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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Research Project #424595

Research Project: Genetic Improvement of Durum and Spring Wheat for Quality and Resistance to Diseases and Pests

Location: Cereal Crops Research

2014 Annual Report

The proposed research involves the use of genetics and genomics to gain understanding of the genes associated with mechanisms of disease resistance or susceptibility and end use quality, and the identification, characterization, and development of genetic stocks, germplasm, and tools for the improvement of wheat and other small grains. Specific objectives are: 1. Identify new genes and sources for resistance and end-use quality in wheat. 1A. Identify new sources of Hessian fly resistance among wheat wild relatives of the Aegilops genus and newly developed synthetic hexaploid wheats. 1B. Identify new sources of stem rust resistance among wheat relatives of the Thinopyrum genus and newly developed synthetic hexaploid wheats. 1C. Identify new sources of Fusarium head blight (FHB), tan spot, and Stagonospora nodorum blotch (SNB) resistance among newly developed synthetic hexaploid wheats. 1D. Identify novel genes for resistance to stem rust, tan spot, SNB, and Hessian fly among the National Small Grains Collection and a collection of domesticated emmer accessions using association mapping. 1E. Identify novel genes for end-use quality among entries of the Uniform Regional Nursery using association mapping. 2. Identify and develop molecular markers for rusts, necrotrophic diseases, and pre-harvest sprouting in wheat. 2A. Determine the chromosomal locations of novel genes conferring sensitivity to newly identified host-selective toxins produced by S. nodorum using molecular markers. 2B. Develop molecular markers suitable for MAS of the S. nodorum toxin sensitivity genes Snn3-B1 and Snn3-D1 through genomic analysis and fine-mapping. 2C. Determine the chromosomal location of a new Ug99 stem rust resistance gene using molecular markers. 2D. Develop markers and populations for the fine-mapping and initiation of the map-based cloning of the Ug99 stem rust resistance gene Sr47. 2E. Develop molecular markers suitable for MAS of pre-harvest sprouting resistance QTLs on chromosome 2B in tetraploid wheat. 3. Characterize the genetic mechanisms of resistance involved in wheat-necrotrophic pathogen interactions. 3A. Determine the structural and functional diversity of the Tsn1 gene among accessions of the wild wheat ancestor Aegilops speltoides. 3B. Identify genes and/or genetic mechanisms involved in the Tsn1-ToxA interaction. 3C. Characterize the structure and function of families of Pr-1 and Pr-2 genes in wheat. 4. Develop genetic resources and tools for the improvement of wheat and other small grains. 4A. Develop HRSW lines nearly isogenic for S. nodorum toxin sensitivity genes. 4B. Develop adapted solid-stem durum wheat germplasm for resistance to sawfly. 4C. Develop durum and wheat germplasm with FHB and stem rust resistance. 4D. Develop a reference SNP map for durum wheat. 4E. Develop a SNP marker set for MAS in wheat. 4F. Provide genotyping services for barley, wheat, and oat varietal development.

Durum and hard red spring wheat (HRSW) varieties with improved end-use quality and resistance to abiotic and biotic stresses are needed to meet the nutritional demands of the world’s growing population. This challenge must be met through the discovery and deployment of genes for disease resistance and traits that effect quality such as kernel texture, protein content, flour yield, dough strength, and baking performance. In this project, we will identify new sources of resistance to diseases and pests, and improved quality. Molecular mapping populations will be generated and used to identify genes and quantitative trait loci governing resistance to Stagonospora nodorum blotch, stem rust, and pre-harvest sprouting. This work will yield knowledge of the genetic mechanisms controlling these traits, the development of markers for marker-assisted selection, and genetic stocks and germplasm useful forgene deployment. Additional work on the molecular characterization of the genes and genetic pathways associated with wheat-necrotrophic pathogen interactions will be conducted as part of this project and will yield basic knowledge useful for devising novel strategies for developing crops with resistance to necrotrophic pathogens. Finally, genetic resources and tools for the development of improved wheat and durum cultivars will be generated, including stocks for the genetic analyses of Stagonospora nodorum blotch susceptibility genes, adapted germplasm with resistance to sawfly, Fusarium head blight, and stem rust, and high-throughput molecular marker sets for genomic selection in durum and common wheat. In addition, genotyping services will be provided to regional wheat, durum, barley, and oat breeders to expedite the development of improved varieties.

