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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Improvement of Hard Winter Wheat to Biotic and Abiotic Stresses

Location: Hard Winter Wheat Genetics Research

2014 Annual Report


1a. Objectives (from AD-416):
Objective 1: Identify and develop adapted hard winter wheat germplasm with improved resistance to leaf rust, stripe rust, stem rust, Hessian fly, Fusarium head blight, and with tolerance to heat and drought stress. Sub-objective 1.A: Develop germplasm with resistance to leaf rust, yellow rust, and stem rust. Sub-objective 1.B: Develop germplasm with resistance to Hessian fly. Sub-objective 1.C: Develop germplasm with resistance to Fusarium head blight. Sub-objective 1.D: Develop germplasm with tolerance to post-anthesis heat stress. Sub-objective 1.E: Develop germplasm with tolerance to drought stress. Sub-objective 1.F: Conduct cooperative development of hard winter wheat cultivars. Objective 2: Develop more efficient wheat breeding techniques based on high-throughput phenotyping and genotyping methods as well as genomic selection models. Sub-objective 2.A: Develop new high-throughput phenotyping platform for rapid assessment of agronomic and physiological traits in field trials. Sub-objective 2.B: Identify high-throughput markers for important traits. Sub-objective 2.C: Conduct collaborative development of genomic selection models for prediction of yield, agronomic traits, and grain quality and evaluate prediction accuracy. Objective 3: Increase knowledge of the molecular basis for virulence and resistance for leaf rust and Hessian fly, and tolerance to heat stress in wheat. Sub-objective 3.A: Identify mechanisms of virulence and resistance for leaf rust. Sub-objective 3.B: Identify mechanisms of virulence and resistance for Hessian fly. Sub-objective 3.C: Identify mechanisms of tolerance for heat stress.


1b. Approach (from AD-416):
Production of hard winter wheat is limited by recurring intractable problems such as diseases, insects, heat stress, and drought stress. In addition, emerging problems, such as Ug99 stem rust, threaten the sustainability of production. The first objective of this project is to identify and develop adapted hard winter wheat germplasm with improved resistance to leaf rust, yellow rust, stem rust, Hessian fly, Fusarium head blight, and tolerance to heat and drought stress. We will identify sources of resistance, transfer the resistance genes into adapted backgrounds, identify linked markers, validate the gene effects, and release new germplasm lines for cultivar development. The second objective is to develop more efficient wheat breeding techniques based on high throughput phenotyping and genotyping methods as well as genomic selection models. High-throughput phenotyping platforms will be developed using proximal sensing and georeferenced data collection for rapid assessment of field plots. Genotyping-by-sequencing will be used to characterize genome-wide molecular markers on breeding material and apply genomic selection in wheat breeding. New high-throughput markers will be developed for marker-assisted selection of traits of interest. The third objective is to increase our knowledge of the molecular basis for virulence/avirulence and resistance for leaf rust and Hessian fly, and tolerance to heat stress in wheat. Greater understanding of avirulence effectors in the Hessian fly and the leaf rust pathogen may lead to better strategies for durable resistance. Likewise, uncovering the mechanisms of abiotic stress tolerance may lead to discovery of new tolerance genes with improved or complementary effects.


