Location: Cereal Crops Research
2022 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 was screened for reaction to the disease tan spot to identify resistant lines and conduct genetic analysis to discover genes associated with resistance or susceptibility. The panel was screened with five races of the fungal pathogen, and genetic analysis revealed several known and several previously unknown genes governing reaction to the disease. A manuscript describing these results is currently being written. This research provides knowledge of the importance of tan spot disease in durum wheat, identified lines useful for breeding tan spot resistant durum varieties, and revealed individual genes responsible for governing resistance to tan spot, which can be used to improve modern durum varieties. This work aligns with Sub-objective 1B.
A worldwide collection of durum wheats referred to as the Global Durum Panel was screened for reaction to the disease septoria nodorum blotch (SNB) as well as individual proteins known as effectors produced by the SNB fungus to identify resistant lines and conduct genetic analysis to discover genes associated with resistance or susceptibility. The panel was screened with three isolates of the fungal pathogen and five protein effectors. The results revealed durum lines resistant to SNB and the protein effectors. Subsequent genetic analysis revealed how the pathogen-produced effector proteins and the durum genes that interact with them are involved in conditioning SNB susceptibility. A manuscript describing these results is currently being written. This research provides knowledge regarding the genetic basis of SNB resistance and susceptibility in durum wheat, identified lines useful for breeding SNB resistant durum varieties, and revealed individual genes responsible for governing resistance to SNB, which can be used to improve modern durum varieties. This work aligns with Sub-objective 1C.
A collection of durum wheat from the National Small Grains Collection was screened for reaction to six stem rust isolates to identify novel sources of resistant germplasm. These new individuals were investigated more thoroughly and several genomic loci determining the resistance to stem rust were uncovered. A manuscript describing these results is currently being written. This research provides knowledge regarding the location of genomic loci and molecular markers for the introgression of these loci to breed elite durum cultivars. This work aligns with Sub-objective 1A.
High density single nucleotide polymorphism (SNP) genotyping was acquired and provided to 35 different small grains researchers and breeders with an average monthly throughput of 55 million data points for gene discovery and 18,000 data points for screening germplasm. This information was used for many applications such as mapping new sources of resistance to fungal pathogens, developing genomic selection models, and screening wheat breeding germplasm for superior end-use quality. We developed and just started offering a new genotyping platform – the USDA-SoyWheOatBar -3K - to provide cost-effective, durable genotyping to support fingerprinting and genomic selection applications in wheat, barley, and oat. This work aligns with Subobjective 4E.
Research has been conducted to identify the Snn5 gene in wheat, which recognizes a protein produced by the fungal pathogen that causes the disease septoria nodorum blotch (SNB). When Snn5 recognizes the fungal protein, which is an effector known as SnTox5, it activates a susceptible response in the wheat plant. Toward the identification of the Snn5 gene, we conducted genetic experiments to delineate the location of the gene on its chromosome and developed molecular markers for use in tracking the gene. The markers developed will serve as useful tools for the identification of the Snn5 DNA sequence and for tracking the movement of the gene in cross hybridization experiments, where breeders will strive to eliminate the gene from their material to render plants resistant to SNB. This work aligns with Sub-objective 2C.
To identify the barley resistance gene (TaHRC) and develop plants with resistance to the disease Fusarium head blight (FHB), we used the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology to disrupt the HvHRC gene in barley. Genetically modified plants have been obtained for three different varieties, and the derived mutations are being analyzed by DNA sequencing. We have developed an FHB-inoculation protocol for greenhouse conditions, and the mutants have shown enhanced resistance to FHB. A manuscript describing these results is currently being written. This research will confirm the identity of TaHRC, and it will provide stable gene transformation or gene editing system for barley geneticists, as well as FHB-resistant germplasm for breeding teams. This work aligns with Subobjective 5A.
Accomplishments
1. Genetic analysis of a gene governing disease susceptibility in wheat. Tan spot is a devastating disease of wheat and causes significant losses in yield and revenue in most wheat-growing regions of the world. ARS researchers in Fargo, North Dakota, conducted genetic analysis of tan spot resistant and susceptible wheat plants to identify a gene governing tan spot susceptibility. The researchers determined the position of the gene in the genome and developed molecular markers for the gene that can be used to determine if other wheat lines contain the gene. Wheat breeders and geneticists will benefit from this research in that they will now be able to efficiently characterize their wheat lines for tan spot susceptibility and use the markers to eliminate the susceptibility gene from high-performing wheat varieties, which, as a result, will benefit farmers in that their crops will suffer less yield losses due to tan spot.
