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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

2018 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. For developing germplasm with resistance to rusts, approximately 5000 wheat lines were screened annually for resistance to stripe rust at Rossville, Kansas. The tests included entries from the regional nurseries, gene mapping populations, and advanced lines from 17 public and private breeding programs. Approximately 2000 lines were screened annually for resistance to stem rust at Manhattan, Kansas; and approximately 1500 lines were screened annually for resistance to leaf rust at Manhattan and Hutchinson, Kansas. Spring wheat variety ‘Kingbird’ has some of the highest known levels of durable, minor gene resistance to stem rust. Rust resistance genes in Kingbird were mapped and transferred to adapted hard winter wheat lines that can be used as parents by breeders. Durable, minor gene resistance to leaf rust in a slow rusting line, CI13227, was mapped and a new slow rusting gene on chromosome 2D was discovered. Combinations (pyramids) of major resistance genes to stem rust should provide much greater durability than single genes. A combination of stem rust resistance genes Sr22, Sr26, Sr35, Sr38/Yr17, Sr57/Lr34, and Sr58/Lr46 was assembled in several adapted winter wheat backgrounds for use as parents by wheat breeders. In collaboration with ARS and university colleagues, three new stem rust resistance genes, SrTA10171, SrTA10187, and SrTA1662 from Aegilops tauschii, a wild wheat relative, were discovered. Germplasm with these new genes in adapted backgrounds was produced. A large proportion of our crossing effort was dedicated to novel sources of stripe rust resistance. Donor germplasm included 12 ARS-developed spring wheats from the Pacific Northwest; 6 spring wheat accessions from the National Small Grains Germplasm Collection project; 4 Australian spring wheats carrying resistance genes Yr47, Yr51, Yr57, and Yr63; Yr40 from Aegilops geniculata; seedling resistance genes Yr5+Yr15 in combination; 10 winter wheats from the Pacific Northwest; 29 complex sources of adult plant resistance in hard winter wheat; and 131 winter wheat landrace accessions from the National Small Grains Collection. In collaboration with university colleagues, race-specific resistances to stripe rust in cultivars ‘TAM 111’, ‘Jagger’, and ‘Heyne’ were mapped. For Hessian fly, approximately 5,500 wheat lines were screened for public and private breeding programs annually in greenhouse tests. Studies were completed on heat-sensitivity of different Hessian fly resistance genes. Cultivars carrying resistance genes H15, H26, and H32 exhibited the best temperature stability, whereas cultivars containing H17, H18, and H19 had the worst temperature stability. In collaboration with university researchers, a novel gene for Hessian fly resistance was discovered in the popular hard red winter wheat variety, ‘Duster’. Crosses and backcrosses to an adapted winter wheat variety were made with 19 spring durum wheats that have temperature-stable resistance to Hessian fly. For Fusarium head blight (FHB), genes for resistance were mapped from Chinese wheat landraces ‘Huangfangshu’ and ‘Huangcandou’ and two new resistance genes were found. A dominant male-sterile facilitated recurrent selection population has been developed using 16 Asian sources of resistance and a select group of regionally-adapted resistance sources. Combinations of Fhb1, an important Fusarium head blight resistance gene, and Fhb6, a new resistance gene introduced from Elymus tsukushiensis, into regional winter wheats have been constructed. Fhb1 was also pyramided with two resistance genes on chromosome 5A by marker-assisted backcrossing. Three new mapping populations for native FHB resistance were developed from crosses of ‘CI13227’/’Lakin’, ‘Lyman’/’Overley’, and ‘Overland’/’Everest’. For heat tolerance, breeding populations have been constructed using several heat tolerant winter wheat donor lines. A dominant male-sterile-facilitated recurrent selection population has also been initiated using these sources of tolerance. A new initiative has been launched to capture the heat and drought tolerance of wild emmer wheat (Triticum dicoccoides) for the improvement of bread wheat. This species, which is the wild ancestor of durum wheat, is adapted to exceptionally hot, dry environments and should carry useful stress tolerance genes. More than 10,000 wheat breeding samples from 12 breeding programs were analyzed annually for molecular markers in our genotyping lab. More than 60 million genome-wide and 150,000 sequence-specific data points were generated for wheat geneticists and breeders. The regional wheat nurseries were also characterized with more than 100 sequence-specific markers linked to important traits of interest to breeders. The genotypic data were used in conjunction with phenotypic data by wheat researchers for characterizing and selecting breeding lines with desired combinations