Progress Report
The wheat Snn1 gene, which confers sensitivity to a toxin produced by the fungal pathogen Stagonospora nodorum, was cloned using a molecular genetics approach. Candidate genes were identified and validated by mutagenesis. The gene is a member of the wall-associated kinase class of receptors. Snn1 is tightly regulated by the circadian clock and light, and it likely arose in the tetraploid progenitor of common wheat. This work relates directly to objective 3. Identification of molecular markers for a new Ug99 stem rust resistance gene in goatgrass. A total of 710 progeny plants from a cross between resistant and susceptible goatgrass (Ae. tauschii) accessions were evaluated for reaction to stem rust at the seedling stage, and then a subset of 179 susceptible plants were selected to conduct molecular genetic analysis to identify the chromosomal location of the gene conferring stem rust resistance. A single dominant gene for resistance was mapped to the short arm of wheat chromosome 2D. Five molecular markers were then developed for the gene region based on sequencing resources. This work relates directly to objective 2. Development of hard red spring wheat lines nearly isogenic for S. nodorum toxin sensitivity genes. The synthetic hexaploid wheat line LDNsyn2377, wheat line AF89, and tetraploid wheat line LP749-29, which carry the toxin sensitivity genes Snn3-D1, Snn4, and Snn5, respectively, were used as donors of the three genes in backcrosses to BR34 as the recurrent parent. The first generation progeny from each of backcrosses were directly evaluated for reactions to respective toxins and second generation progeny for the three genes were produced. This work relates directly to objective 4. A set of 497 landrace and cultivated durum wheat accessions deposited at the USDA-ARS National Small Grains Collection, Aberdeen, ID, was evaluated for resistance to stem rust and leaf rust pathogens. Stem rust resistance was evaluated both at the seeding stage against three races at the Cereal Disease Lab, St. Paul, MN, and at the adult plant stage under field conditions in Ethiopia. Leaf rust resistance was also evaluated both at the seedling stage against a virulent race at CIMMYT in Mexico, and at the adult plant stage in the field at ICARDA, Morocco. Results from preliminary association mapping analysis have revealed novel resistance loci against these two diseases. Lines resistant to both diseases have also been identified. This work relates directly to Objective 1. A method based on determining the DNA sequence of many small, targeted regions of the barley genome was developed and optimized to replace Illumina's GoldenGate assay containing 384 molecular markers known as single nucleotide polymorphism (SNP) markers. The targeted regions were selected based on the known DNA sequences obtained from previous screening of barley lines. Bioinformatics pipelines were developed to evaluate and analyze the sequence data from the targeted regions for marker development. The information and technology was then used to genotype barley breeding populations to support breeders' genomic selection efforts. This work relates to Objective 4.

1. Characterization of a wheat protein mediating sensitivity to a fungal toxin. ToxA is a fungal protein that is toxic to wheat plants and a major determinant of some fungal diseases, but how this protein becomes toxic to wheat is still not well understood. ARS researchers in Fargo, ND, identified a protein in wheat that physically interacts with the ToxA protein, and when this interaction occurs it results in plant cell death followed by disease, which leads to yield losses. These findings provide the first evidence that certain fungal proteins may act as toxins by targeting specific plant proteins to induce cell death, which might be essential for the toxin-producing fungi to colonize the host plants. These studies will help to develop better strategies to combat fungal pathogens that exploit plant proteins to cause diseases.

