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United States Department of Agriculture

Agricultural Research Service


Location: Hard Winter Wheat Genetics Research

2013 Annual Report

1a. Objectives (from AD-416):
Objective 1: Develop adapted hard red or white wheat germplasm lines with improved resistance to emerging or intractable problems in wheat production and marketing. Objective 2: Increase understanding of the molecular basis of parasite virulence, host resistance, and stress tolerance for these problems. Objective 3: Develop and apply phenotypic and genotypic selection technology for these traits to hard red or white winter wheat germplasm or cultivar development.

1b. Approach (from AD-416):
Production of high quality hard red or white winter wheat is limited by recurring intractable problems such as leaf rust, Fusarium head blight, Hessian fly, and heat stress during the grain filling period. In addition, new emerging problems such as stripe rust, stem rust, and Karnal bunt threaten the production or marketing of high quality grain. The first objective of this project is to develop adapted hard red or white wheat germplasm lines with improved resistance or tolerance to these problems. We will utilize existing sources and identify new sources of resistance, introgress them into desirable backgrounds, and then release them for use as parents of commercial cultivars. The second objective is to increase our understanding of the molecular basis of parasite virulence, host resistance, and stress tolerance to support strategic development and deployment of genetic resistance. Greater understanding of secreted virulence/avirulence effectors in the Hessian fly and the leaf rust pathogen may lead to better strategies for durability. Greater understanding of the mechanisms of durable rust resistance and heat tolerance may lead to discovery of new genes or alleles with complementary mechanisms and to optimized gene combinations in new cultivars. The third objective is to develop and apply phenotypic and genotypic selection technology for these traits to hard red or white winter wheat germplasm and cultivar development. This is an essential component of the technology transfer effort. Large-scale phenotypic screening data for Hessian fly and Karnal bunt resistance and genotypic marker data will be provided to cooperators.

3. Progress Report:
Project #5430-21000-006-00D entitled Genetic Enhancement for Resistance to Biotic and Abiotic Stresses in Hard Winter Wheat expired in FY13. This is a summary of the major accomplishments. (New #5430-21000-010-00D) Six hard red and white winter wheat germplasm lines were developed and released with high levels of minor gene, adult plant resistance to leaf and stripe rust. Five lines were released with high levels of minor gene, adult plant resistance to stem rust. Twenty adapted hard winter wheat lines were released carrying single genes Sr22, Sr32, Sr35, Sr39, or Sr40. Four adapted hard winter wheat lines were released carrying the combination of Sr22 plus Sr35. One germplasm line was released carrying the combination of Sr22, Sr26, Sr35, and Lr34, which should be more durable than lines with single or double Sr genes. In collaboration with ARS researchers in St. Paul, MN and KSU researchers, six stem rust resistance genes, Sr51, Sr52, Sr53, SrTa1662, SrTa10171, and SrTa10187, were discovered and transferred to bread wheat from wild wheat relatives. Improved germplasm with shorter alien segments were developed for Sr22 and Sr35. An improved compensating translocation was developed for Sr44. All of these genes are effective against the Ug99 group of stem rust races. Genes for resistance to Fusarium head blight (FHB) were identified in three wheat varieties including Chinese wheat landraces ‘Huangfangzhu’, ‘Haiyanzhong’, and Kansas variety ‘Heyne’. A novel QTL for FHB was discovered on chromosome 7A of variety ‘Sumai#3’. In collaboration with KSU researchers, a novel FHB resistance gene was found in Leymus racemosus and named Fhb3. Three adapted hard red winter wheat lines were released carrying Fhb1. Two hard red winter wheat germplasm lines were released carrying a shorter alien segment with the Hessian fly resistance gene H21. A wheat gene called Mds-1 was found to be a susceptibility gene for Hessian fly parasitism of wheat, thus potentially opening new strategies for durable resistance. Hessian fly secreted salivary gland proteins, which are potential effectors of resistance reactions, were characterized and found to evolve rapidly. Levels of proteins EF-Tu and rubisco activase were both associated with heat stress tolerance. Heterologous expression of a plastid EF-Tu reduced protein thermal aggregation and enhanced CO2 fixation in wheat following heat stress. Four wheat lines were identified with tolerance to post-anthesis heat stress. In collaboration with several land grant universities, seventeen new wheat cultivars for the Great Plains were developed and registered. ARS researchers helped select the varieties for resistance to rust diseases, Hessian fly, Fusarium head blight, aluminum tolerance, pre-harvest sprouting, etc. using a combination of traditional screening and molecular marker techniques. Genotyping-by-sequencing (GBS) was developed to leverage the power of next-generation sequencing technology to discover and assay thousands of DNA markers. Genomic selection using GBS markers was successfully used to predict the performance of breeding lines for grain yield, heading date, and thousand kernel weight of wheat.