of agronomic and pest resistance traits. During this project, 31 cultivars and 22 germplasm lines were cooperatively developed by this unit, other ARS units, and university breeding programs. We also provided data for cultivar development by private breeding programs. Objective 2. To make breeding more efficient, we were the first to apply a high throughput marker technology called genotyping-by-sequencing (GBS) to wheat and barley. We showed that GBS is useful for performing genome-wide association mapping and genomic selection in wheat. We also designed a high throughput method called genotyping by multiplexing amplicon sequencing (GBMAS) that optimizes conditions for sequencing barcoded sets of informative sequence-specific amplicons simultaneously from different wheat samples. A large effort was made to develop new sequence-specific markers and to convert old markers from obsolete marker platforms to new high throughput marker technologies based on single nucleotide polymorphisms. Based on the candidate gene that we cloned, TaHRC, we developed a new competitive allele-specific PCR (KASP) DNA marker for Fhb1. We showed that the marker is highly diagnostic in worldwide wheat germplasm. An important sprouting tolerance gene, TaPHS1, was cloned and new diagnostic markers were developed to select for sprouting tolerance without the laborious mist bench method that was used previously. A new KASP marker was developed for the highly effective Sbm1 resistance gene for wheat soilborne mosaic virus so that difficult field testing for resistance is no longer needed. We recently discovered a gene controlling wheat grain size on chromosome 7A in soft winter wheat. New KASP markers have been developed to select for this gene and move it into hard winter wheat varieties to improve yield potential. In addition, new high throughput markers were developed for rust resistance genes Sr22, Sr26, Sr35, Lr42, Lr77, Lr78, and a new slow rusting gene for leaf rust on chromosome 2D. In total, we have developed more than 80 new KASP markers. Objective 3. In the cereal rusts, pathogen gene products called effectors are secreted into plant cells. When effectors are recognized and trigger host resistance, the effector is called an avirulence factor. Identification of avirulence factors in the pathogen is key to understanding the mechanisms of virulence and resistance and, ultimately, designing more durable resistance strategies. A chemical mutagen was used to knock-out avirulence factors in the leaf rust pathogen race BBBD. Mutants were identified with changes in virulence to resistance genes Lr2a, Lr2c, Lr11, Lr16, Lr17, Lr26, and Lr52. DNA was isolated from all of the mutants and sequenced to identify candidate effector genes. Candidate effectors will be tested for ability to trigger race-specific resistance reactions. Different races of the leaf rust fungus are expected to express different effectors. These effectors are, in turn, expected to differentially affect gene expression patterns in the wheat host. Six different races of leaf rust fungus were used to infect susceptible wheat plants. RNA was sequenced from infected tissues to determine gene expression patterns in the wheat. Forty-seven wheat genes were verified to have differential expression patterns for the six races. Two wheat genes were correlated with race-specificity and could be important targets of manipulation by the pathogen. An important tool for understanding the rust pathogen’s arsenal is to obtain the complete genomic sequence. In collaboration with an international consortium, we produced a complete assembly of the genome of leaf rust fungus race BBBD in 2016. Subsequently, BBBD was re-sequenced using new platforms to try to improve the genome assembly and separate the two haplotypes of the genome. The different sequence datasets were assembled to produce a virtually complete whole genomic sequence of BBBD. For Hessian fly, insect larvae secrete effectors into wheat plant cells, much like the rust pathogens. Understanding Hessian fly effectors is key to designing more durable strategies for resistance. In cooperation with university and ARS collaborators, we cloned the first Hessian fly avirulence gene, vH13, which is recognized by resistance gene H13. It was also the first effector ever cloned from an arthropod. We also cloned the avirulence gene vH24 that is recognized by resistance gene H24. This work may open the door to cloning additional avirulence factors in this insect. To develop more durably resistant cultivars, we need a better understanding of the host targets of Hessian fly effectors. We showed that the wheat gene Mds-1 is expressed at high levels during parasitism by the larvae. Silencing of Mds-1 by RNA interference conferred immunity to all Hessian fly biotypes on normally susceptible wheat genotypes. Therefore, Mds-1 appears to be a major susceptibility gene in wheat for the Hessian fly. Modification of susceptibility genes may provide broad spectrum and durable sources of resistance to Hessian fly.

