This is the final report for this project, which as been replaced by project 6070-22000-018-00D, "Genetic Improvement of Small Grains and Characterization of Pathogen Populations." A large study of the U.S. wheat powdery mildew population revealed that it is different in the Plains hard wheat area and the eastern soft wheat area. The study confirmed that the hard wheat population remains avirulent to genes long defeated in the soft wheat area, and more sensitive to triazole fungicides. It also demonstrated that five resistance (Pm) genes recently introgressed from wild wheat relatives should be effective throughout both regions. Additionally, through an international collaboration, we identified which wheat resistance genes (Pm genes) are effective against the wheat powdery mildew population of Egypt. Also, a collaboration led to publication of Pm 59, a new powdery mildew resistance gene from Aegilops tauschii. Through an international collaboration, we conducted and submitted for publication research comparing levels of disease and secondary metabolites, including mycotoxins, produced by Fusarium graminearum and three other, relatively less aggressive Fusarium species that also cause Fusarium head blight of wheat and barley. Our study compared 4 infection timings spanning a 10-day period of wheat flowering, which is the period when wheat is susceptible to Fusarium infection. We showed that the other species, some of which have been detected in FHB-infected wheat in the U.S., caused the highest disease and mycotoxin levels when they infected relatively later in flowering. Our results suggest that mycotoxins produced by the weaker Fusarium species are relatively more abundant when environmental conditions promote spore liberation and infection later in anthesis, whereas mycotoxins produced by F. graminearum are likely favored by earlier conducive conditions. The genomic selection effort in collaboration with breeders continued to expand for the 2018 growing season. DNA was isolated and SNP data analyzed for a large number of lines that entered the genomic selection program. ARS scientists were able to develop genomic data sets for predictions more than 5,000 lines for grain yield, test weight and Fusarium head blight resistance traits, along with other traits such as resistance to powdery mildew, stripe rust and leaf blotch. In October and November 2017, we planted uniform, elite, and advanced trials at 7 locations in North Carolina (Plymouth, Kinston, Goldsboro, Raleigh, Salisbury, Laurel Springs, and Mills River). Soon after planting Laurel Springs, the location received heavy rains and flooding due to hurricanes Nate and Maria, and we abandoned the location for 2017-18. Over years, we have been able to better identify lines having superior bread-making quality. One of these lines was ARS10-389; we supplied about 210 pounds of seed of this line to the North Carolina State University, Foundation Seed Organization in Rocky Mount for increased. The line is being released as an improved hard red winter wheat variety. The description is - ARS10-389 is a hard red winter wheat developed by USDA-ARS. Juvenile plant growth is semi-erect, plant color at boot stage is green and the flag leaf is erect, twisted, and wax is absent. ARS10-389 is 5 days earlier than TAM 303 and 4 days later than USG 3120. Anther color is yellow and plant height averages 82cm, which is 3cm shorter than USG 3120 and 7cm taller than Shirley. Stems are absent anthocyanin, waxy bloom and hairiness. Internodes are hollow, the peduncle is erect, and auricle hairs are absent. Heads are middense, tapering and awnleted. ARS10-389 is resistant to stripe rust, stem rust, powdery mildew, and Hessian Fly biotype B; moderately resistant to Fusarium Head Blight and leaf rust; and moderately susceptible to glume blotch and yellow dwarf. ARS10-389 has hard grain with protein content of 12% and high molecular weight glutenin subunits 5+10 at the Glu-D1 locus. Among the unique characteristics of ARS10-389, is it’s high level of moderate resistance to scab (Fusarium Head Blight). Most all hard wheats adapted to the U.S. have poor levels of scab resistance. Internationally, our program in Pakistan (WPEP, Wheat Production Enhancement Program) released 3 new rust resistant wheat varieties, bringing the total released to 32 new varieties over an 8 year time period. In Kenya, we continued to evaluate U.S. wheat and barleys; in 2018, the nursery consisted of over 6,000 entries. Barley and oat germplasm were evaluated at 9 and 13 locations respectively, worldwide. Twenty-six barley and 9 oat experimental lines were evaluated. 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. In collaboration with North Carolina State over 10,000 SNP markers, identified through an iSelect 6K beadchip SNP array and through genotyping-by-sequencing (GBS), were 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 213 diverse winter oats, were evaluated for their response to crown freezing using controlled environment growth chambers and their survival was correlated with the SNP markers.


