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ARS Home » Plains Area » Manhattan, Kansas » Center for Grain and Animal Health Research » Hard Winter Wheat Genetics Research » Research » Research Project #424855

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

Location: Hard Winter Wheat Genetics Research

2015 Annual Report

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.

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.

Progress Report
Objective 1. More than 13,000 wheat breeding samples from 10 breeding programs were analyzed for molecular markers in the USDA-ARS Central Small Grains Genotyping Laboratory. The SRPN, NRPN, and RGON regional wheat nurseries were also characterized with more than 60 gene-specific markers linked to important traits of interest to breeders. A total of over 130,000 gene-specific marker data points were generated in 2015. In addition, over 50,000,000 genome-wide GBS marker data points were generated for wheat and barley genetics programs for the Triticeae Coordinated Agricultural Project. The data were used by wheat and barley researchers for characterizing and selecting breeding lines with desired combinations of agronomic and pest resistance traits. More than 5,000 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 with good resistance. In some cases, resistant lines were selected and then shipped back to the breeders for further evaluation. More than 3500 wheat lines from wheat breeders and geneticists in the Great Plains region were screened for resistance to stripe rust at Rossville, KS. The test also included the SRPN, NRPN, and RGON regional nurseries and four mapping populations for resistance to stripe rust. This was the fifth 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 resistance genes Sr22, Sr26, Sr35, and Lr34 in combination. Objective 2. Genotyping-by-sequencing (GBS), a new high-density genetic marker technology, was used to map and identify markers for different traits including resistance to wheat Fusarium head blight, leaf rust, stem rust, stripe rust, pre-harvest sprouting, and Hessian fly. GBS markers for key traits are being converted into KASP markers, a user-friendly marker system, for marker-assisted selection. Twenty-seven GBMAS (genotyping by multiple amplicon sequencing) markers were developed for 10 important agronomic and pest resistance traits in wheat. The new markers were validated by comparison of results with traditional markers for each trait. GBMAS has relatively simple protocols, fast turnaround times, high reliability, and low costs. An irrigated stem rust field screening nursery was conducted in 2014/2015. 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. 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; 3) heat stress tolerance, and 4) adult plant leaf rust and stripe rust on a diverse panel of 305 hard winter wheat lines from the Great Plains. Objective 3. 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 correlated with differences in the protein-coding sequences. The goal is to determine which genes in the pathogen explain the differences in virulence patterns. We have identified two leaf rust proteins that appear to be recognized by wheat resistance genes Lr9 and Lr26. We will now be able to study how the plant recognizes the proteins as well as what amino acid changes are responsible for changes in virulence. Hessian fly is a destructive pest of wheat and a model organism to study gall midges. Hessian fly has six developmental stages including eggs, three instars of larvae, pupae and adults. The molecular mechanisms controlling the transition between different stages are not known and could provide useful information to develop new means to control this destructive pest. We have used the recently developed technology called RNA-Seq to have systematically analyzed genes that are differentially expressed between two successive stages of Hessian fly. We found that there was a massive shift in gene expression when the insect transitioned from one stage to the next, and each stage expressed a unique combination of genes. The large data sets of differentially expressed genes identified in this study should be very useful to provide targets for further research that could eventually lead to new means to control this insect pest. The information reported in this study should also be very useful for comparative research for other insect species as well as for non-insect organisms. Hessian fly is a destructive pest of wheat and can overcome wheat resistance relatively quickly (within 3-8 years after the initial deployment of a resistance gene). To develop wheat cultivars with more durable resistance, we need a better understanding of the molecular mechanisms for Hessian fly avirulence or virulence. The first step to reveal the mechanism for Hessian fly avirulence/virulence is to map and clone Hessian fly avirulence/virulence genes. To map and clone Hessian fly avirulence genes, we need to identify useful molecular markers. During this year, we identified over 7,000 single nucleotide polymorphisms (SNPs) from three different Hessian fly populations. These observations indicate that the identified SNPs could be converted into genetic markers for mapping Hessian fly avirulence and other interesting traits.

1. New DNA markers found for pre-harvest sprouting resistance gene in white wheat. Pre-harvest sprouting (PHS), which occurs when mature wheat spikes are dampened by rainy weather, reduces both wheat grain yield and end-use quality. It is an especially big concern in white wheat varieties, which tend to be more susceptible to PHS. Growing PHS-resistant cultivars is the most effective approach to reduce PHS damage. ARS researchers in Manhattan, KS identified new DNA markers for a PHS resistance gene on wheat chromosome arm 4AL. These new markers can be easily used for marker-assisted selection to improve PHS resistance in white wheat varieties.

