2011 Annual Report
1a.Objectives (from AD-416)
Identify novel sources of resistance to Fusarium head blight (FHB), Stagonospora nodorum blotch (SNB), tan spot (TS), stem rust (SR) and Hessian fly (HF) among accessions of the primary gene pool of wheat. Develop and characterize synthetic hexaploid wheat lines, genetic stocks, and mapping populations useful for the genetic analysis of resistance to FHB, SNB, TS, SR, and HF. Identify novel QTL associated with resistance to FHB, SNB, TS, and end-use quality in tetraploid and/or hexaploid mapping populations. Isolate genes associated with host-pathogen interactions involving host-selective toxins produced by the SNB and TS pathogens. Conduct genomic analysis and fine mapping of genomic regions harboring genes conferring sensitivity to host-selective toxins and for Hessian fly resistance, and develop markers suitable for marker-assisted selection. Introgress genes/QTL for resistance to FHB, SNB, and TS into adapted germplasm using marker-assisted selection. Develop small grains germplasm and varieties with improved disease resistance and end-use quality using high-throughput genotyping and marker-assisted selection.
1b.Approach (from AD-416)
Survey tetraploid relatives of wheat for resistance to FHB, SNB, TS, SR, and HF. Develop synthetic hexaploid lines, near-isogenic lines, and mapping populations using conventional techniques. Develop genetic linkage maps in the segregating mapping populations using molecular markers and identify genomic regions harboring QTL associated with resistance or improved quality. Use QTL analysis to determine the chromosomal locations of genes governing resistance and quality traits. Target genomic regions harboring disease resistance loci, sensitivity to host-selective toxins, and Hessian fly resistance with PCR-based markers to identify markers suitable for marker-assisted selection. Isolate the Tsn1 gene using positional cloning techniques. Develop a high-resolution map of the H26 gene for genomic analysis and positional cloning. Develop improved germplasm through the use of conventional and marker-assisted selection. Release enhanced germplasm to wheat breeders and deposit germplasm stocks in the National Germplasm System. Utilize high-throughput marker platforms for genotyping lines for the small grains breeding community, and develop new high-throughput markers for important agronomic traits. BL-1; 04/04/08
To further characterize the Tsn1-ToxA interaction, EMS mutant-based gene expression profiling revealed that Tsn1 controls at least five PR-1 genes in response to challenge by ToxA, the disease-inducing toxin produced by Stagonospora nodorum. One Tsn1-controled PR-1 gene was found to encode a protein that interacts with both ToxA and PR-2, a second well-known defense protein. The possibility that Tsn1 interacts with a ToxA/PR-1/-PR-2 protein complex will be further investigated.
Several PR-1 proteins have been expressed in the yeast Pichia pastoris to evaluate their function. Antibodies specific to two of them were developed and successfully used to detect the native proteins produced in the host. Western blot analysis confirmed that the Tsn1-controled PR-1 protein is indeed induced and accumulated upon ToxA-treatment in susceptible wheat lines. Virus-induced gene silencing suggested that the PR-1 function is likely required for ToxA-triggered susceptibility.
A mapping population generated from a cross between Grandin and BR34 was grown in six field environments, and end-use quality traits including kernel characteristics, flour and milling yield, dough quality, and bread-baking characteristics were evaluated. Also, the storage protein genes for high molecular weight and low molecular weight glutenins, as well as kernel hardness genes encoding puroindoline a and b proteins were placed on the existing genetic linkage maps. Initial analysis has led to the identification of several genes or genomic regions with large effects on the different end-use quality traits.
Hard red spring wheat lines nearly isogenic for genes conferring sensitivity to host-selective toxins produced by Stagonospora nodorum are being developed to evaluate the role of individual host-toxin interactions. Four lines used as donors of the toxin sensitivity genes Tsn1, Snn1, Snn2, and Snn3 were backcrossed to the universal insensitive line BR34 as the recurrent parent. The BC3F1 progeny from each of backcrosses were directly evaluated for reaction to the respective toxins and BC4F1 progeny for the four genes were produced.