4. Accomplishments
1. Three new genes for resistance to Ug99 stem rust transferred from a wild wheat relative. Wheat stem rust is a serious threat to global wheat production due to the emergence of new highly virulent races in Africa, known collectively as the Ug99 group. In collaboration with Kansas State University, ARS researchers in Manhattan, KS and St. Paul, MN identified three new resistance genes to Ug99 in the wild wheat relative, Aegilops tauschii, and transferred them to bread wheat. The new genes were designated SrTA1662, SrTA10187, and SrTA10171 and were mapped to chromosomes 1D, 6D, and 7D, respectively. These genes can be used in combinations with other resistance genes to develop new wheat varieties with more durable resistance to stem rust.

2. A gene controlling pre-harvest sprouting in hard white winter wheat identified. When harvest of mature wheat is delayed by rain, pre-harvest sprouting often occurs, especially in some hard white winter wheat cultivars. Sprouted wheat is low in quality and is often suitable only for animal feed. A sprouting tolerance gene called TaPHS1 was identified on chromosome 3A by researchers from ARS and Kansas State University in Manhattan, KS. Many white wheat cultivars carry a nonfunctional version of this gene and thus are susceptible to pre-harvest sprouting. A DNA marker developed from the gene will allow breeders to easily and accurately select future varieties that carry tolerance to pre-harvest sprouting.

3. Wheat gene Mds-1 governs susceptibility to Hessian fly. Hessian fly is a type of gall midge that stunts and kills wheat seedlings and also causes lodging of adult plants. Many resistance genes against Hessian fly have been deployed. However, most have been rapidly overcome by new biotypes of the Hessian fly, so new strategies are needed. In collaboration with Kansas State University, ARS researchers in Manhattan, KS found a wheat gene called Mds-1 that is commandeered and up-regulated by the Hessian fly when it parasitizes the wheat plants. When the Mds-1 gene was experimentally deactivated in a susceptible cultivar, plants became immune to all biotypes of Hessian fly. Thus, Mds-1 is a susceptibility gene that is required by the Hessian fly to parasitize wheat. Modification of susceptibility genes like Mds-1 may provide a potentially broad and durable source of resistance to Hessian fly and other pests.

4. Genotyping-by-sequencing proves to be a useful tool for genomics. Genotyping-by-sequencing (GBS) is a new technique that uses next-generation sequencing for simultaneously discovering and scoring thousands of inexpensive, high-density genetic markers with no prior genomic information required. One of the problems with whole genome sequencing is assembling the resulting data into the correct order. ARS researchers in Manhattan, KS and collaborators showed that GBS can be used in ordering whole genome sequence data using genetic linkage information from segregating populations. This new method, called PopSeq, is independent of prior genomic resources and is much more rapid and inexpensive than the conventional approach. PopSeq will allow the cost-efficient assembly of well-ordered genomic sequence information for any sexually reproducing species.