2. Susceptibility to pre-harvest sprouting is a result of wheat domestication. Pre-harvest sprouting (PHS) is a major problem in wheat that is grown in humid regions. Previously, ARS researchers in Manhattan, KS cloned a gene named TaPHS1 for PHS resistance from chromosome 3AS and found that two mutations in the gene turned PHS-resistant genotypes into PHS-susceptible genotypes. PHS assay of wheat progenitor accessions showed that the wild types were highly PHS resistant, while domesticated types gained increased PHS susceptibility during domestication. DNA markers were developed based on these mutations and can be used to increase sprouting tolerance through marker-assisted selection.

3. New DNA marker found for leaf rust resistance gene. Leaf rust is a common wheat disease that is found all over the world. In the United States, the most cost-effective way to combat the disease is to use resistance genes. One of these resistance genes, Lr16, provides resistance to many races of leaf rust and is very desirable in wheat breeding programs. Since it is difficult to accurately score resistance using visual methods, plant breeders need DNA markers that they can use to follow Lr16 in their breeding programs. ARS researchers in Manhattan, KS described a new technique to develop markers that takes advantage of the similarities among resistance genes and new high throughput DNA sequencing technology. A new DNA marker was developed for Lr16 that is easy to use and expected to be efficient for identifying resistant plants.

4. Heat tolerance found in primitive cultivars of emmer and durum wheat. Compared to many other crops, bread wheat is very susceptible to high temperature stress during the grain filling period. Heat stress is currently one of the biggest constraints on wheat yields in the Great Plains region of the US, often resulting in losses of 50% or more. The problem is expected to get worse as atmospheric carbon dioxide levels increase. ARS researchers in Manhattan, KS investigated the variation for heat tolerance in five primitive cultivated subspecies of emmer and durum wheat. Several lines with good tolerance to high temperature stress were identified. These will be useful to breeding programs for the improvement of heat tolerance in bread wheat.

5. Glutathione metabolic pathway involved in resistance to Hessian fly. Hessian fly is a destructive pest of wheat. The insect pest is mainly controlled by deploying resistant wheat cultivars. Unfortunately, resistance conferred by major resistance genes is usually short-lived, lasting only for 3-8 years. To develop more durable resistant cultivars, we need a better understanding of the resistance mechanism in wheat to Hessian fly. Glutathione is a small peptide that plays a role in various physiological processes in nearly all organisms. ARS researchers in Manhattan, KS examined the changes in glutathione abundance and metabolic pathways in both resistant and susceptible plants following Hessian fly attack. They found that the abundance of total glutathione increased up to 60% in resistant plants within 72 hours following Hessian fly attack, but no increase in susceptible plants. The results provide a foundation for elucidating the molecular processes involved in glutathione-mediated plant resistance to Hessian fly and potentially other pests as well.

6. Three new wheat cultivars co-developed by ARS and universities. New wheat cultivars are needed by producers to maintain and increase yield and grain quality. In collaboration with Montana State University and Texas A&M University, ARS researchers in Manhattan, KS participated in the development and registration of three new wheat cultivars for the Great Plains including cultivars ‘Colter’, ‘TAM 305’, and ‘Warhorse’. These new high yielding cultivars are now available for wheat producers.