To increase the levels of Fusarium head blight (FHB) resistance in durum wheat, six cultivated emmer lines were used as donors of FHB resistance and backcrossed to durum cultivars (Alkabo, Ben, Divide, Grenora). A total of 59 BC1F4-6 lines from each of backcrosses were evaluated in the greenhouse and their BC1F5-7 lines were evaluated in field nurseries at two locations. Six BC1F5 lines and one double haploid have been crossed and backcrossed with the new ND durum cultivar Tioga and two elite durum lines.
Development of DNA markers for breeding against an important disease of wheat. Plant breeders are beginning to use molecular markers for desirable traits to speed the development of new varieties. Wheat cultivars that carry a gene called Tsc2 are susceptible to the disease tan spot, because the gene confers sensitivity to a toxin produced by the tan spot fungus. Development of DNA markers closely associated with the gene would provide useful tools for eliminating it from wheat cultivars in a rapid and efficient manner. ARS researchers in Fargo, ND, used sophisticated genetic analyses to develop DNA markers tightly linked to the disease susceptibility gene. They showed that the markers could be used as effective indicators of the presence/absence of the gene. These new markers should be useful for developing varieties of wheat with improved levels of tan spot disease resistance. Given wheat’s importance as a worldwide food crop, increased disease resistance will be important for food security of the increasing world population.
Discovery of related wheat genes that govern susceptibility to a major fungal pathogen of wheat. The pathogen that causes the disease Stagonospora nodorum blotch (SNB) is a serious threat to wheat production because it produces numerous toxins that kill leaf tissue resulting in disease. ARS researchers in Fargo, ND, discovered a novel gene in wheat designated Snn3-D1 that governs reaction to an SNB toxin known as SnTox3. They also showed that the Snn3-D1 gene was related by ancestry to another previously identified gene that confers sensitivity to SnTox3 known as Snn3-B1. Through sophisticated genetic and genomic analyses, the researchers laid the groundwork necessary to clone the Snn3 genes, which will provide valuable insights regarding how the SNB pathogen interacts with the wheat plant to cause disease. They also developed DNA markers that can be used to efficiently remove the Snn3 genes, and thus SNB susceptibility, from elite wheat varieties. This work provides important knowledge that can be used to provide food security under a changing global climate, in which the SNB pathogen is expected to thrive.
Characterization of a pathogenesis-related protein gene family in bread wheat. Pathogenesis-related protein 1 (PR-1) genes are associated with disease resistance and are induced in plants attacked by fungi, bacteria, viruses, nematodes, and insects. ARS researchers in Fargo, ND, determined the chromosomal locations for 23 PR-1 gene family members in common bread wheat. Twelve genes were found to be differentially expressed between disease resistant and susceptible wheat cultivars, demonstrating their involvement in pathogen responses. The development of DNA markers and chromosome maps for these genes provides a way to evaluate the roles of individual family members in disease resistance. Understanding how these genes confer resistance may lead to new methods for breeding and engineering disease resistant crops.
Development of a high density DNA marker panel in wheat for genetic and breeding applications. Due to the complex nature of the wheat genomes, the number of useful DNA markers has been limited and insufficient to make adequate breeding progress through marker-assisted selection. An ARS scientist in Fargo, ND, in collaboration with wheat scientists in the U.S. and Australia, developed a high density DNA marker panel containing 9,000 genetic variations discovered at the single nucleotide level from the gene-containing regions of the wheat genomes. This high density marker panel was used to characterize 5,000 wheat lines, including cultivars, advanced breeding lines and various germplasm collections contributed from wheat breeders in the U.S., Canada, and Mexico. The results provide a vast amount of genetic information allowing U.S. wheat breeders to explore genetic diversity that can be used for wheat improvement.
Genetic similarity of wheat lines with Hessian fly resistance genes. Hessian fly is a very destructive pest of wheat and other cereals. Eight wheat lines were previously developed by individually transferring eight Hessian fly resistance genes into the wheat cultivar Newton, and they have been extensively used for studying wheat-Hessian fly interactions because it was presumed that they were genetically very similar. However, the degree of genetic similarity among the eight lines and Newton has not been directly investigated. ARS scientists in Fargo, ND, and West Lafayette, IN, collaborated with scientists at North Dakota State University to investigate the genetic similarity among the eight lines and Newton. They concluded that some of the lines had highly uniform genetic backgrounds nearly identical to that of Newton, but other lines had highly dissimilar backgrounds compared to Newton. This information is useful for wheat geneticists and entomologists who use these lines for investigating expression of H genes and wheat-Hessian fly interactions.