2. Identification of genes governing yield in durum wheat. Durum wheat is used to make pasta and other semolina-based products. Durum relatives may provide a source of genes and genetic variation that can be used to improve yield in durum wheat. ARS researchers in Fargo, North Dakota, conducted genetic analysis of yield-related traits in durum and a relative of durum known as emmer wheat. Greenhouse and field-based studies revealed the positions of genes within the genome of emmer wheat that improved the yields of durum wheat under multiple environments. Durum breeders will benefit from this study because it provides them with knowledge of emmer genes that can be used to improve durum wheat through conventional hybridization means. Ultimately, higher yielding durum varieties will lead to increased income for producers and more food for pasta consumers.
3. Identification of disease resistance genes in barley. A disease known as spot form net blotch (SFNB) is one of the most destructive leaf diseases of barley in the United States and worldwide. Identification of effective disease resistance genes is important for the development of SFNB-resistant barley varieties. ARS researchers in Fargo, North Dakota, along with collaborators at North Dakota State University and Washington State University, conducted genetic analysis of barley resistance to SFNB. The researchers identified a total of ten genes that contributed different levels of SFNB resistance, with one of the genes contributing high levels of resistance. DNA markers associated with the genes were developed and will be useful to expedite the transfer of the resistance genes into new barley varieties. Therefore, the knowledge and tools developed in this research will help to mitigate losses in barley yields due to SFNB, which will lead to increased income for barley producers.
Review Publications
Gaurav, K., Arora, S., Silva, P., Sanchez-Martinez, J., Horsnell, R., Gao, L., Brar, G., Widrig, V., Raupp, J., Singh, N., Xu, S.S., Brown Guedira, G.L., Faris, J.D., Wulff, B.B., et al. 2021. Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement. Nature Biotechnology. 40:422-431. https://doi.org/10.1038/s41587-021-01058-4.
Peters Haugrud, A., Zhang, Z., Friesen, T.L., Faris, J.D. 2022. Genetics of resistance to septoria nodorum blotch in wheat. Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-022-04036-9.
Somegowda, V.K., Prasad, K.V., Naravula, J., Vemula, A., Selvanayagam, S., Rathore, A., Jones, C.S., Gupta, R., Deshpande, S.P. 2022. Genetic dissection and quantitative trait loci mapping of agronomic and fodder quality traits in Sorghum under different water regimes. Frontiers in Plant Science. 13. Article 810632. https://doi.org/10.3389/fpls.2022.810632.
Carlson, C.H., Choi, Y., Chan, A.P., Town, C.D., Smart, L. 2021. Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow (Salix spp.). G3, Genes/Genomes/Genetics. https://doi.org/10.1093/g3journal/jkab436.
Running, K., Momotaz, A., Kariyawasam, G., Zurn, J., Acevedo, M., Carter, A., Liu, Z., Faris, J.D. 2022. Genomic analysis and delineation of the tan spot susceptibility locus Tsc1 in wheat. Frontiers in Plant Science. 13:1-10. https://www.frontiersin.org/articles/10.3389/fpls.2022.793925/full.
Nandety, R.S., Gill, U.S., Krom, N., Dai, X., Dong, Y., Zhao, P., Mysore, K.S.2022. Comparative genome analysis of plant rust pathogen genomes reveal a confluence of pathogenicity factors to quell host plant defense responses. Plants. 11. https://doi.org/10.3390/plants11151962.
Alhashel, A., Poudel, R., Fiedler, J.D., Carlson, C.H., Rasmussen, J., Baldwin, T., Friesen, T.L., Brueggeman, R., Yang, S. 2021. Genetic mapping of host resistance to the Pyrenophora teres f. maculata isolate 13IM8.3. Genes, Genomes, Genetics. https://doi.org/10.1093/g3journal/jkab341.
Gaddameedi, A., Sheraz, S., Are, A., Kexue, L., Pellny, T., Gupta, R., Wan, Y., Moore, K., Shewry, P. 2022. The location of iron and zinc in grain of conventional and biofortified lines of sorghum. Journal of Cereal Science. https://doi.org/10.1016/j.jcs.2022.103531.