Review Publications
Shen, X., Ma, L., Zhong, S., Liu, N., Zhang, M., Chen, W., Zhou, Y., Li, H., Zhang, Z., Li, X., Bai, G., Zhang, H., Tan, F., Ren, Z., Luo, P. 2015. Identification and genetic mapping of the putative Thinopyrum intermedium-derived dominant powdery mildew resistance gene PmL962 on wheat chromosome arm 2BS. Theoretical and Applied Genetics. doi: 10.1007/s00122-014-2449-x.
Liu, S., Sehgal, S., Li, J., Lin, M., Trick, H., Yu, J., Gill, B.S., Bai, G. 2013. Cloning and characterization of a critical regulator for pre-harvest sprouting in Wheat. Genetics. doi: 10.1534/genetics.113.152330.
Aggarwal, R., Subramanyam, S., Zhao, C., Chen, M., Harris, M.O., Stuart, J.J. 2014. Avirulence effector discovery in a plant galling and plant parasitic arthropod, the Hessian fly (Mayetiola destructor). PLoS One. 9(6):e100958.
Liu, X., Khajuria, C., Li, J., Trick, H.N., Huang, L., Gill, B.S., Reeck, G.R., Antony, G., White, F.F., Chen, M. 2013. Wheat Mds-1 encodes a heat-shock protein and governs susceptibility towards the Hessian fly gall midge. Nature Communications. 4:2070.
Kono, T., Kiran, S., Poland, J.A., Morrell, P. 2013. SNPMeta: SNP annotation and SNP metadata collection without a reference genome. Molecular Ecology Resources. 14, 419-425.
Li, C., Bai, G., Carver, B., Chao, S., Wang, Z. 2015. Single nucleotide polymorphism markers linked to QTL for wheat yield traits. Euphytica. Published online 30 May 2015. DOI: 10.1007/s10681-015-1475-3.
Yu, X., Pijut, P., Byrne, S., Asp, T., Bai, G., Jiang, Y. 2015. Candidate gene association mapping for winter survival and spring regrowth in perennial ryegrass. Plant Science. 235:37-35.
Lin, M., Cai, S., Wang, S., Liu, S., Zhang, G., Bai, G. 2015. Genotyping-By-Sequencing (GBS) identified SNP tightly linked to QTL for pre-harvest sprouting resistance. Theoretical and Applied Genetics. DOI: 10.1007/S00122-015-2513-1.
Talukder, S.K., Prasad, V., Todd, T., Poland, J.A., Bowden, R.L., Fritz, A.K. 2015. Effect of cytoplasmic diversity on post anthesis heat tolerance in wheat. Euphytica. 204:383-394. DOI:10.1007/s10681-014-1350-7.
Ibrahim, A., Rudd, J., Devkota, R., Baker, J., Sutton, R., Simoneaux, B., Opena, G., Herrington, R., Rooney, L., Dykes, L., Awika, J., Nelson, L.R., Fritz, A., Bowden, R.L., Graybosch, R.A., Jin, Y., Seabourn, B.W., Chen, X., Kolmer, J.A., St Amand, P., Bai, G., Duncan, R. 2015. Registration of 'TAM 305' hard red winter Wheat. Journal of Plant Registrations. doi:10.3198/jpr2014.08.0054crc.
Johnson, A.J., Shukle, R.H., Chen, M., Srivastava, S., Subramanyam, S., Schemerhorn, B.J., Weintraub, P.G., Moniem, H., Flanders, K.L., Williams, C.E. 2015. Differential expression of candidate salivary effector proteins in field collections of Hessian fly, Mayetiola destructor. Insect Molecular Biology. 24(2):191-202. DOI: 10.1111/imb.12148.
Li, G., Wang, Y., Chen, M., Edae, E.A., Poland, J.A., Akhunov, E., Chao, S., Bai, G., Carver, B.F., Yan, L. 2015. Precisely mapping a major gene conferring resistance to Hessian fly in bread wheat using genotyping-by-sequencing. Biomed Central (BMC) Genomics. 16:108. doi:10.1186/s12864-015-1297-7.
Harris, M.O., Friesen, T.L., Xu, S.S., Chen, M.S., Giron, D., Stuart, J.J. 2015. Pivoting from Arabidopsis to wheat to understand how agricultural plants integrate responses to biotic stress. Journal of Experimental Botany. 66(2):513-531.
Zhao, C., Escalanta, L.N., Chen, H., Benatti, T.R., Qu, J., Chellapilla, S., Waterhouse, R.M., Wheeler, D., Andersson, M.N., Bao, R., Batterton, M., Behura, S.K., Blankenburg, K.P., Caragea, D., Carolan, J.C., Coyle, M., El-Bouhssini, M., Francisco, L., Friedrich, M., Gill, N., Grace, T., Grimmelikhuijzen, C.J., Han, Y., Hauser, F., Herndon, N., Holder, M., Ioannidis, P., Jackson, L., Javaid, M., Jhangiani, S.N., Johnson, A.J., Kalra, D., Korchina, V., Kovar, C.L., Lara, F., Lee, S.L., Liu, X., Lofstedt, C., Mata, R., Mathew, T., Muzny, D.M., Nagar, S., Nazareth, L.V., Okwuonu, G., Ongeri, F., Perales, L., Peterson, B.F., Pu, L., Robertson, H.M., Schemerhorn, B.J., Scherer, S.E., Shreve, J.T., Simmons, D., Subramanyam, S., Thornton, R.L., Xue, K., Weissenberger, G.M., Williams, C.E., Worley, K.C., Zhu, D., Zhu, Y., Harris, M.O., Shukle, R.H., Werren, J.H., Zdobnov, E.M., Chen, M., Brown, S.J., Stuart, J.J., Richards, S. 2015. A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor. Current Biology. 25:613-620. DOI: 10.1016/j.cub.2014.12.057.
