Progress 12/01/23 to 11/30/24
Outputs
Target Audience:We have reached a very broad audience. Through field days we did presentations to growers, milling and baking industries, and consumers using wheat products. Through professional meetings and publications, we did presentations to scientists and students in academic sectors. Changes/Problems:We made an one year extension, and the project will end in Nov. 30 in 2025.? What opportunities for training and professional development has the project provided?Student and postdoctoral fellows received extensive training in the assessment of dwarf and common bunt resistance and completed disease assessment in dwarf bunt nurseries at USU, Logan, UT for two consecutive years. The students have been trained in molecular biology, including molecular cloning and CRISPR technique, training in operating field equipment in cultivar development. Also, they have been trained in genotyping techniques, fine-mapping, genomic selection, analyzing data using different softwares and packages. Students did presentations at professional meetings and field day presentations to growers and stakeholders to disseminate the information about the disease bunt and its identification. How have the results been disseminated to communities of interest?The lead PI at UI made an oral presentation on dwarf bunt cultivar development to the Idaho Wheat Commissioners and growers field day. The lead PI and Co-PIs as well as two graduate students did oral presentations at The Western Wheat Workers Meeting.? What do you plan to do during the next reporting period to accomplish the goals?For objective 1, two large F2 populations will be used in fine mapping of 6DL QTL and phenotyped in the USU disease nursery in 2025. The resequencing data of the parental lines will be used to understand the dwarf bunt resistance mechanisms in the two parents. The mutant derived F1s will be back-crossed twice, and the derived populations will be used to identify candidate genes for the 6DL QTL using MutRen Sequencing. We are going to continue CRISPR-CAS9 to validate the candidate genes. For objective 2, we will target a third-year assessment of dwarf bunt and common bunt resistance in the winter wheat panel. Under objective 3, the agronomic performance of the selected lines will be assessed for grain yield and other agronomic performance in various field trials and added to the cultivar development pipeline. For objective 4, we are going to continue training to one postdoc and one MS student. We are going to do two oral presentations at the ASA-CSSA-SSSA International Annual Meetings in San Antonio, TX, in November 2024 and publish two papers in 2025.
Impacts
What was accomplished under these goals?
To meet the proposed objectives, two different populations were evaluated for dwarf bunt infection in the field nursery at Utah State University for two consecutive years (2023, 2024). The protocol for green-house screening of common bunt disease has been optimized and used in phenotyping the two mapping populations. Phenotyping of these populations along with the high throughput genotyping facilitated candidate gene validation, genomic selection model development, and the bunt resistance cultivar development in this project. Under objective 1: fine-mapping and candidate gene analysis. In the past two years, we have identified the QTLs on chromosome arms 6DS, 6DL, and 7DS. Using exome capture sequence data, we have retrieved several tentative candidate genes for the 7DS QTL. In 2024, we have validated the 6DL and 6DS QTL in a diverse winter wheat panel and retrieved four tentative candidate genes for the 6DL QTL. To validate these candidate genes, we made three different approaches: 1) Sequenced the four candidate genes in the two parental lines; 2) Developed fine-mapping populations targeting the QTL on the 6DL; 3) Selected 6DL knock-out mutants. Additionally, the high-quality genome resequencing of the parental lines has been used to target and understand the role of the genomic differences in the candidate genes and their regulatory region in dwarf bunt resistance. We have also confirmed some knockout mutation lines in UI Silver, the resistant parent in the population the 6DL QTL was retrieved. The crosses of these mutant lines with UI Silver wild type have been initiated this year. Candidate genes identified from capture sequencing of the 7DS QTL have been validated in parental lines by sequencing and in fine-mapping populations. We expect to have CRISPR-CAS9 edited plants for the candidate genes by the end of 2025. Under objective 2, Genomic selection to select for dwarf and common bunt resistance. Dwarf bunt resistance has estimated broad sense heritability of 0.70 and narrow sense heritability of 0.31, suggesting significant environmental effects and genomic selection would facilitate the selection in cultivar development. Using the two years' data and five-fold cross-validation, a basic genomic BLUP (GBLUP) prediction model yielded an average prediction accuracy of 0.80. An alternative approach treated entries from specific breeding programs as the test set, using the remaining entries at the training set. The GBLUP model predicted entries from the UI, USU, and Washington State University breeding programs with accuracies of 0.64, 0.51, and 0.30, respectively. The USU program assessed whether using the most informative SNP marker as a fixed effect in the GBLUP model could improve accuracy. The results showed there is a neglect change with the fixed effect included for two major QTL on chromosome arm 6DL and 7DS. Under objective 3, Cultivar improvement for durable dwarf bunt resistance, we selected three doubled haploid winter wheat lines that showed dwarf bunt resistance and good agronomic performance. These three lines have been advanced to elite nursery and western wheat regional trials for this planting season. Under objective 4, Graduate student and postdoctoral training, this project has been training two Ph.D. and one MS students, one and a half postdoctoral fellows this year with additional matching fund from the lead PI's university. MS student associated with project at USU graduated in May of 2024, the Ph.D student at UI plans to graduate in December of 2024.