5. Genotyping-by-sequencing becomes the method of choice for large scale genotyping of wheat. ARS researchers in Manhattan, KS and their collaborators recently solved several technical issues for using genotyping-by-sequencing (GBS) in wheat. Advanced algorithms were developed for correctly identifying locations of polymorphisms in the polyploid wheat genome. GBS genotyping typically results in missing data for some individuals for some markers so new robust procedures were developed for imputing missing GBS data. These innovations have allowed GBS to become the platform of choice for large-scale genotyping projects in wheat and other crops. GBS was also shown to be superior for genetic diversity studies in wheat due to lack of bias in selecting genomic markers compared to other methods. Finally, GBS was shown to be compatible with two completely different next-generation sequencing platforms and thus is likely to be suitable for future developments in sequencing technologies.

6. Genomes of wheat leaf rust and stem rust fungi differ significantly. The rusts of wheat, caused by fungi in the genus Puccinia, cause significant yield losses each year and are found wherever wheat is grown around the world. To better understand how the rusts evolve and overcome host plant resistance, ARS researchers in Manhattan, KS and their collaborators compared three large stretches of DNA from leaf rust and stem rust fungi. Gene order was similar, but gene sequence identity varied from 26-99%. Numerous repetitive elements called retrotransposons were also found in the leaf rust fungus DNA sequence, which probably explains why the leaf rust genome is 50% larger than the stem rust fungus genome. Identification of genes that are highly conserved between the two pathogens may reveal vulnerable targets for future control strategies. Comparisons may also reveal important differences in how leaf rust and stem rust fungi have adapted to cause disease in wheat

7. Three resistance genes effective against Ug99 wheat stem rust were stacked in one germplasm line. One of the best strategies to prolong the useful life of resistance genes is to stack them together in the same line. In that way, the genes can help protect each other from defeat. ARS researchers in Manhattan, KS used DNA markers to combine stem rust resistance genes Sr22, Sr26, and Sr35 into one adapted hard red winter wheat line. The line also contains a gene called Lr34, which provides some additional resistance to stem rust as well as leaf rust and stripe rust. The germplasm line will be used by breeders to develop new hard winter wheat cultivars with more durable resistance to stem rust.

8. 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 Montana State University, Kansas State University, and Oklahoma State University, ARS researchers in Manhattan, KS participated in the development and registration of four new wheat cultivars for the Great Plains including cultivars ‘Bearpaw’, ‘Billings’, ‘Judee’, and ‘Tiger’. ARS researchers helped select the varieties for resistance to diseases and insects and quality using a combination of traditional and molecular marker techniques. These new high yielding cultivars are now available for wheat producers.

9. Software application developed for using hand-held tablets as field research notebooks. One of the difficulties faced by breeding programs is collecting and managing huge amounts of field notes with rapid turnaround times and low error rates. An application was developed by ARS researchers in Manhattan, KS for hand-held Android(TM) tablets that can be used as a replacement for paper field books. The ‘Field Book’ application is very flexible and can be used to record a variety of numeric, percentage, Boolean, date, and text data in a suitable format for field plot research. Data can then be uploaded to a local computer or to a cloud-based server. The application is available as a free download at:

Review Publications
Fellers, J.P., Soltani, B., Bruce, M.A., Linning, R., Cuomo, C.A., Szabo, L.J., Bakkeren, G. 2013. Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements. Biomed Central (BMC) Genomics. doi:10.1186/1471-2164-14-60.

Yu, X., Bai, G., Liu, S., Luo, N., Wang, Y., Richmond, D., Pijut, P.M., Jackson, S., Yu, J., Jiang, Y. 2013. Association of candidate genes with drought tolerance traits in diverse perennial ryegrass accessions. Journal of Experimental Botany. doi:10.1093/jxb/ert018.

Liu, Z., Bai, G., Bowden, R.L. 2013. Molecular markers for leaf rust resistance gene Lr42 in Wheat. Crop Science. doi: 10.2135/cropsci2012.09.0532.

Yanshi, X., Li, R., Ning, Z., Bai, G., Siddique, K., Yan, G., Baun, M., Varshney, R., Guo, P. 2013. Single nucleotide polymorphisms in HSP17.8 and their association with agronomic traits in barley. PLoS One. 8(2): e56816.

