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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

2017 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:
For Objective 1, approximately 4500 wheat lines were screened for resistance to stripe rust in an inoculated field nursery at Rossville, Kansas. The test included the Southern Regional Performance Nursery, Northern Regional Performance Nursery, and Regional Germplasm Observation Nursery as well as entries from 12 cooperators and three mapping populations. Regional nurseries were also screened for field resistance to stem rust at the Rocky Ford experiment field. Approximately 20% of the 960 crosses made in FY17 were to improve stem rust resistance in regional germplasm. This includes a marker-assisted selection project, which advanced two generations of backcrosses of combinations of major stem rust resistance genes Sr22, Sr26, Sr35, Sr38/Yr17, and Sr57/Lr34 into elite germplasm lines from several cooperating breeding programs. The largest proportion (26%) of the crossing effort in FY17 was dedicated to 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 spring wheats from a cooperator in Australia (carrying resistance genes Yr47, Yr51, Yr57, and Yr63), Yr40 from Aegilops geniculata, seedling resistance genes Yr5+Yr15 in combination provided by a university cooperator, 10 winter wheats from the Pacific Northwest, and 29 complex sources of adult plant resistance in hard winter wheat. In the search for new, unexploited sources stripe rust resistance, 131 winter wheat landrace accessions from the National Small Grains Collection, which had a previous report of resistance, were evaluated at Rossville, Kansas and Hutchinson, Kansas. Selections were made from the most promising 15 accessions, which have been planted in the greenhouse for crossing in FY18. Twenty-two inbred wheat lines with new sources of rust resistance were evaluated in multi-location replicated yield trials in Kansas and Nebraska. For Hessian fly, we screened approximately 5,500 wheat lines for resistance this year in greenhouse tests. We previously identified high-temperature Hessian fly resistance in spring durum wheats. Crosses of 19 of these durum wheats to a regionally-adapted winter wheat variety, and some first backcrosses, were constructed in FY17. The first screening of the populations derived from this effort will occur in FY18. For Fusarium head blight, a dominant male-sterile facilitated recurrent selection population has been developed using 16 Asian sources of resistance (all spring types) 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, and segregating populations will be evaluated in the field in 2018. Fusarium head blight resistance breeding efforts ranked third among the total crosses made in FY17 (17% of total). A collection of 300 doubled haploid lines from crosses of hard winter wheat to Fhb-resistant eastern soft red lines was evaluated under severe disease pressure, and selections were made based on FHB, stripe rust, and leaf rust resistance, as well as agronomic type. These selections will be advanced to replicated testing for yield, disease resistance, and quality in FY18. Heat tolerance crosses accounted for 7% of the crossing effort in FY17. Breeding populations have been constructed using several heat tolerant donor lines and elite cultivars from cooperators. A 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 germplasm, which is the wild ancestor of durum wheat, has a winter habit, and is adapted to exceptionally hot, dry environments. As part of our support for cultivar development, more than 10,000 wheat breeding samples from 10 breeding programs were analyzed for molecular markers in the USDA-ARS Central Small Grains Genotyping Laboratory. The regional wheat nurseries were also characterized with more than 70 gene-specific markers linked to important traits of interest to breeders. A total of over 50,000 gene-specific marker data points was generated in 2017. The data were used by wheat researchers for characterizing and selecting breeding lines with desired combinations of agronomic and pest resistance traits. For Objective 2, we previously developed a Kompetitive Allele Specific Polymerage chain reaction (KASP) DNA marker for Fhb1, a major wheat Fusarium head blight resistance gene, based on the candidate gene we cloned. We validated this marker in 1600 lines in a worldwide wheat collection and showed that it is highly diagnostic in worldwide wheat germplasm. We continue to work to establish cooperative research and development or material transfer agreements (CRADA or MTA) with cooperating Land Grant institutions to provide a functional framework for ARS scientists to use the most promising wheat germplasm from the public sector in our efforts to introduce new genetics into regional germplasm. Twelve wheat genotypes currently are being converted to male sterility using the gene Ms3 for use in breeding. We have begun working with regional breeders to provide, upon request, Ms3 germplasm in their own backgrounds under the terms of the ARS Breeding MTA. We continue to work to establish CRADA-MTAs with cooperating Land Grant institutions to provide a functional framework for ARS scientists to use the most promising wheat germplasm from the public sector in our efforts to introduce new genetics into regional germplasm. For Objective 3, thirty-one chemically-induced knock-out mutants of the leaf rust fungus were identified that give a susceptible reaction on common resistance genes. Mutants are expected to have new mutations in the avirulence effector genes that condition resistance when interacting with host plant resistance genes. Genomic sequencing of mutants is being performed to identify candidate genes for the avirulence effector genes. Identifying and characterizing the effectors in the leaf rust fungus is considered to be a key to designing more durable resistance. Work is continuing to improve the genomic sequence database for the leaf rust fungus using new sequencing technologies. Another key to durable resistance could be to identify the susceptibility genes to leaf rust in wheat. The susceptible spring wheat variety Thatcher was treated with the mutagen ethyl methanesulfonate (EMS) to create a population of 3500 mutant lines. These lines were screened for expression of resistance to the leaf rust pathogen in the field and 25 resistant lines were selected. Resulting resistant lines may have mutations in genes that control susceptibility to the pathogen. Such lines will be characterized to identify candidate susceptibility genes. For Hessian fly, we comprehensively analyzed microRNAs in different stages of Hessian fly development. MicroRNAs are small noncoding molecules involved in regulation of gene expression and could be important modulators of virulence.