The development of stem rust resistant wheat using novel approaches. The strain of wheat stem rust known as Ug99 has the potential to cause worldwide catastrophic losses in wheat production because very few wheat varieties are resistant. Some wild grasses that are distantly related to wheat possess useful Ug99 resistance genes, but the transfer of these genes to modern wheat varieties by conventional means is extremely time consuming and laborious. ARS scientists at Fargo, ND, and St. Paul, MN, developed a novel but efficient approach to transfer genes from distant relatives to wheat by combining traditional chromosome engineering techniques together with modern DNA marker technologies. Using this approach, they developed several wheat lines possessing Ug99 resistance genes from wheat relatives in a timely and efficient manner. These wheat lines will be highly beneficial in the ongoing global effort to combat Ug99 and ultimately provide a significant level of worldwide food security.
Characterization of seed storage proteins in wild relatives of wheat. Seed storage proteins of wheat consist mainly of two classes: glutenins and gliadins. The glutenins play an important role in determining dough-quality and bread-making properties of wheat varieties. The glutenins in widely grown wheat varieties have been extensively characterized. However, they have not been investigated in the wild relatives of wheat, which may possess unique glutenins with desirable properties that could be used to improve the bread-making quality of modern wheat varieties. In cooperation with scientists at North Dakota State University and CSRIO Plant Industry in Australia, ARS scientists in Fargo, ND, and Logan, UT, analyzed the glutenin compositions in five distant relatives of wheat and identified 28 novel glutenin genes. These novel genes may prove useful for the improvement of wheat end-use quality and the enhancement of its nutritional value.
Cloning of a gene responsible for susceptibility of wheat to fungal diseases. Fungal diseases of crops are an insidious threat to the production of food crops like wheat, a major food crop worldwide. Wheat varieties that carry a gene called Tsn1 are particularly susceptible to fungal pathogens that cause leaf diseases called tan spot and Stagonospora nodorum blotch. This gene governs wheat’s sensitivity to a toxin produced by the pathogens. ARS researchers in Fargo, ND, used sophisticated methods to isolate the gene from wheat and determine its DNA sequence, and they resolved how these toxin-producing pathogens acquired the ability to subvert wheat’s disease defense mechanisms. This work provides significant understanding of how these wheat pathogens interact with the crop to cause disease. These insights will lead to novel methods for developing disease resistant crops, particularly for food crops like wheat that are critical to world food security.
Xu, S.S., Chu, C.G., Harris, M., Williams, C.E. 2010. Comparative analysis of genetic background in eight near-isogenic wheat lines with different H genes conferring resistance to Hessian fly. Genome. 54:81–89.
Simons, K.J., Abate, Z., Chao, S., Zhang, W., Rouse, M., Jin, Y., Elias, E., Dubcovsky, J. 2011. Genetic mapping of stem rust resistance gene Sr13 in tetraploid wheat (Triticum turgidum subsp. durum L.). Theoretical and Applied Genetics. 122:649-658.
Zhang, Z., Friesen, T.L., Xu, S.S., Shi, G., Liu, Z., Rasmussen, J., Faris, J.D. 2011. Two Putatively Homoeologous Wheat Genes Mediate Recognition of SnTox3 to Confer Effector-triggered Susceptibility to Stagonospora nodorum. Plant Journal. 65:27-38.
Lu, S., Platz, G., Edwards, M.C., Friesen, T.L. 2010. Mating Type (MAT) Locus -Specific PCR Markers for Differentiation of Pyrenophora teres f. teres and P. teres f. maculata, the Causal Agents of Barley Net Blotch. Phytopathology. 100(12):1298-1306.
Martin, T., Lu, S., Tilbeurgh, H., Ripoll, D., Dixelius, C., Turgeon, B.G., Debuchy, R. 2010. Tracing the Origin of the fungal Sex a1 domain places its ancestor in the HMG-box superfamily: implication for fungal mating-type evolution. PLoS One. 5(12):e15199.
Cistué, L., Chao, S., Chutimanitsakun, Y., Corey, A., Cuesta-Marcos, A., Echávarri, B., Filichkina, T., Garcia-Mariño, N., Romagosa, I., Hayes, P.M. 2011. Comparative Mapping of the Oregon Wolfe Barley Using Doubled Haploid Lines Derived from Female and Male Gametes. Theoretical and Applied Genetics. 122:1399-1410.