Bakhsh, A., Mengistu, N., Baenziger, P., Dweikat, I., Wegulo, S., Rose, D., Bai, G., Eskridge, K. 2013. Effect of fusarium head blight (FHB) resistance gene Fhb1 on agronomic and end-use quality traits of hard red winter wheat. Crop Science. doi: 10.2135/cropsci2012.06.0364.

You, M., Yue, Z., He, W., Yang, X., Yang, G., Xie, M., Zhan, D., Baxter, S.W., Vasseur, L., Gurr, G.M., Douglas, C.J., Bai, J., Wang, P., Cui, K., Huang, S., Li, X., Zhou, Q., Wu, Z., Chen, Q., Liu, C., Wang, B., Li, X., Xu, X., Lu, C., Hu, M., Davey, J.W., Smith, S.M., Chen, M., Xia, X., Tang, W., Ke, F., Zheng, D., Hu, Y., Song, F., You, Y., Ma, X., Peng, L., Zheng, Y., Liang, Y., Chen, Y., Yu, L., Zhang, Y., Liu, Y., Li, G., Fang, L., Li, J., Zhou, X., Lou, Y., Gou, C., Wang, J., Wang, J., Yang, H., Wang, J. 2013. A heterozygous moth genome provides insights into herbivory and detoxification. Nature Genetics. doi:10.1038/ng.2524.

Li, W., Danilova, T., Rouse, M.N., Bowden, R.L., Friebe, B., Gill, B.S., Pumphrey, M.0. 2013. Development and characterization of a compensating wheat-Thinopyrum intermedium Robertsonian translocation with Sr44 resistance to stem rust (Ug99). Theoretical and Applied Genetics. 126:1167-1177.

Olson, E., Rouse, M.N., Pumphrey, M.O., Bowden, R.L., Gill, B., Poland, J.A. 2013. Simultaneous transfer, introgression and genomic localization of genes for resistance to stem rust race TTKSK Ug99 from Aegilops tauschii to wheat. Theoretical and Applied Genetics. 126:1179-1188.

Olson, E.L., Rouse, M.N., Bowden, R.L., Pumphrey, M.O., Gill, B., Poland, J.A. 2013. Introgression of stem rust resistance genes SrTA10187 and SrTA10171 from Aegilops tauschii to wheat. Theoretical and Applied Genetics. doi: 10.1007/s00122-013-2148-z.

Chen, H., Zhu, Y., Whitworth, J.R., Reese, J.C., Chen, M. 2013. Serine and cysteine protease-like genes in the genome of a gall midge and their interactions with host plant genotypes. Insect Biochemistry and Molecular Biology. 43: 701-711.

Graybosch, R.A., St Amand, P., Bai, G. 2013. Evaluation of genetic markers for prediction of pre-harvest sprouting tolerance in hard white winter wheats. Plant Breeding. doi:10.1111/pbr.12071.

Cavanagh, C., Chao, S., Wang, S., Huang, B.E., Stephan, S., Kiani, S., Forrest, K., Saintenac, C., Brown Guedira, G.L., Akhunova, A., See, D.R., Bai, G., Pumphrey, M.O., Tomar, L., Wong, D., Kong, S., Reynolds, M., Lopez Da Silva, M., Bockelman, H.E., Talbert, L., Anderson, J.A., Dreisigacker, S., Baenziger, S., Carter, A., Korzun, V., Morrell, P.L., Dubcovsky, J., Morell, M., Sorrells, M., Hayden, M., Akhunov, E. 2013. Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landrace and cultivars. Proceedings of the National Academy of Sciences. 110:8057-8062.

Carlson, G.R., Berg, J.E., Kephart, K.D., Wichman, D.M., Lamb, P.F., Miller, J.H., Stougaard, R.N., Eckhoff, J.L., Riveland, N.R., Nash, D.L., Grey, W.E., Jin, Y., Kolmer, J.A., Chen, X., Bai, G., Bruckner, P.L. 2013. Registration of ‘Judee’ wheat. Journal of Plant Registrations. 7:191-194.