4. Accomplishments
1. Comparative analysis highlights variable genome content of wheat rusts. Wheat is grown around the world and has been plagued by three species of rust fungi for centuries. Leaf rust, stripe rust, and stem rust each cause significant damage and can adapt quickly to overcome resistance that is present in wheat cultivars. Using advanced DNA sequencing technology, the genomes of leaf and stripe rust were sequenced and compared to stem rust, and other related fungi. The three genomes vary in size, repetitive DNA elements, and the number of genes. Many genes are common to all three rusts, but many are unique to only one species and may reflect special adaptations to their hosts. The analysis of the genomic sequences may reveal weaknesses that can be exploited for improved control of the rust species that attack cereals.

2. Variation for nitrogen use efficiency traits in current and historical great plains hard winter wheat. Wheat varieties that efficiently capture and convert available soil nitrogen into grain protein are key to sustainably meeting the rising global demand for grain protein. Both historically important and contemporary varieties and breeding lines were included in the set of 299 winter wheat lines that was tested. Differences in plant height and flowering date explained much of the variation in nitrogen use efficiency. A region of the wheat genome on the long arm of chromosome 2D also was important for nitrogen use efficiency. In this case, the most favorable gene(s) were not widely used in current varieties, which indicates that there may be opportunities for improving wheat nitrogen use efficiency by selection using markers in this region of the wheat genome.

3. First survey of microRNAs in Hessian fly. MicroRNAs (miRNAs) are small RNA molecules that are thought to participate in gene regulation and play roles in nearly all biological processes. Therefore, miRNAs may provide opportunities to develop new means to combat the Hessian fly, Mayetiola destructor, a destructive pest of wheat. This study conducted a comprehensive analysis of miRNAs from Hessian fly larvae, pupae and adults. A large number of miRNA species and variants were identified from this study. In addition, we analyzed the expression patterns of the identified miRNA species and variants among different developmental stages of the Hessian fly. We also identified putative target genes and their functions. Our results provide a foundation for future analysis of miRNA functions and application in controlling the Hessian fly pest.