3. Progress Report:
1. More than 11,000 wheat breeding samples from 10 breeding programs were analyzed for molecular markers in the USDA-ARS Central Small Grains Genotyping Laboratory. We also analyzed three regional wheat nurseries with more than 50 specific markers linked to important traits of interest to breeders. A total of over 100,000 allele-specific marker data points were generated in 2014. The data were used by wheat researchers for selecting wheat breeding lines. 2. Genotyping-by-sequencing (GBS), a new high density marker technology, was done for 10 recombinant inbred populations or doubled haploid populations to map resistance in wheat to Hessian fly, soilborne wheat mosaic virus, wheat streak mosaic virus, Fusarium head blight, and other traits. Data are being analyzed to map the genetic loci controlling these traits. 3. We are working to develop methods for GBMAS (genotyping by multiple amplicon sequencing). GBMAS first amplifies up to a few hundred predefined marker targets in a multiplex PCR reaction. Then unique barcodes are ligated to the PCR products for each individual. Samples are then pooled and prepared for high throughput sequencing. Barcodes are used to separate resulting sequence reads and make genotyping calls. This platform has relatively simple execution, fast turnaround times, high reliability, and low costs. 4. More than 3,500 wheat lines from wheat breeders and geneticists in the Great Plains region were screened in the greenhouse for resistance to the Hessian fly. Results were sent to breeders to aid in the selection of elite lines. In some cases, resistant lines were selected, dug up, and were shipped back to the breeders. 5. An irrigated stripe rust screening nursery at Rossville, KS was planted with more than 1500 breeder advanced lines. The nursery also included four mapping populations for resistance to stripe rust. Unfortunately, the nursery was lost due to winterkill due to late planting. 6. An irrigated stem rust field screening nursery was conducted in 2013/2014. Two mapping populations for minor gene resistance to stem rust were scored for resistance reactions. These data will be used in the coming year to map the locations of the resistance genes. In addition, selections were made in segregating populations for resistant germplasm development. 7. This was the fourth year of work under specific cooperative agreements with six public wheat breeding programs to introgress resistance to Ug99 stem rust into elite adapted wheat cultivars. Each breeding program made crosses between resistant donor lines and their own elite breeding lines. The primary goal is to produce new varieties with three-gene or four-gene combinations of resistance genes Sr22, Sr26, Sr35, and Lr34. 8. Association mapping studies are in various stages of completion for: 1) adult plant leaf rust on a core collection of 1414 diverse winter wheat lines from the National Small Grains Collection in Aberdeen, ID; 2) adult plant stem rust, leaf rust, and stripe rust on a panel of 205 hard and soft winter wheat entries from elite nurseries; and 3) heat stress tolerance, and adult plant leaf rust and stripe rust on a diverse panel of 305 hard winter wheat lines from the Great Plains. 9. In collaboration with other researchers, the genomes of one hundred and thirty-four isolates of the leaf rust fungus have been sequenced. Specific virulence of these isolates to different resistance genes is being used to identify differences in the protein-coding sequences that might explain the differences in virulence patterns. To date, 11 candidate genes have been identified by comparative genomics that might mediate the resistance response in the plant. 10. Studies are ongoing on developing synoptic models of resistance gene durability. A model was developed for predicting the occurrence of new virulent races for combinations of resistance genes based on the exponential failure distribution. This model accounts for rates of mutation, sexual recombination, migration, pathogen population size, and the number of genes in the combination. A second synoptic model for predicting plant disease resistance gene durability singly and in combinations has been developed based on the balance of effectiveness of resistance and fitness costs. Together, these synoptic models will be useful for developing improved strategies for resistance gene stewardship. A manuscript is in preparation.


4. Accomplishments
1. Genes for resistance to Fusarium head blight mapped in new Chinese source of resistance. Fusarium head blight (FHB) is a devastating disease of wheat worldwide. Growing resistant cultivars is the most effective strategy to control the disease. ARS researchers at Manhattan, KS genetically mapped resistance genes in a population developed from a cross between the highly resistant Chinese landrace ‘Huangcandou’ and ‘Jagger’, a moderately susceptible hard red winter wheat from Kansas. Marker analysis identified three genes from Huangcandou and two from ‘Jagger’ that were associated with scab resistance. Markers associated with the resistance genes were identified and can be used to enhance scab resistance in wheat breeding programs.

2. Study identifies the most effective wheat resistance genes for the Hessian fly. The Hessian fly is a major pest of wheat, and is controlled mainly through deploying resistant wheat cultivars. Change in Hessian fly populations in the field is often rapid and wheat cultivars may lose resistance within 6-8 years. To ensure continuous success of host plant resistance, Hessian fly populations in the field need to be constantly monitored to determine which resistance genes remain effective in different geographic regions. ARS researchers and university colleagues investigated five Hessian fly populations collected from Texas, Louisiana, and Oklahoma, where infestation by Hessian fly has been high in recent years. Eight resistance genes including H12, H13, H17, H18, H22, H25, H26, and Hdic, were found to be highly effective against all tested Hessian fly populations in this region, conferring resistance to 80% or more of plants containing one of these resistance genes. This information will help breeders select the best combinations of genes to control Hessian fly.