Publications
- Type:
Journal Articles
Status:
Accepted
Year Published:
2024
Citation:
Joshi P, G.S. Dhillon, Y. Gao, A. Kaur, J. Wheeler, X. Chen, W. Krause, M. Krause, and J. Chen*. 2024. Identification and validation of two quantitative trait loci for dwarf bunt in the resistant cultivar UI Silver. Theor Appl Genet. In revision.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Chen, J. M. R. Krause, Joshi, P, W. Krause, G.S. Dhillon, A. Kaur, and F. Xiao. 2024. Plant Breeding Partnership Genomics-enabled wheat breeding to accelerate development of dwarf bunt resistant cultivars. Oral presentation at 2024 Western Wheat Workers meeting. Idaho Falls, ID, June 18-19, 2024.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Chen, J. 2024. Unlocking Genes for Dwarf Bunt Resistance in Winter Wheat - Current Progress and Outlook. 2024 NIFA AFRI project meeting and National Association of Plant Breeders Annual Conference, San Louis, MO. July 20-25, 2024.
- Type:
Conference Papers and Presentations
Status:
Awaiting Publication
Year Published:
2024
Citation:
Joshi P, G.S. Dhillon, Y. Gao, A. Kaur , J. Wheeler ,W. Krause, M. R. Krause, X. Chen and J. Chen. 2024. Identification and Validation of Quantitative Trait Loci for Dwarf Bunt in the Resistant Cultivar UI Silver. Poster presentation at 2024 National Association of Plant Breeders Annual Conference, San Louis, MO. July 20-25, 2024.
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Progress 12/01/22 to 11/30/23
Outputs
Target Audience:We have reached a very broad audience. Through field days we did presentations to growers, milling and baking industries, and consumers using wheat products. Through professional meetings and publications, we did presentations to scientists and students in academic sectors. Changes/Problems:The co-PI at the USU is leaving for Oregon State University in November. She will transfer her responsibilities to another faculty in the department. Her student has collected two years data for his thesis. Therefore, the effect of the co-PI leave will be minimum. What opportunities for training and professional development has the project provided?Students and postdoctoral fellows received extensive training in assessment of dwarf and common bunt resistance and completed disease assessment in more than 4000 headrows in Logan, UT. Theyalso received training in genotyping, fine-mapping, and analyzed data using R and other softwares, training in molecular biology, including molecular cloning and CRISPR technique, training in operating field equipment in cultivar development and did a field day presentation to growers and stakeholders. In addition, two graduate students received training on genomic selection organized by USDA-ARS NIFA WheatCAP project. This year, we conducted 20 project meetings in-person or with zoom. How have the results been disseminated to communities of interest?The lead PI at UI made an oral presentation on dwarf bunt cultivar development to Idaho Wheat Commissioners. The Ph.D student and postdoctoral fellow each did oral presentation at the XII International bunt and smut workshops at Boku, Autria, and a poster presentation at the state growers field day. The MS student at USU did an oral presentation at the XII International bunt and smut workshops at Boku, Austria and a poster presentation on genomic selection of dwarf bunt at the ASA-CSSA-SSSA International Annual Meetings in St. Louis, MS. Wheat Growers/U.S. What do you plan to do during the next reporting period to accomplish the goals?We are going to continue CRISPR-CAS9 and EMS knockout mutants to validate the candidate genes for objective 1; assess on the third year for dwarf bunt and common bunt resistance in the winter wheat panel under objective 2; assess grain yield and other agronomic performance for newly developed bunt resistant lines in multiple environments under objective 3; train one and a half postdoc and three graduate students under objective 4. We are going to present our finding at the 3rd International Wheat Congress in Perth, Western Australia in September 22 to 27, 2024. The Ph.D students will get trainings on sequence analysis to identify candidate genes and develop informative molecular markers to select the resistant genes identified. MS student at USU plan to graduation in May of 2024 and Ph.D student at UI plans to graduate in winter of 2024.
Impacts
What was accomplished under these goals?
