Location: Plant Stress and Germplasm Development Research
2024 Annual Report
Objectives
Objective 1. Use traditional and molecular breeding techniques to develop superior sorghum breeding germplasm and hybrids adapted to diverse environments including improved thermal tolerance and improved water use efficiency.
Sub-objective 1A: Development and agronomic testing of grain and forage inbreds and hybrids with the dominant multiple tiller trait.
Objective 2. Utilize diverse germplasm and sorghum mutants to discover and characterize genes and traits such as cold and drought tolerance, and improved hybrid yield, required for superior sorghum production.
Sub-objective 2A: Characterize phenology and biomass accumulation of a dominant multiple tiller mutant (mtl-d1).
Sub-objective 2B: Using remote sensing via small unoccupied aircraft systems (sUAS) as a high-throughput method to screen stay-green and sugarcane aphid (SCA) tolerance.
Sub-objective 2C: Identify the causal mutation for mtl-d1 and genes associated with biomass production.
Sub-objective 2D: Evaluation and analyses of morphological variation in grain composition and total seed protein and quality for 256 sequenced AIMS sorghum mutants.
Sub-objective 2E: Identification of candidate genes and development of DNA markers for increased seed protein content in sorghum.
Objective 3. Discover and characterize sorghum physiological adaptation traits such as modified leaf angle, variable stomatal density, and stay-green drought tolerance, in diverse sorghum germplasm.
Sub-objective 3.A: Characterizing radiation use efficiency (RUE) in sorghum through erect leaf architecture and plant height.
Sub-objective 3B: Exploring potential increase in sink size and strength by characterizing components of panicle architecture using automated tools.
Approach
Sorghum (Sorghum bicolor, L. Moench) is an important C4 crop that is grown in a variety of environments worldwide for food, feed, forage, and cellulosic biomass production. The crop is known for its inherent drought tolerance, especially compared to other cereal crops like maize and rice. More recently, sorghum has gained attention as a health food crop with desirable market characteristics such as gluten-free grain, and as a sustainably grown product that is rich with beneficial compounds such as antioxidants. Sorghum, as a crop commodity in the United States, is of critical importance in major grain production regions of the country where water is limited. Unfortunately, sorghum crop improvement has remained relatively stagnant for the last 40 years. This stagnation in yield improvements is partially due to minimal research investments by public and private institutions. As climate change effects agricultural production worldwide, and specifically the U.S. Great Plains, it is imperative that scientists improve sorghum in terms of yield potential and end-user utilization. The objective of this research is to integrate recent advances in plant breeding and molecular biology with next generation phenotyping technologies to accelerate the rate of genetic gain in grain and forage sorghum. This project aims to elucidate the genes and gene networks controlling novel agronomic and compositional traits such as leaf erectness, altered and optimized plant height, multi-tillering, and grain protein enhancement. The products of this research will include improved sorghum germplasm, trait-specific genetic markers, and an improved understanding of the physiological traits that enhance sorghum productivity.
Progress Report
For Sub-objective 1A, ARS scientists in Lubbock, Texas developed and tested 8 experimental sorghum hybrids containing the multiple tiller trait. Initial hybrid evaluation confirms that the trait is dominant, and that it is expressed in different genetic backgrounds. Preliminary data show that there is an increase in tillers and above-ground biomass, but more research is needed to confirm yield increases, especially for grain sorghum. For Sub-objective 2A, we evaluated above-ground and below-ground biomass of the multiple tiller mutant in two environments. Researchers have identified that the multiple tiller mutant produces an increase in both leaf and root biomass. Researchers also confirmed that anthesis for the mutant is delayed approximately 18-21 days compared to the wild-type. The delay in anthesis has been confirmed in multiple diverse environments. Researchers are evaluating the potential agronomic consequences of delayed anthesis and are also evaluating if the anthesis timing can be shortened through breeding. For Sub-objective 2B, ARS scientists in Lubbock, Texas, utilized drones to accurately screen diverse sorghum germplasm for post-flowering drought tolerance. The newly developed methods allowed for researchers in Lubbock, Texas to screen large numbers of breeding lines very quickly. Results indicate that unmanned aerial vehicle screening for drought tolerance is very similar to ground-truth data in terms of accuracy. This research will advance the improvement of sorghum by allowing breeders to screen many thousands of sorghum breeding lines quickly and cost-effectively. For Sub-objective 2C, ARS scientists in Lubbock, Texas created mapping populations to identify the casual gene for the multiple tiller trait in sorghum. Researchers also began development of single nucleotide polymorphism markers associated with the trait. Molecular markers will assist the breeding program in trait introgression and selection, especially in forage germplasm where the tillering trait may be less obvious visually. For Sub-objective 2D, ARS scientists in Lubbock, Texas grew-out and collected grain for 256 fully sequenced sorghum mutants. Each mutant line was analyzed by near infrared spectroscopy for important grain quality traits such as protein and starch composition. This vital data will allow researchers to investigate the genetic control of important grain composition traits in sorghum. For Sub-objective 2E, ARS scientists in Lubbock, Texas, initiated the development of genetic mapping populations for identifying genes controlling grain protein in sorghum. Initial backcrossing to the wild-type parent has been completed. For Sub-objective 3A, ARS scientists in Lubbock, Texas evaluated leaf angle traits in the sorghum association panel (SAP), as well as a collection of sorghum mutants. A LI-600 porometer with GPS accelerometer/magnetometer was used to calculate angle of incidence to sun, leaf pitch, roll, heading, slope, and the effects on stomata conductance, transpiration, photosystem II, electron transport rate, lead vapor pressure deficit, and leaf temperature. Preliminary results show that there is significant variation for leaf angle in sorghum, and that some lines express an erect leave phenotype in multiple environments. Additionally, a set of mutants were identified as having the erect leaf phenotype. Further research will test the hypothesis that the erect leaf phenotype increases yield potential in sorghum. For Sub-objective 3B, ARS scientists in Lubbock, Texas, collected panicles from the SAP and measured agronomically important traits such as panicle shape, branch number, grain color, grain size, and grain number using automated deep learning tools. These data will provide details on branching characteristics and grain development of diverse sorghum, which will help researchers improve grain size and grain number in sorghum.
