Research Project: Improvement of Biotic Stress Resistance in Durum and Hard Red Spring Wheat Using Genetics and Genomics

Location: Cereal Crops Research

2021 Annual Report

Objectives
OBJECTIVE 1: Identify novel sources of disease and pest resistance in durum wheat and goatgrass to enhance crop resilience. OBJECTIVE 2: Map and characterize novel genes governing resistance/susceptibility to tan spot, Septoria nodorum blotch, stem rust, and Hessian fly in wheat and goatgrass to develop the knowledge and tools for their deployment in the development of wheat varieties with improved resistance. OBJECTIVE 3: Characterize genetic mechanisms associated with wheat-pathogen interactions to increase our understanding and knowledge of the biological mechanisms associated with resistance and susceptibility. OBJECTIVE 4: Utilize and develop genetic resources and molecular tools for the improvement of wheat and provide genotyping services to expedite the development of improved wheat, barley and oat varieties. OBJECTIVE 5: Genetically improve barley by the application of molecular genetics and genomics to increase resistance to head and foliar diseases such as Fusarium head blight, net blotch and spot blotch.

Approach
Durum, hard red spring wheat (HRSW) and barley varieties with improved resistance to diseases and pests are needed to meet the demands of the world’s growing population. This challenge must be met through the discovery, characterization, and deployment of genes for resistance to biotic stresses. In this project, we will identify new sources of resistance to Septoria nodorum blotch, tan spot, and stem rust in durum, to Hessian fly in goatgrass, and to Fusarium head blight and spot-form net blotch in barley. Molecular mapping and genetic analyses will be used to identify and characterize genes and quantitative trait loci governing resistance to tan spot, Septoria nodorum blotch, stem rust, Fusarium head blight and spot-form net blotch. 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 for gene deployment. Additional work on the molecular characterization of the genes and genetic pathways associated with wheat/barley-pathogen interactions will be conducted as part of this project and will yield basic knowledge useful for devising novel strategies for developing disease and pest resistant varieties. Finally, genetic resources and tools for the development of improved wheat, durum and barley cultivars will be generated, including stocks for the genetic analyses of Septoria nodorum blotch susceptibility genes and Hessian fly resistance genes, adapted germplasm with low cadmium and resistance to sawfly, Fusarium head blight, and stem rust, and a reference sequence-based genetic map for durum 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
A worldwide collection of durum wheats referred to as the Global Durum Panel (GDP) has been assembled, but it is unknown if the lines are resistant or susceptible to tan spot disease. The panel has been screened with fungal isolates representing five different races of the tan spot fungus, and the data is currently being analyzed. This research will provide knowledge on the importance of tan spot disease in durum wheat, and it will lead to the identification of tan spot-resistant durum lines. This work is aligned with Subobjective 1B. A worldwide collection of durum wheats referred to as the Global Durum Panel (GDP) has been assembled, but it is unknown if there is any resistance in the lines to Septoria nodorum blotch. We screened the panel with five unique fungal-produced proteins (effectors) that cause cell death and three fungal isolates to determine which durum lines were resistant or susceptible to the effectors and/or fungal isolates. We have begun to analyze the data. This work will provide information on the prevalence of the known effector sensitivity genes in durum wheat accessions, information on how the fungus and plant interact in different durum lines and reveal durum lines that have high levels of resistance to SNB. This work is aligned with Subobjective 1C. Research has been initiated to characterize tan spot resistance in the durum variety Kronos. A genetic mapping population has been screened for reaction to Ptr ToxB, a protein that interacts with the durum susceptibility gene Tsc2. The gene was determined to be on the short arm of chromosome 2B. The genetic markers that were used were developed by comparing the genome sequence of Kronos to the wheat genome reference sequence. Candidate Tsc2 genes have been identified and will be characterized. This research will help in the understanding of how Ptr ToxB and Tsc2 interact in the plant. This work aligns with Subobjective 2A. A synthetic wheat line SW8 (PI 639730) was found to have two genes for resistance to Hessian Fly. The two genes, H26A and H26B, are very close in the genome and were moved into a more adapted wheat variety, Newton, by making six rounds of backcrossing. Three genetically similar lines were developed, two with either H26A or H26B, and one with both genes. Now each gene can be evaluated for Hessian Fly resistance and the lines can be used as germplasm for wheat breeders. This work aligns with Subobjective 4B. Saw Fly-resistant durum wheat with solid-stems and durum with low cadmium accumulation are being developed. The genes Sst1 for solid stem from the durum landrace ‘Golden Ball’ and Cdu1 for low-cadmium accumulation from the Canadian durum cultivars ‘Strongfield’ and ‘Transcend’ were transferred into six North Dakota durum cultivars, Alkabo, Carpio, Divide, Joppa, Grenora, ND Riveland, and five breeding lines through six backcrosses and using genetic markers. A total of 200 durum lines containing both genes have been selected and are now available for use in breeding programs. This work aligns with Subobjective 4C. Thirty-eight small grains researchers and breeders were provided access to the most advanced genetic marker technology for wheat, barley and oats. Because of the availability of reference genomes, high density single DNA letter differences across the wheat barley and oat genomes, were used to identify new genes or used to select lines from genetic mapping populations. Each month, 51 million single DNA nucleotide changes were identified and provided for gene discovery and 9,000 for screening germplasm. This information was used for many applications such as identifying new sources of resistance to rust pathogens in oat and durum, developing breeding selection models in barley, and screening wheat breeding germplasm for resistance to Fusarium head blight. Proof of concept studies in wheat and barley are also progressing to develop new DNA sequencing technology as genetic tools for crop improvement. This work aligns with Subobjective 4E. Research to determine if barley has a gene similar to the wheat FHB1 (aka TaHRC) gene, which provides resistance to the major pathogen Fusarium head blight (FHB), is being conducted so that resistance can be developed in barley varieties. We used CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) gene editing technology to induce mutations to disrupt the barley copy, HvHRC. Gene-edited plants have been obtained and the mutations are being verified by DNA sequencing. This work will not only help verify that TaHRC is comparable to FHB1 in wheat and that barley has a similar gene for FHB resistance, but it will also establish the protocols for gene editing in barley for the benefit of barley genetics and improvement. This work aligns with Subobjective 5A. To identify barley resistance/susceptibility genes to spot form net blotch (SFNB) caused by the fungal pathogen Pyrenophora teres f. maculata (Ptm), we conducted quantitative trait loci (QTL) mapping with two different genetic populations using the Ptm isolate 13IM8.3. We identified ten regions in the barley genome that provide either resistance or susceptibility. Two of these regions were common in both genetic mapping populations. Genetic markers easily used by barley breeders were developed for each important genomic region and will be useful for developing SFNB resistant barley varieties. This work aligns with Subobjective 5B.