We got very uniform dwarf bunt infection in the field nursery at Utah State University, evaluated dwarf bunt resistance in more than 4000 lines. Protocol for common bunt screening in greenhouse has been optimized and used in phenotyping of two mapping populations. These nurseries and methods facilitated candidate gene validation, genomic selection model development, and the bunt resistance cultivar development. We have accomplished five presentations at the international and national meetings this year. Under objective 1, fine-mapping and candidate gene analysis. Candidate genes identified from capture sequencing of the 7DS QTL have been validating in parental lines by sequencing and in fine-mapping populations. The wheat transformation system and CRISPR-based gene knockout have been optimized at the main campus of UI. The CRISPR constructs targeting the first group of candidate genes have been generated. We expect to start gene editing experiments in 2024. We also confirmed some knockout EMS mutation lines in the resistant cultivar UI Silver this year. These EMS mutation lines will be used to identify candidate genes for the 6DL QTL using MutloSeq technology. Under objective 2, genomic selection, we successfully obtained the second-year dwarf bunt infection data this year. Using the two years' data and five-fold cross-validation, a basic genomic BLUP (GBLUP) prediction model yielded an average prediction accuracy of 0.78. This study suggests that dwarf bunt resistance is high heritability trait and genomic selection can be used in cultivar improvement. Under objective 3, we selected two doubled haploid winter wheat lines that showed dwarf bunt resistance and good agronomic performance. The two lines were advanced to elite nursery and planted for seed increase. Under objective 4, this project has been training two Ph.D and one MSstudents, one and a half postdoctoral fellows this year with additional matching fund from the lead PI's university.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Joshi P, G.S. Dhillon, Y. Gao, A. Kaur, J. Wheeler, and J. Chen. 2023. Comparative mapping of Dwarf Bunt and Common Bunt Resistance QTL in Winter Wheat Doubled Haploid Population. Oral presentation at 2023 ASA, CSSA, SSSA international annual meeting, San Louis, MO. Oct. 29 Nov. 1, 2023.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Joshi, P., G. Dhillon, D. Hole, T. Gordon, H. Burstmayr, M. Ehn, W. Krause, M. Krause, and J. Chen. 2023. Assessment of Dwarf Bunt and Common Bunt Resistance in Wheat Differential Lines. Proceeding of XXII international bunt and smut workshop. Boku, Austria. June 13 15, 2023. Https://short.boku.ac.at/bunt.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Krause, W., J. Chen, P. Joshi, D. Hole, R. Nelson, J. Clawson, T. Gordon, M.R. Krause. 2023. Genomic selection for dwarf bunt resistance in wheat. Poster presentation at 2023 ASA, CSSA, SSSA international annual meeting, St. Louis, MO. Oct. 29 Nov. 1, 2023.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Dhillon, G., P. Joshi, Y. Yan, F. Xiao, W. Krause, M. Krause, and J. Chen. 2023. Candidate gene analysis of the 7DS QTL for dwarf bunt resistance using targeted capture sequencing. Proceeding of XXII international bunt and smut workshop. Boku, Austria. June 13 15, 2023. Https://short.boku.ac.at/bunt.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Krause, W., J. Chen, P, Joshi, D. Hole, P. Nelson, J. Clawson, T. Gordon, and M. Krause. 2023. Genomic selection for dwarf bunt resistance in wheat. Proceeding of XXII international bunt and smut workshop. Boku, Austria. June 13 15, 2023. Https://short.boku.ac.at/bunt.
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Progress 12/01/21 to 11/30/22
Outputs
Target Audience:We have reached a very broad audience. Through field days we did presentations to growers, milling and baking industries, and consumers using wheat products. Through professional meetings and publications,we did presentations to scientists and students in academic sectors. Changes/Problems:One Ph.D student started in the fall of 2022, a half year later than the expected targeting date. This delay didn't have very much impact on the project progress.? The postdoctoral fellow at UI was hired one year later than the expected targeting date. There is no impact on the project progress because one Ph.D student has been doing the work that the postdoc was supposed to do. What opportunities for training and professional development has the project provided?Student received extensive training in assessment of dwarf and common bunt resistance and completed disease assessment in 4,800 headrows in Logan, UT. The students also received training in genotyping, fine-mapping, and analyzed data using JMP Genomics and R softwares, and training in molecular biology, including molecular cloning and CRISPR technique. In addition, the students received training in operating field equipment in cultivar development and did a field day presentation to growers and stakeholders. How have the results been disseminated to communities of interest?The lead PI at UI made an oral presentation on dwarf bunt cultivar development to Idaho Wheat Commissioners. The lead PI and co-PIs did an electronic poster presentation at the 2nd International Wheat Congress, oral presentation at Pacific Northwest Tri-state Growers Convention, and oral presentation on dwarf bunt resistant cultivars at the state growers field day. The co-PI at USU made an oral presentation that discussed preliminary results of the genomic selection analyses at the ASA-CSSA-SSSA International Annual Meetings in Baltimore, MD. A similar oral presentation was given virtually at the Simposio de Ciencias Agrarias of the Instituto Nacional de Tecnología Argentina. Finally, the co-PI at USU also described the goals of the project during an invited virtual presentation titled "Emerging breeding technologies to improve wheat production in Utah and the U.S." at the National Association of Wheat Growers/U.S. Wheat Associates fall meeting on November 8th, 2022. What do you plan to do during the next reporting period to accomplish the goals?We are going to use CRISPR-CAS9 and EMS knockout mutants to validate the candidate genes for objective 1; assess on the second year for dwarf bunt and common bunt resistance in the winter wheat panel under objective 2; assess grain yield and other agronomic performance for newly developed bunt resistant lines in multiple environments under objective 3; train one postdoc and three graduate students under objective 4. We are going to present our finding at the XXII International Bunt Workshop being held in Austria and at the 2023 International ASA, CSSA, SSSA meetings in Texas. The M.S. student will attend the Tucson Plant Breeding Institute at the University of Arizona to receive in-depth training in quantitative genetics during January, 2023. The Ph.D students will get trainings on sequence analysis to identify candidate genes and develop informative molecular markers to select the resistant genes identified.?
