Location: Wheat Health, Genetics, and Quality Research
2021 Annual Report
Accomplishments
1. Molecular marker developed to select for the mutant ERA8 (Enhanced Response to ABA8) gene. Wheat grain undergoes preharvest sprouting or germination on the mother plant when rain occurs before harvest, resulting in substantial discounts for farmers due to low falling numbers from elevated grain alpha-amylase. There is a major need for new wheat cultivars with resistance to low falling numbers. ARS researchers at Pullman, Washington, and collaborators at Washington State University and John Innes Centre, performed a bulked segregant analysis of exome-DNA-sequence data that mapped ERA8, a new mutant allele in wheat that improves resistance to low falling numbers, to a specific single nucleotide change in the TaMKK3-A sequence. This perfect DNA marker for ERA8 is being used by wheat breeders to select for increased preharvest sprouting tolerance to avoid farmers’ risk of discounts due to low falling number test results.
2. Alternative method of emergence from deep sowing identified in reduced height wheat varieties. The commercial product Release-LC uses the plant hormone gibberellic acid (GA) to improve yield by stimulating grain germination and efficient seedling emergence in farmers’ fields, but also caused a problem because crown root systems were pushed out of the soil putting seedlings at risk of drying out. There was a need to explain why this chemical caused this problem because the manufacturer thought this problem could not occur in wheat lines carrying the GA-insensitive Rht-1 (reduced height) dwarfing genes. ARS researchers in Pullman, Washington, along with Washington State University collaborators, characterized a collection of wheat lines that varied for Rht-1 alleles and found that some GA-insensitive Rht-1 lines could respond to GA with excessive seedling elongation, especially if they had been selected for better emergence. These results provided farmers with information about how to use GA to enhance germination and identified an alternative method to develop wheat with better emergence.
3. Wide-spread late maturity alpha-amylase (LMA) susceptibility is a likely cause of low falling numbers in North American wheat. Farmers lose money when their wheat grain is discounted due to low falling numbers caused by the starch-degrading enzyme alpha-amylase in the grain and the two causes of low falling numbers are difficult to differentiate, but have different genetic control. While U.S. breeding programs focus selection for resistance to preharvest sprouting, they did not know the extent or genetic control of late maturity alpha amylase in North American germplasm. ARS researchers in Pullman, Washington, in collaboration with collaborators at Washington State University, evaluated varieties from 10 North American spring wheat breeding programs and found that most of the late maturity alpha-amylase (LMA) susceptibility mapped to the same loci as LMA in Australian wheat. US wheat breeders now know that selection for LMA resistance is critical to improve falling numbers and have molecular markers to use for this selection.
4. Genotyping by multiplexed sequencing (GMS) method developed to identify multiple known genes in barley. Barley breeders and geneticists need cost effective and efficient methods to identify multiple known genes in breeding populations. Although genotyping methods based on resequencing and analysis of individual genes are popular, there is a need for a cost-effective genotyping platform that can simultaneously identify multiple known genes. ARS researchers at Pullman, Washington, in collaboration with U.S. barley breeders, developed and tested a new genotyping by multiplexed sequencing (GMS) method combined with a data analysis pipeline that can accurately identify alleles at 267 genes of interest to barley breeders. This platform is being used by barley breeders to conduct genetic analysis and select for winter tolerance, improved malting quality, and agronomic traits in barley.
5. Changes in genetic diversity in wheat over time examined to determine if diversity remained for major economic traits. Crop breeders need genetic diversity to improve agronomic traits and to select for pest resistance. Due to long term selection for high grain yield and adaptation, genetic diversity can be lost and breeding progress reduced. ARS researchers at Pullman, Washington, examined population structure and changes in genomic-level and agroecosystem-level genetic diversity of Pacific Northwest (PNW) wheat over the past 120 years. Long-term shifts in gene diversity were not detected, but fluctuations were significant within market classes and within a subset of the most widely grown spring and winter varieties. At the agroecosystem level, diversity has been on a rising trend since the 1990s as the dominance of acreages by a few varieties has become less common. Cultivation of multiple market classes and periodic incorporation of new germplasm by breeding programs have been able to maintain useful levels of genetic diversity in PNW wheat over time indicating that breeding progress will continue.
Review Publications
Hagerty, C., Lutcher, L., Mclaughlin, K.R., Hayes, P., Garland Campbell, K.A., Paulitz, T.C., Graebner, R.C., Kroese, D.R. 2021. Reaction of winter wheat and barley cultivars to Fusarium pseudograminearum inoculated fields, 2018 and 2019. . Agrosystems, Geosciences & Environment. 4(2). Article e20173. https://doi.org/10.1002/agg2.20173.