Accomplishments
1. A new type of wheat gene governing disease susceptibility. Septoria nodorum blotch (SNB) is a severe fungal disease of wheat worldwide. ARS researchers in Fargo, North Dakota, isolated a new gene in wheat, Snn3-D1, that makes wheat susceptible to SNB. The researchers found that a portion of the Snn3-D1 gene involved in the recognition of the SNB pathogen in wheat plants has similarity to a component of a nematode gene involved in sperm movement. This is the first research to show common features between a nematode sperm-movement gene and a pathogen resistance gene in plants. This knowledge will allow researchers to devise appropriate strategies for the development of disease resistant crops.

2. A new type of wheat gene governing disease resistance. Septoria tritici blotch (STB) is a severe fungal disease of wheat worldwide. ARS researchers in Fargo, North Dakota, along with collaborators in France and The Netherlands discovered a gene from wheat that provides resistance to STB. The gene, Stb16, belongs to a class of genes that have not previously been associated with disease resistance in plants. This gene is important because it makes wheat resistant to many strains of the STB fungus and very useful for plant breeders as they develop new STB resistant varieties.

3. A new form of a durum wheat gene for controlling stem rust resistance. Stem rust is one of the most damaging diseases in durum and bread wheat and a threat to wheat production worldwide. New strains of the fungal pathogen, such as Ug99, have caused epidemics in East Africa, Europe and Central Asia in the last two decades. ARS researchers in Fargo, North Dakota, identified two new forms of Sr13, one of the most important stem rust resistance durum wheat genes. Stem rust testing with multiple strains of the pathogen showed one of the forms, Sr13c, to be the strongest and provided resistance to all current strains of the pathogen. The second new form, Sr13d, did not provide resistance to Ug99. Therefore, Sr13c can be used by breeders to develop new wheat varieties with robust stem rust resistance.

4. Stem rust resistance genes in the wheat line Largo. A synthetic wheat line Largo, created by reconstructing in a laboratory setting the ancestral hybridization of three wild species to combine the A, B, and D genomes, was found to have resistance to stem rust. ARS researchers in Fargo, North Dakota, identified five stem rust resistance genes in Largo. Among these genes, three were previously identified genes (Sr9e, Sr13c, and Sr46) and two are potentially new Sr genes. Knowledge of the Sr genes present in Largo will help wheat breeders to design breeding experiments aimed at the development of new stem rust-resistant wheat varieties.

5. A barley gene regulating chloroplast development. Plant chloroplasts are miniature factories of photosynthesis and critical for crop biomass and grain yield. However, chloroplast development is a complicated process, and the underlying chloroplast formation pathways have not been fully revealed. ARS researchers in Fargo, North Dakota, genetically characterized a mutated strain of barley known as grandpa1 (gpa1) that is defective in chloroplast formation. Genetic analysis revealed chromosome 2H to be the chromosomal location of the defective Gpa1 gene and provided possible function. This research provides knowledge for barley geneticists to potentially manipulate Gpa1 to improve photosynthesis for higher yields.