Impacts
What was accomplished under these goals?
The dwarf bunt nursery established in Logan on the Utah State University campus has been serving as an international nursery and evaluated materials used in this project and materials from the Western Regional Nursery, from USDA-ARS and from breeders from Austria. We have also developed a common bunt nursery in Aberdeen, ID and developed protocols for screening common bunt resistance in growth chamber. These nurseries and methods will facilitate the bunt resistance cultivar development, candidate gene validation, and genomic selection model development in this project. Under objective 1, fine-mapping and candidate gene analysis, we have initiated CRISPR-CAS9-based gene editing system to determine the dwarf bunt resistance genes. Three NB-LRR type candidate resistance genes located on the 7DS QTL are identified and six CRISPR constructs targeting the corresponding genes have been generated. Introduction of the CRISPR constructs into a resistant cultivar UI SIlver is in progress. We also identified some knockout EMS mutation lines in the resistant cultivar UI Silver. These knockout mutation lines will facilitate the candidate gene identification for the 6DL QTL and validate the candidate genes for the 7DS QTL. We developed fine-mapping population for the 6DL QTL. Under objective 2, two replicates of 384 winter wheat cultivars and breeding lines with varying levels of resistance to dwarf bunt were sown in the disease nursery on 5 October 2021 and were inoculated on 17 November 2021. This population contains lines from the CO, ID, MT, OR, UT, and WA wheat production areas. This population was genotyped by Wheat 90K iSelect platform and by a "genotyping by multiplex sequencing" (GMS) platform. The USU program analyzed the phenotypic data from the training population evaluated during the 2022 growing season. Disease resistance showed a line-mean heritability of 0.65. The program also performed a preliminary genomic prediction analysis using the phenotypic and GMS data. Using five-fold cross-validation, a basic genomic BLUP (GBLUP) prediction model yielded an average prediction accuracy of 0.57. An alternative approach treated entries from specific breeding programs as the test set, using the remaining entries at the training set. The GBLUP model predicted entries from the UI, USU, and Washington State University breeding programs with accuracies of 0.40, 0.46, and 0.44, respectively. Finally, the USU program assessed whether using the most informative SNP marker as a fixed effect in the GBLUP model could improve accuracy. The most informative marker, IWA8562_30, showed an adjusted r-squared value of 0.15. However, when it was included in the GBLUP prediction model as a fixed effect, the prediction accuracy was reduced slighty from 0.57 to 0.55. Under objective 3, we selected two doubled haploid winter wheat lines that showed dwarf bunt resistance and good agronomic performance. The two lines were advanced to elite nursery and planted for seed increase. Under objective 4, we hired one Ph.D and one M.S students in spring and another Ph.D student in fall this year. We also hired the postdoctoral fellow in the end of this year, and he will start on the project in January of 2023.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Jianli Chen, Margaret Krause, Fangming Xiao, Tyler Gordon, Rui Wang, Juliet Marshall, Blair Goates, and David Hole. 2022. Research progress on dwarf bunt resistance in winter wheat in the Western US. E-Poster. Beijing, P.R. China. Sep.11-15, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Margaret Krause. 2022. Big data for small breeding: insights from the Utah State University small grains breeding program. Oral presentation. ASACSSASSSA International Annual Meetings. Baltimore, MD. Nov. 8.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Margaret Krause. 2022. Emerging breeding technologies to improve wheat production in Utah and the U.S. Virtual oral presentation. National Association of Wheat Growers/U.S. Wheat Associates Fall Meeting. Baltimore, MD. Nov. 8.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Margaret Krause. 2022. Big data for small breeding: leveraging emerging breeding technologies to benefit small-scale breeding programs. Virtual oral presentation. Simposio de Ciencias Agrar�as, Instituto Nacional de Technolog�a Argentina. Nov. 4.
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