Niu, Z., Klindworth, D.L., Friesen, T.L., Chao, S., Jin, Y., Cai, X., Xu, S.S. 2011. Targeted introgression of a wheat stem rust resistance gene by DNA marker-assisted chromosome engineering genetics. Genetics. 187(4):1011-1021.
Chao, S., Dubcovsky, J., Dvoral, J., Luo, M., Baenziger, S.P., Matnyazov, R., Clark, D.R., Talbert, L., Anderson, J.A., Dreisigacker, S., Glover, K., Chen, J., Campbell, K., Bruckner, P.L., Rudd, J.C., Haley, S., Carver, B.F., Sims, R., Sorrells, M.E., Akhunov, E.D. 2010. Population-Specific Patterns of Linkage Disequilibrium and SNP Variation in Spring and Winter Polyploid Wheat. Biomed Central (BMC) Genomics. 11:727.
Zitzewitz, J., Condon, F., Corey, A., Cuesta-Marcos, A., Filichkin, T., Haggard, K., Fisk, S.P., Smith, K.P., Muehlbauer, G.J., Karsai, I., Veisz, O., Chao, S., Castro, A.J., Gutierrez, L., Hayes, P.M. 2011. The genetics of winterhardiness in barley: Perspectives from genome-wide association mapping. The Plant Genome. 4:76-91.
Lu, S., Friesen, T.L., Faris, J.D. 2011. Molecular characterization and genomic mapping of the pathogenesis-related protein 1 (PR-1) gene family in hexaploid wheat (Triticum aestivum L.). Molecular Genetics and Genomics. 285:485-503.
Faris, J.D., Zhang, Z., Lu, H., Lu, S., Cloutier, S., Fellers, J.P., Meinhardt, S.W., Rasmussen, J.B., Xu, S.S., Oliver, R.P., Simons, K.J., Friesen, T.L. 2010. A Unique Wheat Disease Resistance-like Gene Governs Effector-Induced Susceptibility to Necrotrophic pathogens. Proceedings of the National Academy of Sciences. 107:13544-13549.
Abeysekara, N.S., Friesen, T.L., Liu, Z., Mcclean, P.E., Faris, J.D. 2010. Marker Development and Saturation Mapping of the Tan Spot Ptr ToxB Sensitivity locus Tsc2 in Hexaploid Wheat. The Plant Genome. 3:179-189.
Roy, J.K., Smith, K.P., Muehlbauer, G.J., Chao, S., Close, T.J., Steffenson, B.J. 2010. Association Mapping of Spot Blotch Resistance in Wild Barley . Molecular Breeding. 26:243-256.
Massman, J., Cooper, B., Horsley, R., Neate, S., Dill-Macky, R., Chao, S., Dong, Y., Muehlbauer, G., Smith, K. 2011. Genome-wide Association Mapping of Fusarium Head Blight Resistance in Contemporary Barley Breeding Germplasm. Molecular Breeding. 27:439-454.
Lu, S., Yun, S., Lee, T., Turgeon, B. 2011. Altering sexual reproductive mode by interspecific exchange of MAT loci. Fungal Genetics and Biology. 48:714-724.
Niu, Z., Klindworth, D.L., Wang, R., Jauhar, P.P., Larkin, P.J., Xu, S.S. 2011. Characterization of high molecular weight glutenin subunits in Thinopyrum intermedium, Th. bessarabicum, Lophopyrum elongatum, Aegilops markgrafii, and their addition lines in wheat. Crop Science. 51:667-677.
Lowe, I., Jankuloski, L., Chao, S., Chen, X., See, D.R., Dubcovsky, J. 2011. Mapping and validation of Yr48 and other QTL conferring partial resistance to broadly virulent post-2000 North American races of stripe rust in hexaploid wheat. Theoretical and Applied Genetics. 123:143-157.
Xu, S.S., Khan, K., Klindworth, D.L., Nygard, G. 2010. Evaluation and characterization of high-molecular weight 1D glutenin subunits from Aegilops tauschii in synthetic hexaploid wheats. Journal of Cereal Science. 52:333-336.