Carlson, G.R., Berg, J.E., Stougaard, R.N., Eckhoff, J.L., Lamb, P.F., Kephart, K.D., Wichman, D.M., Miller, J.H., Riveland, N.R., Nash, D.L., Grey, W.E., Jin, Y., Kolmer, J.A., Chen, X., Bai, G., Bruckner, P.L. 2013. Registration of ‘Bearpaw’ wheat. Journal of Plant Registrations. 7:180-183.

Veturi, Y., Kump, K., Walsh, E., Ott, O., Poland, J.A., Kolkman, J., Nelson, R., Balint Kurti, P.J., Holland, J.B., Wisser, R. 2012. Multivariate mixed linear model analysis of longitudinal data: an information-rich statistical technique for analyzing disease resistance data. Phytopathology. 102(11):1017-1025.

Mayer, K., Waugh, R., Langridge, P., Close, T.J., Wise, R.P., Graner, A., Matsumoto, T., Sato, K., Schulman, A., Muehlbaueer, G.J., Stein, N., Ariyadasa, R., Schulte, D., Poursarebani, N., Zhou, R., Steuernagel, B., Mascher, M., Scholz, U., Shi, B., Madishetty, K., Svensson, J.T., Bhat, P., Moscou, M., Resnik, J., Hedley, P., Liu, H., Morris, J., Frenkel, Z., Korol, A., Berges, H., Taudien, S., Felder, M., Groth, M., Platzer, M., Himmelbach, A., Lonardi, S., Duma, D., Alpert, M., Cordero, F., Beccuti, M., Ciardo, G., Ma, Y., Wanamaker, S., Cattonaro, F., Vendramin, V., Scalabrin, S., Radovic, S., Wing, R., Morgante, M., Nussbaumer, T., Gundlach, H., Martis, M., Poland, J.A., Spannagl, M., Pfeifer, M., Moisy, C., Tanskanen, J., Zuccolo, A., Russell, J., Druka, A., Marshall, D., Bayer, M., Sampath, D., Febrer, M., Caccamo, M., Tanaka, T., Platzer, M., Fincher, G., Schmutzer, T. 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature. 491:711-716.

Poland, J.A., Rife, T. 2012. Genotyping-by-sequencing for plant breeding and genetics. The Plant Genome. 5(3):92-102.

Poland, J.A., Endelman, J.B., Dawson, J., Rutkoski, J., Wu, S., Manes, Y., Dreisigacker, S., Crossa, J., Sanchez, H., Sorrells, M., Jannink, J. 2012. Genomic selection in wheat using genotyping-by-sequencing. The Plant Genome. 5(3):103-113.

Bernardo, A., Bowden, R.L., Rouse, M.N., Newcomb, M.S., Marshall, D.S., Bai, G. 2013. Validation of molecular markers for new stem rust resistance (Sr) genes in U.S. hard winter wheat. Crop Science. 53(3):755-764.

Khajuria, C., Williams, C.E., Bohssini, M., Whitworth, J.R., Richards, S., Stuart, J.J., Chen, M. 2013. Deep sequencing and genome-wide analysis reveals the expansion of MicroRNA genes in the gall midge Mayetiola destructor. Biomed Central (BMC) Genomics. 14:187.

Khajuria, C., Wang, H., Liu, X., Wheeler, S., Reese, J.C., El Bohssini, M., Whitworth, J.R., Chen, M. 2013. Defense mechanisms in resistant wheat seedlings in response to hessian fly attack. Biomed Central (BMC) Genomics. 14: 423.

Rutkoski, J., Poland, J.A., Jannink, J., Sorrells, M. 2013. Imputation of unordered markers and the impact on genomic selection accuracy. Genetics. 3(3):427-39.

Martin, T.J., Zhang, G., Fritz, A.K., Miller, R., Chen, M. 2013. Registration of 'Tiger' wheat. Journal of Plant Registrations. 7(2): 201-204.

Last Modified: 06/24/2017
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