1. Temperature stability of Hessian fly resistance genes in wheat. The Hessian fly is one of the most destructive pests of wheat. Host plant resistance is one of the best control measures for this insect pest, but it often fails when warm temperatures prevail. ARS researchers in Manhattan, Kansas examined the temperature sensitivity of resistance in wheat cultivars containing 20 different resistance genes. Cultivars carrying resistance genes H15, H26, and H32 exhibited the best temperature stability of resistance, whereas cultivars containing H17, H18, and H19 were the least temperature-tolerant. Our results should provide useful information for breeders to choose which resistance genes to be incorporated into their breeding lines based on historic temperatures in their regions.

2. New slow rusting resistance gene for wheat leaf rust. Leaf rust is an important wheat disease worldwide. Slow rusting resistance has proven more durable than conventional resistance against new virulent races of the leaf rust fungus. ARS researchers in Manhattan, Kansas identified four slow rusting resistance genes in winter wheat line CI13227. A new resistance gene on chromosome 2D showed the consistently largest effect on slow rusting traits. Genetic markers were developed and made available to select for the new resistance gene and develop new cultivars with more durable resistance to leaf rust.

3. Wheat differential gene expression induced by different races of the wheat leaf rust fungus. Leaf rust is one of the most important diseases of wheat. The leaf rust pathogen population consists of many different races that are each able to overcome particular sets of resistance genes in the host plant. The leaf rust races produce secreted molecules called effectors that are thought to suppress host defenses. Different races are expected to produce different effectors. ARS researchers in Manhattan, Kansas determined that different races of the leaf rust pathogen cause different patterns in wheat gene expression during infection. Two wheat genes were differentially affected by the races and could be important targets of manipulation by the pathogen. This information increases our understanding of host-parasite interactions and may lead to new strategies for more durable resistance.

4. Genetic basis for sprouting tolerance in wheat cultivar ‘Danby’ determined. Pre-harvest sprouting (PHS) causes significant losses in grain yield and end-use quality. Usually white wheat is preferred for Asian noodles and steamed breads, but it is more susceptible to PHS than red wheat. ‘Danby’ is a popular white wheat cultivar and has a high level of PHS resistance. ARS researchers in Manhattan, Kansas found that one major gene on the short arm of chromosome 3A of Danby explained 20 to 44% of the sprouting variation. This gene is the same as a previously cloned gene, TaPHS1. In addition, two new minor genes for PHS resistance were detected on chromosome arms 3B and 5A. DNA markers for all three genes were developed and made available for marker-assisted selection for PHS resistance in future cultivars of white wheat.

5. Wheat midge salivary proteins characterized. The wheat midge is a destructive insect pest that attacks wheat kernels during the grain filling stage of growth. Wheat midge larvae inject saliva into plant tissues during feeding. Some of the components in the saliva are thought to reprogram host metabolic pathways and facilitate parasitism by the larvae. ARS researchers in Manhattan, Kansas analyzed gene expression in the salivary glands of larvae during feeding. They found that about 25% of expressed genes encode secreted proteins. These secreted salivary gland proteins (SSGPs) can be classified into 97 groups based on their sequence similarity. Most SSGP-encoding genes appear to be under strong selection for mutations that generate amino acid changes within the coding region. The identification of the genes encoding SSGPs provides a foundation for further studies on the biological and biochemical functions of these proteins as well as for comparative analyses among different insects that share similar feeding mechanisms, such as the Hessian fly.

6. Wild wheat relative Dasypyrum villosum is a potential source of heat tolerance for wheat. Across wheat growing regions in the U.S. and globally, wheat often experiences terminal heat stress during the post-flowering period that reduces both yield and grain quality. Dasypyrum villosum, a wild relative of wheat, has been a useful genetic resource for the improvement of several traits in wheat. ARS researchers in Manhattan, Kansas found that D. villosum is more heat-tolerant than common wheat and that the single kernel weight was the yield component responsible for the tolerance. Two accessions originating in Italy and one from Turkey showed the highest terminal heat tolerance. D. villosum may be a useful novel resource for the improvement of heat tolerance in common wheat.