3. Resistance in wheat to Hessian fly is surprisingly temperature-sensitive. The Hessian fly is a major pest of wheat and is mainly controlled using resistant wheat cultivars. However, the host resistance strategy is generally less successful in the southern U.S. ARS researchers at Manhattan, KS discovered that different temperatures have a profound impact on Hessian fly resistance in selected wheat cultivars from the Great Plains. Many wheat cultivars that are fly-resistant at 20 ºC become susceptible at higher temperatures, and many other cultivars that are fly-susceptible at 20 ºC become resistant at a lower temperature. This finding is significant in several respects. First, this information is important for wheat growers to make cultivar decisions according to historical temperatures in their regions. Second, the loss of fly-resistance in wheat plants at higher temperatures poses a threat for future success of the host resistance strategy due to global climate change. Third, many cultivars that were classified as fly-susceptible according to standard screening criteria are actually resistant at historical average temperatures in the Great Plains area during the wheat growing season. The impact of wheat cultivars with fly-resistance at low temperatures needs to be evaluated further.

4. New sources of resistance to wheat streak mosaic virus found in synthetic hexaploid wheat. Wheat streak mosaic virus (WSMV) is a serious wheat pathogen that causes stunting, with yellow streaks in the leaves, while reducing the yield of the crop. Unfortunately, there are few resistance genes available for WSMV. ARS researchers at Manhattan, KS screened more than 400 synthetic hexaploids, which are hybrids of a wild species, (Aegilops tauschii) and durum wheat. Four lines were found to have resistance to WSMV. These four lines can now be used as parental lines to transfer the resistance into adapted hexaploid wheat lines.

5. New molecular markers found for resistance to soil-borne wheat mosaic virus. Soil-borne wheat mosaic virus (SBWMV) disease can significantly reduce grain yield by up to 80% in winter wheat in the Great Plains. Developing resistant wheat cultivars is the only feasible strategy to reduce the losses. ARS researchers in Manhattan, KS analyzed an association mapping population of 205 winter wheat accessions from the U.S.A. using wheat single nucleotide polymorphism (SNP) chips and identified six new SNP markers that were significantly associated with the SBWMV resistance gene on chromosome 5D. These new markers are being used for marker-assisted selection of wheat resistance to SBWMV.

6. Study of secreted proteins gives clues to foil the wheat leaf rust fungus. Puccinia triticina is the fungus that causes wheat leaf rust, which is one of the most important wheat diseases worldwide. After the fungus enters the plant, special fungal structures called haustoria begin to secrete proteins (called effectors) that are thought to inhibit the defense response of the plant and facilitate parasitism by the fungus. Some of the secreted effector proteins may be recognized by plant resistance genes and may trigger strong race-specific plant defenses. Therefore, secreted proteins are the key to understanding the interaction between the host and the pathogen. ARS researchers in Manhattan, KS used RNA sequencing to identify the proteins that are secreted by six races of the fungus during infection. Differences in secreted proteins between the races were correlated with race specificity and 15 candidate effectors for controlling race specificity were identified. Strategies that target these effector genes may lead to more durable resistance.

7. Four new wheat cultivars were co-developed by ARS and universities. New wheat cultivars are needed by producers to maintain and increase yield and grain quality. In collaboration with Colorado State University, Kansas State University, and Oklahoma State University, ARS researchers participated in the development and registration of four new wheat cultivars for the Great Plains including cultivars ‘Antero’, ‘Clara’, ‘Cowboy’, and ‘Mattern’. In addition, near isogenic winter wheat germplasm lines contrasting for the presence of Fhb1, a gene for resistance to Fusarium head blight, were registered and released. These new high yielding cultivars and germplasm lines are now available for wheat producers, breeders, and geneticists.


Review Publications
Momcilovic, I., Fu, J. 2013. Protein synthesis alongation factors EF-Tu and eEF1A: biosynthesis, functions and application in the improvement of heat tolerance in plants. In: Bethaz, C., Puma, V.L., editors. New Research on Protein Synthesis. New York, NY: Nova Science Publishers. p. 1-49.