Horgan, A.M., Garland Campbell, K.A., Carter, A.H., Steber, C.M. 2021. The three-way interaction of varietal emergence capabilities, rht semi-dwarfing alleles, and GA3 seed application from deep planted wheat (Triticum aestivum L). Agrosystems, Geosciences & Environment. 4(1). Article e20144. https://doi.org/10.1002/agg2.20144.
Sexton, T.M., Steber, C.M., Cousins, A.B. 2021. Leaf temperature impacts whole plant water use efficiency independent of changes in leaf level water use efficiency. Journal of Plant Physiology. 258-259. Article 153357. https://doi.org/10.1016/j.jplph.2020.153357.
Liu, L., Yuan, C., Wang, M., See, D.R., Chen, X. 2020. Mapping quantitative trait loci for high level resistance to stripe rust in spring wheat PI 197734 using a doubled haploid population and genotyping by multiplexed sequencing. Frontiers in Plant Science. 11. Article 596962. https://doi.org/10.3389/fpls.2020.596962.
Parajuli, A., Yu, L., Peel, M., See, D.R., Wager, S., Norberg, S., Zhang, Z. 2021. Self-incompatibility, inbreeding depression, and potential to develop inbred lines in alfalfa. In: Yu LX., Kole C., editors. The Alfalfa Genome. Compendium of Plant Genomes. Springer. Cham, Switzerland. p.255-269. https://doi.org/10.1007/978-3-030-74466-3_15.
Brandt, K.M., Chen, X., Tabima, J.F., See, D.R., Zemetra, R.S. 2021. QTL analysis of adult plant resistance to stripe rust in a winter wheat recombinant inbred population. Plants. 10(3). Article 572. https://doi.org/10.3390/plants10030572.
Nazarov, T., Chen, X., Carter, A., See, D.R. 2021. Fine mapping of high-temperature adult-plant resistance to stripe rust in wheat cultivar Louise. Journal of Plant Protection Research. 60(2):126-133. https://doi.org/10.24425/jppr.2020.132213.
Garland Campbell, K.A., Allan, R., Burke, A., Chen, X., DeMacon, P., Higginbotham, R., Engle, D., Klarquist, E., Mundt, C., Murray, T., Morris, C.F., See, D.R., Wen, N. 2021. Registration of “ARS Crescent” soft white winter club wheat. Journal of Plant Registrations. 15(3):515-526. https://doi.org/10.1002/plr2.20135.
Garland Campbell, K.A., Carter, A.H., Allan, R., Chen, X., Steber, C.M., DeMacon, P., Esser, A., Higginbotham, R., Engle, D., Klarquist, E., Morris, C.F., Mundt, C., Murray, T., See, D.R., Wen, N. 2021. Registration of Castella soft white winter club wheat. Journal of Plant Registrations. 15(3):504-514. https://doi.org/10.1002/plr2.20132.
Liu, T., Bai, Q., Wang, M., Li, Y., Wan, A., See, D.R., Xia, C., Chen, X. 2021. Genotyping Puccinia striiformis f. sp. tritici isolates with SSR and SP-SNP markers reveals dynamics of the wheat stripe rust pathogen in the United States from 1968 to 2009 and identifies avirulence associated markers. Phytopathology. https://doi.org/10.1094/PHYTO-01-21-0010-R.
Bai, Q., Wan, A., Wang, M., See, D.R., Chen, X. 2021. Population diversity, dynamics, and differentiation of wheat stripe rust pathogen Puccinia striiformis f. sp. tritici from 2010 to 2017 and comparison with 1968 to 2009 in the United States. Frontiers in Microbiology. 12. Article 696835. https://doi.org/10.3389/fmicb.2021.696835.
Martinez, S.A., Shorinola, O., Conselman, S., See, D.R., Skinner, D.Z., Uauy, C., Steber, C.M. 2020. Exome sequencing of bulked segregants identified a novel TaMKK3-A allele linked to the wheat ERA8 ABA-hypersensitive germination phenotype. Theoretical and Applied Genetics. 133:719-736. https://doi.org/10.1007/s00122-019-03503-0.
Ghimire, B., Hulbert, S., Garland Campbell, K.A., Steber, C.M., Sanguinet, K. 2020. Characterization of root traits for improvement of spring wheat in the Pacific Northwest. Agronomy Journal. 112(1):228-240. https://doi.org/10.1002/agj2.20040.