Accomplishments
1. Stacking new genes for resistance to stem, stripe, and leaf rust of wheat. The wheat rusts are the most devastating and widespread diseases of wheat on a global scale. It is only through sustained, mission-focused breeding programs, that we will be able to keep a step or two ahead of the pathogens. ARS researchers at Raleigh, North Carolina, introgressed rust genes that have new and useable molecular markers into superior germplasm lines. Segregating populations of our elite, adapted lines containing Sr13, Sr28, Sr43, Yr5, Yr15, Yr60, Lr32, Lr51, and Lr60 were developed. Additionally, we will combine Sr2 with Fhb1, Lr34, and Lr46 in advanced lines. Selected plants with all the desired rust genes were further genotyped in Raleigh, then phenotyped in Kenya for Ug99 stem rust and stripe rust.

2. Improved understanding of wheat powdery mildew pathogen. Powdery mildew is one of the most common and damaging diseases in global wheat production. Blumeria graminis f. sp. tritici, the fungus that causes the disease, can rapidly overcome host resistance or fungicides used in management. Thus, it is important to monitor which resistance genes are effective in which regions, and to locate a continuous stream of new resistance genes to replace those that are defeated. ARS researchers at Raleigh, North Carolina, conducted a large study of the U.S. wheat powdery mildew population and learned that it is different in the Plains hard wheat area and the eastern soft wheat areas. The study confirmed that the hard wheat population remains controlled by resistance genes that are long defeated in the soft wheat area, and is also more sensitive to two common triazole fungicides. The study also demonstrated that five resistance genes recently introduced into common wheat from wild wheat relatives should be effective throughout both regions.

3. Optimization of genomic breeding methods in wheat using fixed effects. Genomic selection is a tool that allows plant breeders to utilize DNA sequence data to improve the efficiency with which they can identify the best performing lines for release as varieties. ARS researchers at Raleigh, North Carolina, developed DNA markers that can determine allele status of major genes affecting important traits such as flowering time, plant height and disease resistance. ARS scientists worked with wheat breeders in the eastern growing region to combine DNA marker data with nine years of performance data of hundreds of experimental lines in replicated field plots. Researchers determined that the addition of markers predictive of the presence of major genes for resistance to powdery mildew and genes affecting plant development resulted in optimized genomic selection models that had increased predictive ability. This study demonstrated the value of genomic selection to improve selection and this new tool has now been widely adopted by U.S. soft winter wheat breeders.

4. Improved understanding of disease resistance in eastern winter wheat. It is critical to breed for resistance to fungal diseases of wheat in the eastern United States where leaf rust, stripe rust and powdery mildew are responsible for loss of grain yield and end-use quality. ARS researchers at Raleigh, North Carolina, in collaboration with wheat breeders and pathologists, have identified the genomic location of genes contributing to disease resistance in eastern winter wheat. A combination of genome wide association analysis and mapping in biparental populations determined that resistance genes located on chromosomes 7A, 2B, and 6B were important determinants of resistance to powdery mildew, and genes on chromosomes 3B, 4B, and 5B contributed to stripe and leaf rust resistance. As a result, DNA markers predictive for the presence of resistance genes in cultivars and breeding lines were developed and are being used to track genes and develop cultivars having multiple resistances.