Bernardo, A., Bai, G., Yu, J., Kolb, F., Bockus, W., Dong, Y. 2014. Registration of near-isogenic winter wheat germplasm contrasting in Fhb1 for fusarium head blight resistance. Journal of Plant Registrations. 8:106-108.

Lui, H., Bayer, M., Druka, A., Russell, J., Hackett, C., Poland, J.A., Ramsay, L., Hedley, P., Waugh, R. 2014. An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley. Biomed Central (BMC) Genomics. 15:104.

Zhang, X., Fu, J., Hiromasa, Y., Pan, H., Bai, G. 2013. Differentially expressed proteins associated with Fusarium head blight resistance in wheat. PLoS One. 8(12):e82079.

Jin, F., Bai, G., Zhang, D., Dong, Y., Ma, L., Bockus, W., Dowell, F.E. 2014. Fusarium-damaged kernels and deoxynivalenol in Fusarium-infected U.S. Winter Wheat. Phytopathology. 104(5):472-478.

Bruce, M.A., Neugebauer, K.A., Joly, D.L., Bakkeren, G., Migeon, P., Wang, S., Akhunov, E., Cuomo, C.A., Fellers, J.P., Kolmer, J.A. 2014. Using transcription of six Puccinia triticina races to identify the secretome during infection of wheat. Frontiers in Plant Science. 4:520.

Hunger, R., Edwards, J., Bowden, R.L., Yan, L., Rayas-Duarte, P., Bai, G., Horn, G., Kolmer, J.A., Giles, K., Chen, M., Jin, Y., Osburn, R., Bales, M., Seabourn, B.W., Klatt, A., Carver, B. 2013. 'Billings' wheat combines early maturity, disease resistance, and desirable grain quality for the Southern Great Plains of the USA. Journal of Plant Registrations. 8:22-31.

Garces-Carrera, S., Knutson, A., Wang, H., Giles, K.L., Huang, F., Whitworth, R.J., Smith, C.M., Chen, M. 2014. Virulence and biotype analyses of Hessian Fly (Mayetiola destructor) populations from Texas, Louisiana, and Oklahoma. Journal of Economic Entomology. 107(1):417-423.

Martin, T.J., Zhang, G., Fritz, A.K., Miller, R., Chen, M. 2014. Registration of 'Clara CL' Wheat. Journal of Plant Registrations. 8(1):38-42.

Liu, S., Rudd, J.C., Bai, G., Haley, S.D., Ibrahim, A., Xiu, Q., Hays, D.B., Graybosch, R.A., Devkota, R.N., St Amand, P. 2014. Molecular markers linked to genes important for Hard Winter Wheat production and marketing in the U.S. Great Plains. Crop Science. 54:1304-1321. DOI:10.2135/cropsci2013.08.0564.

Haley, S., Johnson, J., Peairs, F., Stromberger, J., Hudson-Ams, A., Seifert, S., Valdez, V., Kottke, R., Rudolph, J., Bai, G., Chen, X., Bowden, R.L., Jin, Y., Kolmer, J.A., Chen, M., Seabourn, B.W., Dowell, F.E. 2014. Registration of 'Antero' Wheat. Journal of Plant Registrations. doi: 10.3198/jpr2013.12.0072crc.

Liu, S., Yang, X., Zhang, D., Bai, G., Chao, S., Bockus, W. 2014. Genome-wide association analysis identified SNPs closely linked to a gene resistant to Soil-borne wheat mosaic virus. Theoretical and Applied Genetics. 127:1039-1047.

Cai, J., Bai, G. 2014. Quantitative trait loci for Fusarium head blight resistance in Huangcandou x 'Jagger' wheat. Crop Science. DOI:10.20135/cropsci2013.12.0835.

Barkley, A., Tack, J., Nalley, L.L., Bergtold, J., Bowden, R.L., Fritz, A. 2013. Weather, disease, and wheat breeding effects on Kansas wheat varietal yields, 1985 to 2011. Agronomy Journal. 106:227-235.