2. Evaluation and characterization of wheatgrass for resistance to stem rust disease of wheat. Among the relative species of wheat, several wild species belonging to the genus Thinopyrum (common name: wheatgrass) have been used as sources of resistance to rusts and other major diseases in wheat. In an effort to identify novel sources of resistance to stem rust race Ug99, ARS researchers at Fargo, ND and St. Paul, MN, evaluated 241 lines representing five different wheatgrass species for reaction to nine different strains of the stem rust pathogen. The results showed that all but one line were resistant to most of the stem rust strains. The lines with high levels of resistance to Ug99 are useful sources of stem rust resistance for wheat improvement.

3. Evaluation of durum wheat proteins on bread making quality. Durum wheat has traditionally been used to make pasta, but it would be advantageous if it could be marketed for bread making as well. ARS researchers at Fargo, ND investigated the effects of protein composition on bread making quality in durum. The proteins studied included glutenin (one of the two protein components of gluten), identified as bands 5+10 and band 8, and two groups of small glutenin proteins identified as LMWI or LMWII. Durum that had bands 5+10 had higher glutenin content, which was associated with exceedingly strong dough, and absence of band 8 resulted in weaker dough. Durum having LMWI had weaker dough than those having LMWII. This study provides useful knowledge for improving durum bread making quality by selecting optimal combinations of protein components.

4. Identification of genes associated with head shape in wheat. The wheat head is important because it is where reproduction occurs and it holds the seeds until harvest. ARS researchers at Fargo, ND, investigated genes from a wild wheat relative that govern a shorter, more compact wheat head. Two different genes, one associated with head length and another associated with the number of seed-bearing bodies per head, were both located to a single chromosome. These genes and the traits they are associated with may be useful for improving drought resistance in modern durum varieties.

5. Identification of a gene mutation critical for the domestication of wheat. The domestication of wheat was instrumental in spawning the civilization of humankind, and it occurred through genetic mutations that gave rise to types with non disarticulating heads, soft glumes, and free-threshing seed, which are traits that made wheat easy to cultivate, harvest, and thresh for early farmers. ARS researchers at Fargo, ND, identified and analyzed a gene from the ancestor of the maternal parent of common wheat known as wild emmer that prohibits the seed from being easily threshed. The research showed that this gene underwent mutation about 8,000 years ago to give rise to our modern free-threshing wheats. Knowledge of the evolutionary events leading to modern day varieties will be useful for devising novel strategies for wheat improvement.

6. Characterization of zinc-DNA interactions potentially involved in wheat genome evolution. The genomes of organisms contain DNA sequences that make up genes, but also repetitive, or so-called "junk," DNA, and the origins and roles of the latter are poorly understood. The wheat genome contains particularly large amounts of "junk" DNA. An ARS researcher in Fargo, ND, conducted DNA analysis of genes in wheat and found that the annealing of complementary DNA sequences (a crucial step in DNA synthesis, repair and recombination) was blocked by zinc, an essential trace element. However, "junk" DNA was resistant to zinc blocking. These findings suggest that zinc-DNA interactions might be among natural forces driving "junk" DNA prevalence in the genome. Further studies may provide further understanding of the evolution of economically important traits such as disease resistance governed by genes associated with "junk" DNA in wheat.