4. Genes expressed differentially in Hessian fly larvae feeding in resistant and susceptible plants. Hessian fly is a destructive pest of wheat and is mainly controlled by resistant cultivars. Hessian fly manipulates susceptible plants extensively, but is unable to manipulate resistant plants, and thus dies in them. In this study, we identified many genes that were expressed differently between Hessian flies feeding in resistant plants and those feeding in susceptible plants. Hessian flies fed in resistant plants expressed more cytochrome P450 genes, which tend to be involved in detoxification processes, suggesting that toxic chemicals from resistant plants may play important roles in Hessian fly larval death. Expression levels of genes involved in energy metabolism and protein synthesis suggested that flies on resistant plants ultimately died of starvation. We also found that many genes encoding secreted salivary proteins were expressed at higher levels in Hessian flies feeding in resistant plants, indicating that these genes may play critical roles for Hessian flies to manipulate host plant metabolism. This study provides a foundation for future research that may lead to a better understanding of the mechanisms for fly larvae to manipulate wheat plants, which may eventually lead to wheat cultivars with more durable resistance to the Hessian fly pest.

5. Multiple minor quantitative trait loci (QTLs) are responsible for Fusarium head blight resistance in Chinese wheat landrace Haiyanzhong. Fusarium head blight (FHB) is a devastating disease in wheat. Cultivar resistance is one of the most effective strategies to minimize the disease damage. Chinese wheat landrace Haiyanzhong (HYZ) is highly resistant to FHB. Using DNA markers, we mapped 6 genes for FHB resistance in HYZ, and found that multiple minor genes on chromosomes 5A, 6B, 7D, 3B, 4B and 4D together can provide a high level of FHB resistance in wheat. Critical SNP markers linked to the genes on chromosomes 5A, 6B, and 7D were converted into breeder-friendly assays, and can be used for marker-assisted selection to pyramid these genes in wheat.

6. Genome-wide association analysis on pre-harvest sprouting resistance and grain color in U.S. winter wheat. Pre-harvest sprouting (PHS) in wheat can cause substantial reductions in grain yield and end-use quality. Grain color and other genetic components affect PHS resistance. We conducted a genome-wide association study on grain color and PHS resistance using a panel of 185 U.S. elite breeding lines and cultivars. We identified 9 genes for grain color on seven chromosomes and 13 genes for PHS resistance on 11 chromosomes. Genes that affect both grain color and PHS resistance were identified on the long arms of the 3A and 3D chromosomes. However, several other genes that do not affect grain color also played significant roles on PHS resistance. Therefore, it is possible to breed PHS-resistant white wheat by pyramiding these non-color related genes.


Review Publications
Cuomo, C.A., Bakkeren, G., Khalil, H., Panwar, V., Joly, D., Linning, R., Sakthikumar, S., Song, X., Goldberg, J., Young, S., Zeng, Q., Bruce, M.A., McCallum, B., Szabo, L.J., Hulbert, S., Chen, X., Fellers, J.P. 2016. Comparative analysis highlights variable genome content of wheat rusts and divergence of the mating loci. Genes, Genomes, Genetics. doi:10.1534/g3.116.032797.

Lin, M., Zhang, D., Liu, S., Zhang, G., Yu, J., Fritz, A., Bai, G. 2016. Genome-wide association analysis on pre-harvest sprouting resistance and grain color in U.S. winter wheat. BMC Genomics. 17:794. doi:10.1186/s12864-016-3148-6.

Ge, L., Yu, J., Wang, H., Luth, D., Bai, G., Wang, K., Chen, R. 2016. Increasing seed size and quality by manipulating BIG SEEDS 1 in legume species. Proceedings of the National Academy of Sciences. doi:10.1073/pnas.1611763113.

Guttieri, M.J., Frels, K., Regassa, T., Waters, B., Baenziger, P. 2017. Variation for nitrogen use efficiency traits in current and historical Great Plains hard winter wheat. Euphytica. 213:87. doi:10.1007/s10681-017-1869-5.