Graybosch, R.A., Baenziger, P.S., Dantra, D., Regassa, T., Jin, Y., Kolmer, J.A., Wegulo, S., Bai, G., St Amand, P., Chen, X., Seabourn, B.W., Dowell, F.E., Bowden, R.L., Marshall, D.S. 2014. Release of ‘Mattern’ waxy (amylose-free) winter wheat. Journal of Plant Registrations. 8:43-48.

Chen, M., Wheeler, S., Wang, H., Whitworth, J.R. 2014. Impact of temperatures to Hessian Fly resistance of selected wheat cultivars in the Great Plains Region. Journal of Economic Entomology. 107(3): 1266-1273.

Anathakrishnan, R., Sinha, D., Murugan, M., Zhu, K., Chen, M., Zhu, Y., Smith, C.M. 2014. Comparative gut transcriptome analysis reveals differences between virulent and avirulent biotypes of the Russian wheat aphid, Diuraphis noxia. Arthropod-Plant Interactions. 8(2):79-88.

Cheng, Y., Wang, Q., Li, Z., Cui, J., Hu, S., Zhao, H., Chen, M. 2013. Cytological and comparative proteomic analyses on male sterility in Brassica napus L. induced by the chemical hybridization agent monosulphuron ester sodium. Arthropod-Plant Interactions. 8(11): e80191.

Chen, M., Wheeler, S., Davis, H., Whiteworth, J.R., Knutson, A., Giles, K.L., Skinner, M. 2014. Molecular markers for identification of Hessian fly males caught on pheromone traps. Journal of Economic Entomology. 107(3):1110-1117.

Currie, Y., Moch, J., Underwood, J., Kharabsheh, H., Quesenberry, A., Miyagi, R., Thomas, C., Boney, M., Wood, S., Chen, M., Zhu, L. 2014. Transient heat-stress compromises the resistance of wheat seedlings to Hessian fly (Diptera: Cecidomyiidae) infestation. Journal of Economic Entomology. 107(1):389-395.

Baenziger, P.S., Graybosch, R.A., Regassa, T., Klein, R., Kruger, G.R., Santra, D.K., Xu, L., Rose, D., Wegulo, S., Jin, Y., Kolmer, J.A., Hein, G.L., Chen, M., Bai, G., Bowden, R.L., Poland, J.A. 2014. Registration of ‘NE06545’ (husker genetics brand freeman) hard red winter wheat. Journal of Plant Registrations. 8:279-284. DOI: 10.3198/jpr2014.02.0009crc.

Zhang, D., Bowden, R.L., Yu, J., Carver, B., Bai, G. 2014. Association analysis of stem rust resistance in U.S. Winter Wheat. PLoS One. 9(7): e103747.

Haley, S., Johnson, J., Peairs, F., Stromberger, J., Hudson-Arns, E., Seifert, S., Kottke, R.A., Valdez, V.A., Nachtman, J.J., Rudolph, J.B., Bai, G., Chen, X., Bowden, R.L., Jin, Y., Kolmer, J.A., Chen, M., Seabourn, B.W. 2014. Registration of 'Cowboy' wheat. Journal of Plant Registrations. 8:169-172.

Eckard, J., Gonzales-Hernandez, J., Chao, S., St Amand, P., Bai, G. 2014. Construction of dense linkage maps "on the fly" using early generation wheat breeding populations. Molecular Breeding. DOI:10.1007/s11032-014-0116-1.

Bansal, R., Hulbert, S., Reese, J., Whitworth, R.J., Stuart, J., Chen, M. 2014. Pyrosequencing reveals the predominance of Pseudomonadaceae in gut microbiome of a Gall Midge. Pathogens. 3(2):459-472.

Basnet, B.R., Ibrahim, A.H., Chen, X., Singh, R.P., Mason, E.R., Bowden, R.L., Liu, S.Y., Devkota, R.N., Subramanian, N.K., Rudd, J.C. 2014. Molecular mapping of stripe rust resistance QTL in hard red winter wheat TAM 111 adapted in the US high plains. Crop Science. 54:1361-1373.

Last Modified: 05/23/2017
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