Review Publications
Li, C., Li, C., Carver, B., Bowden, R.L., Wang, Z., Bai, G. 2017. Mapping of quantitative trait loci for leaf rust resistance in the wheat population Ning7840 x Clark. Plant Disease. 2017(101):1974-1979.
Hussain, W., Baenziger, P., Belamkar, V., Guttieri, M.J., Venegas, J., Easterly, A., Poland, J. 2017. Genotyping-by-sequencing derived high-density linkage map and its Aapplication to QTL mapping of flag leaf traits in bread wheat. Nature Scientific Reports. Scientific Reports 7, Article number: 16394 (2017). doi: 10.1038/s41598-017-16006-z.
Frels, K., Guttieri, M.J., Joyce, B., Baenziger, P. 2017. Evaluating canopy spectral reflectance vegetation indices to estimate nitrogen use traits in hard winter wheat. Field Crops Research. 217 (2018) 82-92.
El-Basyoni, I., Lorenz, A.J., Guttieri, M.J., Frels, K., Baenziger, P., Poland, J., Akhunov, E. 2018. A comparison between genotyping-by-sequencing and array-based scoring of SNPs for genomic prediction accuracy in winter wheat. Plant Science. 270:123-130.
Navrotskyi, S., Baenziger, P., Regassa, T., Guttieri, M.J., Rose, D. 2017. Variation in asparagine concentration in Nebraska wheat. Cereal Chemistry. 95(2):264-273.
Al-Jbory, Z., Anderson, K.M., Harris, M.O., Mittapalli, O., Whitworth, R., Chen, M. 2018. Transcriptomic analyses of the secreted proteins from the salivary glands of the wheat midge larvae. Journal of Insect Science. 18(1):17.
Mourad, A.M., Sallam, A., Belamkar, V., Wegulo, S., Bowden, R.L., Jin, Y., Mahdy, E., Bakheit, B., El-Wafaa, A., Poland, J., Baenziger, P.S. 2018. Genome-wide association study for identification and validation of novel SNP markers for Sr6 stem rust resistance gene in bread wheat. Frontiers in Plant Science. 9:380.
Xia, Y., Li, R., Bai, G., Siddique, K., Varshney, R., Baum, M., Yan, G., Guo, P. 2017. Genetic variations of HvP5CS1 and their association with drought tolerance related traits in barley (Hordeum vulgare L.). Scientific Reports. 7:7870.
Chen, J., Li, R., Xia, Y., Bai, G., Peiguo, G., Zhiliang, W., Hua, Z., Siddique, K. 2017. Development of EST-SSR markers in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee) based on de novo transcriptomeic assemblies. PLoS One. 12(9):e0184736.
Liu, N., Lin, M., Xu, X., Bai, G. 2017. Genome-wide association analysis of powdery mildew resistance in U.S. winter wheat. Scientific Reports. 7:11743.
Zhang, G., Martin, T., Fritz, A., Miller, R., Bai, G., Chen, M., Bowden, R.L. 2017. Registration of ‘Tatanka’ hard red winter wheat. Journal of Plant Registrations. 12(1):74-78.
Pour, H.A., Bihamta, M.R., Mohammadi, V., Peyghambari, S.A., Bai, G., Zhang, G. 2017. Genotyping-by-sequencing (GBS) revealed molecular genetic diversity of Iranian wheat landraces and cultivars. Frontiers in Plant Science. 8:1293.
Lu, Y., Bowden, R.L., Zhang, G., Xu, X., Fritz, A., Bai, G. 2017. Quantitative trait loci for slow-rusting resistance to leaf rust in doubled-haploid wheat population CI13227 × Lakin. Journal of Phytopathology.
Fu, J., Bowden, R.L., Jagadish, K., Gill, B. 2017. Genetic variation for tolerance to terminal heat stress in Dasypyrum villosum. Crop Science. 57:1–7.
Du, C., Whitworth, R., Chen, M. 2017. MicroRNA variants, expression, and putative target genes in the Gall Midge Mayetiola destructor. Journal of Molecular Biology and Techniques. 1(1):103.