Review Publications
Sapkota, S., Mergoum, M., Kumar, A., Fiedler, J.D., Johnson, J., Bland, D., Lopez, B., Sutton, S., Ghimire, B., Buck, J., Chen, Z., Harrison, S. 2020. A novel adult plant leaf rust resistance gene Lr2K38 mapped on wheat chromosome 1AL. The Plant Genome. 13:e20061. https://doi.org/10.1002/tpg2.20061.
Saintenac, C., Cambon, F., Aouini, L., Verstappen, E., Mahmod T. Ghaffary, S., Poucet, T., Marande, W., Berges, H., Xu, S.S., Jaouannet, M., Favory, B., Alassimone, J., Sanchez-Vallet, A., Faris, J.D., Kema, G., Robert, O. 2021. A wheat cysteine-rich receptor-like kinase confers broad-spectrum resistance against Septoria tritici blotch. Nature Communications. 12:433. https://doi.org/10.1038/s41467-020-20685-0.
Mazzucotelli, E., Sciara, G., Mastrangelo, A., Desiderio, F., Xu, S.S., Faris, J.D., Hayden, M.J., Tricker, P.J., Ozkan, H., Echenique, V. 2020. The Global Durum Wheat Panel: An international effort to identify and exchange beneficial alleles. Frontiers in Plant Science. 11:569905. https://doi.org/10.3389/fpls.2020.569905.
Marais, F., Fiedler, J.D., Tao, H., Pirseyedi, S., Hegstad, J., Ganaparthi, V., Liu, Y., Bisek, B., Li, X. 2020. Homoeology of Thinopyrum distichum single chromosome additions in triticale and wheat. Crop Science. https://doi.org/10.1002/csc2.20357.
Yang, S., Overlander, M., Fiedler, J.D. 2021. Genetic analysis of the barley variegation mutant, grandpa1.a. BMC Plant Biology. 21(1):134. https://doi.org/10.1186/s12870-021-02915-9.
Xavier, R.K., Xu, D., McCarthy, P., Yang, S., Wang, G. 2021. Draft genome sequence of Streptomyces sp. HB-N217 isolated from the marine sponge Forcepia sp.. Microbiology Resource Announcements. 10. Article e01410-20. https://doi.org/10.1128/MRA.01410-20.
Zhang, Z., Running, K.L., Sudeshi, S., Peters Haugrud, A.R., Szabo-Hever, A., Shi, G., Brueggeman, R.S., Xu, S.S., Friesen, T.L., Faris, J.D. 2021. A protein kinase-major sperm protein gene hijacked by a necrotrophic fungal pathogen triggers disease susceptibility in wheat. Plant Journal. 106(3):720-732. https://doi.org/10.1111/tpj.15194.
Friesen, T.L., Faris, J.D. 2021. Characterization of effectors and their targets in necrotrophic pathogens reveals trends and variation in host manipulation. Annual Review of Phytopathology. https://doi.org/10.1146/annurev-phyto-120320-012807.
Sharma, J.S., Overlander, M., Faris, J.D., Klindworth, D.L., Rouse, M.N., Kang, H., Long, Y., Jin, Y., Lagudah, E.S., Xu, S.S. 2021. Characterization of synthetic wheat line Largo for resistance to stem rust. Genes, Genomes, Genetics. https://doi.org/10.1093/g3journal/jkab193.
Richards, J.K., Seneviratne, S., Wyatt, N., Xu, S.S., Liu, Z., Faris, J.D., Friesen, T.L. 2021. A triple threat: The Parastagonospora nodorum SnTox267 effector exploits three distinct host genetic factors to cause disease in wheat. New Phytologist. https://doi.org/10.1111/nph.17601.
Gill, B., Klindworth, D.L., Rouse, M.N., Zhang, J., Zhang, Q., Sharma, J.S., Chu, C.N., Long, Y., Chao, S., Olivera, P.D., Friesen, T.L., Zhong, S., Jin, Y., Faris, J.D., Fiedler, J.D., Elias, E.M., Liu, S., Cai, X., Xu, S.S. 2021. Function and evolution of allelic variation of Sr13 conferring resistance to stem rust in tetraploid wheat (Triticum turgidum L.). Plant Journal. 106:1674-1691. https://doi.org/10.1111/tpj.15263.
Kariyawasam, G.K., Richards, J.K., Wyatt, N.A., Running, K., Xu, S.S., Liu, Z., Borowicz, P., Faris, J.D., Friesen, T.L. 2021. The Parastagonospora nodorum necrotrophic effector SnTox5 targets the wheat gene Snn5 and facilitates entry into the leaf mesophyll. New Phytologist. https://doi.org/10.1111/nph.17602.
Zhang, M., Zhang, W., Zhu, X., Sun, Q., Yan, C., Xu, S.S., Fiedler, J.D., Cai, X. 2020. Dissection and physical mapping of wheat chromosome 7B by inducing meiotic recombination with its homoeologues in Aegilops speltoides and Thinopyrum elongatum. Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-020-03680-3.
Hoque, A., Fiedler, J.D., Rahman, M. 2020. Genetic diversity analysis of a flax (Linum usitatissimum L.) global collection. BMC Genetics. 21:557. https://doi.org/10.1186/s12864-020-06922-2.