Tan, C., Assanga, S., Zhang, G., Haley, S.D., Rudd, J.C., Xue, Q., Amir, I., Bai, G., Zhang, X., Byrne, P., Fuentealba, M.P., Lui, S. 2017. Development and validation of kasp markers for wheat streak mosaic virus resistance gene Wsm2. Crop Science. 57:340-349. doi:10.2135/cropsci2016.04.0234.

Rutter, W.B., Salcedo, A., Akhunova, A., Wang, S., Hanquan, L., Bowden, R.L., Akhunova, E. 2017. Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses. Biomed Central (BMC) Genomics. 18:291. doi:10.1186/s12864-017-3678-6.

Li, G., Bai, G., Carver, B.F., Elliott, N.C., Bennett, R.S., Wu, Y., Hunger, R., Bonman, J.M., Xu, X. 2017. Genome-wide association study reveals genetic architecture of coleoptile length in wheat. Theoretical and Applied Genetics. 130(2):391-401.

Li, G., Xu, X., Bai, G., Carver, B.F., Hunger, R., Bonman, J.M., Kolmer, J.A., Dong, H. 2016. Genome-wide association mapping reveals novel QTL for seedling leaf rust resistance in a worldwide collection of winter wheat. The Plant Genome. 9(3):1-12. doi:10.3835/plantgenome2016.06.0051.

Li, G., Xu, X., Bai, G., Carver, B.F., Hunger, R.M., Bonman, J.M. 2017. Novel sources of leaf rust resistance in winter wheat. Crop Science. 57(2):865-876.

Cai, J., Wang, S., Li, T., Bai, G. 2016. Multiple minor QTLs are responsible for Fusarium head blight resistance in Chinese wheat landrace Haiyanzhong. PLoS One. 11(9):e0163292. doi:10.1371/journal.pone.0163292.

Sukumaran, S., Li, X., Li, X., Zhu, C., Bai, G., Perumal, R., Tuinstra, M., Prasad, V., Mitchell, S., Tesso, T., Yu, J. 2016. QTL mapping for grain yield, flowering time, and stay-green traits in sorghum with genotyping-by-sequencing markers. Crop Science. 56:1429-1442. doi:10.2135/cropsci2015.02.0097.

Li, L., Sun, F., Wu, D., Zhen, F., Bai, G., Li, T. 2016. High-throughput development of genome-wide locus-specific informative SSR markers in wheat. Science China Life Science. 60(6):671-673. doi:10.1007/s11427-016-0252-x.

Chen, M., Liu, S., Wang, H., Cheng, X., El Bouhssini, M., Whitworth, R. 2016. Genes expressed differentially in Hessian fly larvae feeding in resistant and susceptible plants. International Journal of Molecular Sciences. 17:1324. doi:10.3390/ijms17081324.

Zhang, M., Liang, Y., Song, A., Yu, B., Zeng, X., Chen, M., Yin, H., Zhang, X., Sun, B., Fan, F. 2017. Loss of soil microbial diversity may increase insecticide uptake by crop. Agriculture, Ecosystems and Environment. 240: 84-91 doi:10.1016/j.agee.2017.02.010.

Chen, J., Guttieri, M.J., Zhang, J., Hole, D., Souza, E., Goates, B. 2016. A novel QTL associated with dwarf bunt resistance in Idaho 444 winter wheat. Journal of Theoretical and Applied Genetics. 129(12):2313-2322. doi:10.1007/s00122-016-2783-2.

Brabec, D.L., Guttieri, M.J., Pearson, T., Carsrud, B. 2017. Effectiveness of an image-based sorter to select for kernel color within early segregating hard winter wheat (Triticum aestivum L.) populations. Cereal Research Communications. 45(3): 488-499. doi: 10.1556/0806.45.2017.034.

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. 2017. Registration of 'Sunshine' hard white winter wheat. Journal of Plant Registrations. doi: 10.3198/jpr2016.12.0075crc.