5. Identification of DNA markers for freeze damage in oat. Winter hardiness is a complex trait involving numerous mechanisms of resistance that are under genetic control. Small segments of DNA that are associated with those mechanisms can be used to select individual genotypes with those mechanisms. ARS researchers at Raleigh, North Carolina, in collaboration with researchers at North Carolina State University identified eight significant markers on five different oat chromosomes (5C, 6C, 11A, 8A 14D) associated with winter hardiness. Combining individual winter hardiness traits from genotypes with these markers will help breeders select freezing tolerant germplasm in the effort to improve winter hardiness in oats.

6. Freezing during reproductive phase of growth. Freezing weather during spring can devastate winter cereal crops when they are in the reproductive phase of growth. ARS researchers at Raleigh, North Carolina, developed a procedure for evaluating large numbers of wheat genotype for spring freeze during field evaluations. The procedure indicated that contrary to existing literature there are genetic differences in spring freeze tolerance between wheat genotypes. In collaboration with researchers at North Carolina State University, the freezing tolerant germplasm that was identified is being crossed with existing cultivars to improve tolerance to unexpected spring freeze events. This will allow farmers to realize the full yield potential of cultivars despite unpredictable freezing weather in early spring.


Review Publications
Zhou, Y., Conway, B., Miller, D., Marshall, D.S., Cooper, A., Murphy, J.P., Chao, S., Brown Guedira, G.L., Costa, J. 2017. Quantitative trait loci mapping for spike characteristics using a genetic map with array-based and genotyping-by-sequencing (GBS) SNP markers in hexaploid wheat. The Plant Genome. https://doi:10.3835/plantgenome2016.10.0101.
Lozada, D.N., Mason, R.E., Babar, M.A., Carver, B.F., Brown Guedira, G.L., Merrill, K., Arguello, M.N., Acuna, A., Vieira, L., Holder, A., Miller, R.G., Addison, C., Moon, D.E., Miller, R.G., Dreisigacker, S. 2017. Association mapping reveals loci associated with multiple traits that affect grain yield and adaptation in soft winter wheat. Euphytica. 213(9):222.
Nice, L., Steffenson, B.J., Brown Guedira, G.L., Akhonuv, E.D., Liu, C., Kono, T.J., Morrell, P.L., Blake, T.K., Horsley, R.D., Smith Kevin, P., Meuhlbauer, G.J. 2016. Development and genetic characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) population of wild × cultivated barley. Genetics. 203(3):1453-1467.
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.
Lukaszewski, A.J., Cowger, C. 2017. Re-engineering of the Pm21 transfer from Haynaldia villosa to bread wheat by induced homoeologous recombination. Crop Science. 57:1-5.
Lookabaugh, E., Shew, B., Cowger, C. 2017. Three pythium species isolated from severely stunted wheat during an outbreak in North Carolina. Plant Health Progress. 18:169-173.
Wiersma, A., Pulman, J., Brown, L., Cowger, C., Olson, E. 2017. Identification of PmTA1662 from Aegilops tauschii. Theoretical and Applied Genetics. 130:1123-1133.
Kuprian, E., Munkler, C., Resnyak, A., Zimmermann, S., Tuong, T.D., Gierlinger, N., Muller, T., Livingston, D.P., Neuner, G. 2017. Complex bud architecture and cell-specific chemical patterns enable supercooling of Picea abies bud primordial. New Phytologist. 40:3101-3112.
Shu, X., Livingston, D.P., Woloshuk, C., Payne, G. 2017. Comparative histological and transcriptional analysis of maize kernels infected with Aspergillus flavus and Fusarium verticillioides. Molecular Plant Pathology. 8:2075-2085.
Carpenter, N.R., Griffey, C.A., Malla, S., Barnett, M., Marshall, D.S., Fountain, M.O., Murphy, J.P., Milus, E., Johnson, J., Buck, J., Chao, S., Brown Guedira, G.L., Wright, E. 2017. Identification of quantitative resistance to puccinia striiformis and puccina triticina in the soft red winter wheat cultivar ‘Jamestown’. Crop Science. 57:2991-3001.