Review Publications
Niu, Z., Klindworth, D.L., Yu, G., Friesen, T.L., Chao, S., Jin, Y., Cai, X., Ohm, J.-B., Rasmussen, J.B., Xu, S.S. 2014. Development and characterization of wheat lines carrying stem rust resistance gene Sr43 derived from Thinopyrum ponticum. Theoretical and Applied Genetics. 127:969-980.
Faris, J.D., Zhang, Z., Garvin, D.F., Xu, S.S. 2014. Molecular and comparative mapping of genes governing spike compactness inherited from wild emmer wheat. Molecular Genetics and Genomics. 289:641-651.
Faris, J.D., Zhang, Z., Chao, S. 2014. Map-based analysis of the tenacious glume gene Tg-B1 of wild emmer and its role in wheat domestication. Gene. 542:198-208.
Klindworth, D.L., Hareland, G.A., Elias, E.M., Ohm, J.-B., Puhr, D.P., Xu, S.S. 2014. Interactions of genotype and glutenin subunit composition on breadmaking quality of durum 1AS•1AL-1DL translocation lines. Cereal Chemistry. 91(3):211-217.
Niu, Z., Jiang, A., Abu Hammad, W., Oladzadabbasabadi, A., Xu, S.S., Mergoum, M., Elias, E.M. 2014. Review of doubled haploid production in durum and common wheat through wheat x maize hybridization. Plant Breeding. 133:313-320.
Niu, Z., Puri, K.D., Chao, S., Jin, Y., Sun, Y., Steffenson, B.J., Maan, S.S., Xu, S.S., Zhong, S. 2013. Genetic analysis and molecular mapping of crown rust resistance in common wheat. Theoretical and Applied Genetics. 127:609-619.
Bassi, F.M., Kumar, A., Zhang, Q., Paux, E., Huttner, E., Kilian, A., Dizon, R., Feuillet, C., Xu, S.S., Kianian, S.F. 2013. Radiation hybrid QTL mapping of Tdes2 involved in the first meiotic division of wheat. Theoretical and Applied Genetics. 126:1977-1990.
Faris, J.D., Liu, Z.H., Xu, S.S. 2013. Genetics of tan spot resistance in wheat. Theoretical and Applied Genetics. 126:2197-2217.
Mujeeb-Kazi, A., Kazi, A.G., Dundas, I., Rasheed, A., Bux, H., Chen, P., Wang, R., Xu, S.S., Mahmood, T. 2013. Genetic diversity for wheat improvement as a conduit to food security. Advances in Agronomy. 122:179-258.
Ogbonnaya, F.C., Abdalla, O., Kazi-Mujeeb, A., Kazi, A.G., Xu, S.S., Gosman, N., Lagudah, E.S., Bonnett, D., Sorrells, M.E. 2013. Synthetic hexaploids: Harnessing species of the primary gene pool for wheat improvement. Plant Breeding Reviews. 37:35-122.
Suttle, J.C., Huckle, L.L., Lu, S., Knauber, D.C. 2014. Potato tuber cytokinin oxidase/dehydrogenase genes: Biochemical properties, activity, and expression during tuber dormancy progression. Journal of Plant Physiology. 171:448-457.
Li, C., Chen, M., Chao, S., Yu, J., Bai, G. 2012. Identification of a novel gene, H34, in wheat using recombinant inbred lines and single nucleotide polymorphism markers. Theoretical and Applied Genetics. 126:2065-2017.
Somo, M., Chao, S., Acevedo, M., Zurn, J., Cai, X., Marais, F. 2014. A genomic comparison of homoeologous recombinants of the Lr19 (T4) translocation in wheat. Crop Science. 54:565-575.
Lu, S. 2014. Zn2+ blocks annealing of complementary single-stranded DNA in a sequence-selective manner. Scientific Reports. 4:5464. Available:
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.
Lu, Y., Wang, M., Chen, X., See, D.R., Chao, S., Jing, J. 2014. Mapping of Yr62 and a small effect QTL for high-temperature adult-plant resistance to stripe rust in spring wheat PI 192252. Theoretical and Applied Genetics. 127:1449-1459.
Munoz-Amatrian, M., Cuesta-Marcos, A., Endelman, J.B., Comadran, J., Bonman, J.M., Bockelman, H.E., Chao, S., Russell, J., Waugh, R., Hayes, P.M., Muehlbauer, G.J. 2014. The USDA collection of barley landraces and cultivars: genetic diversity, population structure, and potential for genome-wide association studies. PLoS One. 9(4):394688. doi:10.137/journal.pone.0094688.