Shoup Rupp, J.L., Simon, Z.G., Gilett-Walker, B., Fellers, J.P. 2014. Resistance to Wheat streak mosaic virus identified in synthetic wheat lines. Euphytica. 198:223-229.
Xu, X., Bai, G., Carver, B.F., Zhan, K., Huang, Y., Mornhinweg, D.W. 2015. Evaluation and reselection of wheat resistance to Russian wheat aphid biotype 2. Crop Science. 55(2):695-701.
Jin, F., Zhang, D., Bockus, W., Baenziger, S., Carver, B., Bai, G. 2013. Fusarium head blight resistance in U.S. winter wheat cultivars and elite breeding lines. Crop Science. 53:2006-2013.
Berg, J.E., Lamb, P.E., Miller, J.H., Wichman, D.M., Stougaard, R.N., Eckhoff, R.N., Kephart, K.D., Nash, D.L., Grey, W.E., Gettel, D., Larson, R., Jin, Y., Kistler, H.C., Chen, X., Bai, G., Bruckner, P.L. 2014. Registration of Warhorse wheat. Journal of Plant Registrations. 8(2):173-176.
Berg, J.E., Wichman, D.M., Kephart, K.D., Eckhoff, R.N., Stougaard, R.N., Lamb, P.F., Miller, J.H., Nash, D.L., Grey, W.E., Johnston, M., Gettel, D., Larson, R., Jin, Y., Kolmer, J.A., Chen, X., Bai, G., Bruckner, P.L. 2014. Registration of Colter wheat. Journal of Plant Registrations. 8(3):285-287.
Gore, M.A., Fang, D.D., Poland, J.A., Zhang, J., Percy, R.G., Cantrell, R.G., Thyssen, G.N. 2014. Linkage map construction and QTL analysis of agronomic and fiber quality traits in cotton. The Plant Genome. 7(1):1-10.
Rutkoski, J.E., Sorrells, M., Poland, J.A., Singh, R.P., Huerta-Espino, J., Bhavani, S., Barbier, H., Rouse, M.N., Jannink, J. 2014. Genomic selection for quantitative adult plant stem rust resistance in wheat. The Plant Genome. DOI: 10.3835/plantgenome2014.02.0006.
Rife, T.W., Wu, S., Bowden, R.L., Poland, J.A. 2015. Spiked GBS: A unified, open platform for single marker genotyping and whole-genome profiling. Biomed Central (BMC) Genomics. 16:248. DOI:10.1186/s12864-015-1404-9.
Talukder, S.K., Babar, A.M., Vijayalakshmi, K., Poland, J.A., Prasad, V., Bowden, R.L., Fritz, A.K. 2015. Mapping QTL for the traits associated with heat tolerance in Wheat (Triticum Aestivum L.). Crop Science. 15:97. DOI:10.1186/s12863-014-0097-4.
Currie, Y., Chen, M., Nickolov, R., Bai, G., Zhu, L. 2014. Impact of transient heat stress on polar lipid metabolism in seedlings of wheat near-isogenic lines contrasting in resistance to hessian fly (Cecidomyiidae) infestation. Journal of Economic Entomology. 107(6):2196-2203. doi:10.1603/EC14286.
Underwood, J., Moch, J., Chen, M., Zhu, L. 2014. Exogenous salicylic acid enhances the resistance of wheat seedlings to hessian fly (Diptera: Cecidomyiidae) infestation under heat stress. Journal of Economic Entomology. 107(5): 2000-2004. doi:10.1603/EC14223.
Liu, X., Zhang, S., Whitworth, J., Stuart, J.J., Chen, M. 2015. Unbalanced activation of glutathione metabolic pathways suggests potential involvement in plant defense against the gall midge mayetiola destructor in wheat. Scientific Reports. 5, Article number: 8092. doi:10.1038/srep08092.
Fu, J., Bowden, R.L., Prasad, V., Ibrahim, A. 2015. Genetic variation for heat tolerance in primitive cultivated subspecies of Triticum turgidum L. Journal of Crop Improvement. 29:565-580. DOI: 10.1080/15427528.2015.1060915.
Hiralshi, H., Oatmin, J., Blunk, L., Gutierrez, W., Fellers, J.P., Gordon, M., Bokhari, W., Ikeda, Y., Miles, D., Asano, M., Tazi, L., Rothenburg, S., Brown, S.J., Asano, K. 2014. Essential role of eIF5-mimic protein in animal development is linked to control of ATF4 expression. Nucleic Acids Research. 42(16):10321-10330.
Rezac-Harrison, N., Fritz, A.K., Glasscock, J., Ahmed, S., Messina, D.N., Fellers, J.P. 2015. Using RNA-seq and in silico subtraction to identify resistance gene analog markers for Lr16 in wheat. The Plant Genome. 8(2):1-9. doi: 10.3835/plantgenome2014.08.0040.