Kaur, J., Fellers, J.P., El-Mounadi, K., Nersesian, N., Clemente, T., Shah, D. 2016. Expression of apoplast-targeted plant defensin MtDef4.2 confers resistance to leaf rust pathogen Puccinia triticina but does not affect mycorrhizal symbiosis in transgenic wheat. Transgenic Research.
Kassa, M.T., You, F.M., Hiebert, C.W., Pozniak, C.J., Fobert, P., Sharpe, A., Menzies, J.G., Humphreys, G., Rezac Harrison, N., Fellers, J.P., Mccallum, B.D., Mccartney, C.A. 2017. Highly predictive SNP markers for efficient selection of the wheat leaf rust resistance gene Lr16. Biomed Central (BMC) Plant Biology. 17:45.
Momcilovic, I., Pantelic, D., Zdravkovic-Korac, S., Oljaca, J., Rudic, J., Fu, J. 2016. Heat-induced accumulation of protein synthesis elongation factor 1A indicates an important role in heat tolerance in potato. Functional Plant Biology. 244:671.
Bai, G., Su, Z., Jin, C. 2018. Wheat resistance to Fusarium Head Blight. Canadian Journal of Plant Pathology.
Shao, M., Bai, G., Rife, T., Poland, J., Lin, M., Liu, S., Kumssa, T., Zhang, G. 2018. QTL mapping of pre-harvest sprouting resistance in white wheat cultivar Danby. Journal of Theoretical and Applied Genetics. 131:1683-1697.
Huang, L., Deng, X., Li, R., Xia, Y., Bai, G., Siddique, K., Guo, P. 2018. A fast silver staining protocol enabling simple and efficient detection of SSR markers in a non-denaturing polyacrylamide gel. Journal of Visualized Experiments. 134:E57192(1-7).
Ando, K., Rynearson, S., Muleta, K.T., Gedamu, J., Girma, B., Bosque-Perez, N.A., Chen, M., Pumphrey, M.O. 2018. Genome-Wide associations for multiplepest resistances in a Northwestern United States elite spring wheat panel. PLoS One. 13(2):e0191305.
Wang, Z., Ge, J., Chen, H., Cheng, X., Yang, Y., Lin, J., Whitworth, R.J., Chen, M. 2018. An insect nucleoside diphosphate kinase (NDK) functions as an effector protein in wheat - Hessian fly interactions. Journal of Insect Biochemistry and Molecular Biology. 100:30-38.
Hussain, W., Guttieri, M.J., Belamkar, V., Poland, J., Sallam, A., Baenziger, P. 2018. Registration of a bread wheat recombinant inbred line mapping population derived from a cross between 'Harry' and 'Wesley'. Journal of Plant Registrations.
Neugebauer, K., Bruce, M., Todd, T., Trick, H.N., Fellers, J.P. 2018. Wheat differential gene expression induced by different races of Puccinia triticina. PLoS One. 13(6):e0198350.
Tang, G., Liu, X., Chen, G., Whitworth, R., Chen, M. 2018. Increasing temperature reduces wheat resistance mediated by major resistance genes to the gall midge Mayetiola destructor (Diptera: Cecidomyiidae). Journal of Economic Entomology. 111(3):1433-1438.
Haley, S.D., Johnson, J.J., Peairs, F.B., Stromberger, J.A., Hudson-Arns, E.E., Seifert, S.A., Anderson, V.A., Rosenow, A.A., Bai, G., Chen, X., Bowden, R.L., Jin, Y., Kolmer, J.A., Chen, M., Seabourn, B.W. 2018. Registration of 'Langin' hard red winter wheat. Journal of Plant Registrations. 12:232-236.
Haley, S.D., Johnson, J.J., Peairs, F.B., Stromberger, J.A., Hudson-Arns, E.E., Seifert, S.A., Anderson, V.A., Bai, G., Chen, X., Bowden, R.L., Jin, Y., Kolmer, J.A., Chen, M., Seabourn, B.W. 2018. Registration of Avery hard red winter wheat. Journal of Plant Registrations. https://10.3198/jpr2017.11.0080crc.
Al-Jbory, Z., Chen, M. 2018. Indirect plant defense against insect herbivores: a review. Review Article. 25(1):2-23.