Location: Wheat Health, Genetics, and Quality Research
2022 Annual Report
Accomplishments
1. Development of environomic prediction to predict spring wheat performance. Changing climate conditions have profound impacts on crop performance from natural fields, but machine learning algorithms specifically designed to capture such impacts are scarce. ARS researchers at Pullman, Washington, in collaboration with researchers at Washington State University, University of Idaho, and Iowa State University, developed a novel machine learning algorithm, environomic prediction (EP), enabling the accurate forecast prediction of performance trend based on daily weather conditions. The potential of EP was demonstrated by six important traits (including yield and quality trait) from the Idaho variety testing trials spanning 16 years at five locations. This EP model can be used to forecast crop performance so growers will be able to adjust the management practices based on the prediction.
2. Plant UBX-domain containing protein 1 (PUX1) is a new gibberellic acid (GA) hormone signaling gene. The GA receptor GID1 controls all aspects of GA response in plants, but not all of its functions can be explained by interaction with DELLA proteins (a short stretch of amino acids that are known to regulate GA signaling). ARS researchers at Pullman, Washington, and colleagues at Washington State University, and the University of Wisconsin, identified PUX1 as a GID1-interacting protein and found that it acted via both DELLA-dependent and independent mechanisms to negatively regulate GA responses including seed germination, stem elongation, and the transition to flowering. These results fundamentally improve our understanding of how the GA hormone controls these responses which are essential to agricultural traits including preharvest sprouting tolerance, emergence, and earliness.
3. Development of a 96-well alpha-amylase enzyme assay. It is difficult to characterize late maturity alpha-amylase (LMA), the expression of alpha-amylase during grain maturation in response to cold temperatures, using the falling numbers test because it requires too much grain for the carefully staged single-spike LMA induction assays. ARS researchers at Pullman, Washington, and colleagues at Washington State University, developed a high throughput 96-well assay using the Phadebas chemistry allowing accurate screening in single-spike samples. This result will provide rapid screening for LMA and preharvest sprouting tolerance in wheat breeding programs that will facilitate selection for resistance to low falling numbers.
4. Loci, effective in resistance to Stripe Rust in U.S. wheat, identified. Stripe rust is a devastating global wheat disease and the hexaploid club spring wheat cultivar JD contains both all-stage and adult plant resistance but the genes controlling this resistance are unknown. A population derived from a cross between JD and a susceptible wheat was assayed in the field and a major gene for resistance was identified on the short arm of chromosome 1B and a marker, wmc708, was closely linked. Additional resistance genes were detected on chromosomes 3A, 3B, 4A, 6B, and 7A which, together contribute to resistance. This research provides molecular markers and targets to combine new genes for stripe rust resistance into other classes of wheat and will reduce grower dependence on fungicides to control this disease.
5. Genetic diversity in wheat has not declined; on the contrary, it actually seems to be slightly increasing. Wheat is a major human food crop and continued wheat improvement, and resilience depends on maintenance of genetic diversity. ARS researchers in Pullman, Washington, examined trends in genetic diversity in wheat cultivars released from the late nineteenth century until the present and discovered that population structure was defined by market class and that genetic diversity had not decreased after the release of the first semidwarf wheat varieties in 1961. In fact, diversity estimates have increased in several wheat market classes indicating that sufficient variation exists in wheat for continued genetic improvement to meet future needs.
6. Plant height determinants characterized. Understanding mechanisms underlying plant height, the iconic trait of the Green Revolution, has significant bearings on improving crops, however, how gene, environmental conditions, and development process, and their interaction in determining plant height are inter-connected remain unclear. ARS researchers in Pullman, Washington, in collaboration with researchers at Iowa State University identified the novel genetics controlling plant height and the explicit environmental condition (early season temperature) these plant height genes responded to, and then depicted how these two determinants interacted with the developmental process. The research outcome presented the first case of illustrating the plant height in the defined gene-environment-development three-dimension space and results in specific targets to match plant growth to optimal growing environments.
Review Publications
Mu, Q., Guo, T., Li, X., Yu, J. 2022. Phenotypic plasticity in plant height shaped by interaction between genetic loci and diurnal temperature range. New Phytologist. 233(4):1768-1779. https://doi.org/10.1111/nph.17904.
Li, X., Guo, T., Bai, G., Zhang, Z., See, D.R., Marshall, J., Garland Campbell, K.A., Yu, J. 2022. Genetics-inspired data-driven approaches explain and predict crop performance fluctuations attributed to changing climatic conditions. Molecular Plant. 15(2):203-206. https://doi.org/10.1016/j.molp.2022.01.001.
Wu, D., Li, X., Tanaka, R., Wood, J., Tibbs-Cortes, L., Magallanes-Lundback, M., Bornowski, N., Hamilton, J., Vaillancourt, B., Diepenbrock, C., Li, X., Deason, N., Schoenbaum, G., Yu, J., Buell, R., Dellapenna, D., Gore, M. 2022. Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain. Genetics. 221(4). Article iyac091. https://doi.org/10.1093/genetics/iyac091.
Li, R., Char, S., Liu, B., Liu, H., Li, X., Yang, B. 2021. High-efficiency plastome base editing in rice with TAL cytosine deaminase. Molecular Plant. 14(9):1412-1414. https://doi.org/10.1016/j.molp.2021.07.007.