Accomplishments
1. High-throughput phenotyping of stay-green in sorghum using unmanned aerial vehicles and machine learning. In sorghum, the stay-green trait is of particular importance as a measure of how well a genotype can tolerate post-anthesis drought conditions, which is critical for grain yield in many environments. Despite its importance, there is a pressing need for a more efficient, accurate, and precise method to phenotype stay-green in sorghum to enhance breeding efforts. To address this need, ARS researchers in Lubbock, Texas, investigated the application of random forest and XGBoost machine learning models for phenotyping the stay-green trait in sorghum. These models provide quantitative measurements that have the potential to enhance genomic studies and reduce phenotyping burdens associated with manual evaluation of thousands of breeding lines. Overall, the models developed serve as a promising foundation for improving the efficiency of stay-green breeding programs in sorghum. This work drastically improves the efficiency of screening for drought tolerance in sorghum.
2. Development of prussic-acid free grain and forage sorghum. Sorghum contains a cyanogenic glucoside known as dhurrin that can produce toxic hydrogen cyanide (HCN) gas once animals feed on the leaves and stems of the sorghum plant. Many strategies are used to minimize the potential HCN toxicity in livestock, including delayed grazing and silage. Even with mitigation strategies in place, the potential for HCN poising in livestock limits sorghum as a forage. ARS researchers in Lubbock, Texas, have developed grain and forage sorghum that do not have the cyanogenic glucoside dhurrin, and therefore, do not produce HCN gas during grazing. Further agronomic testing of these new sorghum lines will include agronomic performance compared to other sorghums, nitrate levels in forage, and forage composition. This work has the potential to significantly improve sorghum as a forage crop and could lead to increased acres for forage-type sorghum hybrids.
Review Publications
Pugh, N.A., Young, A.C., Oijha, M., Emendack, Y., Sanchez, J., Xin, Z., Puppala, N. 2024. Yield prediction in a peanut breeding program using remote sensing data and machine learning algorithms. Frontiers in Plant Science. 15. https://doi.org/10.3389/fpls.2024.1339864.
Smith, A., Gentile, B.R., Xin, Z., Zhao, D. 2023. The effects of heat stress on male reproduction and tillering in Sorghum bicolor. Food and Energy Security. 12(6). Article e510. https://doi.org/10.1002/fes3.510.
Xin, Z., Jiao, Y., Burow, G.B., Hayes, C.M., Chen, J., Burke, J.J., Pugh, N.A., Ware, D. 2023. Registration of 252 sequenced sorghum mutants as a community reverse genetic resource. Journal of Plant Registrations. 17(3):599-604. https://doi.org/10.1002/plr2.20296.
Ostmeyer, T.J., Somayanda, I.S., Bean, S.R., Dhillon, R., Hayes, C.M., Ritchie, G., Asebedo, A.R., Emendack, Y., Jagadish, K.S. 2023. Impact of in-season split application of nitrogen on intra-panicle grain dynamics, grain quality and vegetative indices that govern nitrogen use efficiency in sorghum. Plant and Soil. https://doi.org/10.1002/jpln.202200325.
Hayes, C.M., Emendack, Y., Sanchez, J., Burke, J.J., Pugh, N.A., Xin, Z., Rooney, W.L. 2023. Evaluation of diverse sorghum for leaf dhurrin content and post-anthesis (stay-green) drought tolerance. Crops. 3(3):241-250. https://doi.org/10.3390/crops3030022.
Triplett, E., Hayes, C.M., Emendack, Y., Longing, S., Monclova, C., Simpson, C., Laza, H. 2023. Leaf structural traits mediating pre-existing physical innate resistance to sorghum aphid in sorghum under uninfested conditions. Planta. 258. Article 46. https://doi.org/10.1007/s00425-023-04194-0.
Knoll, J.E., Uchimiya, S.M., Hayes, C.M., Punnuri, S.M., Harris-Shultz, K.R., Smith, J.S. 2023. Registration of three sweet sorghum lines with high tolerance to sorghum aphid (Melanaphis sorghi). Journal of Plant Registrations. 17:551-560. https://doi.org/10.1002/plr2.20310.
Patil, N., Hoffmann, L., Perumal, R., Hayes, C.M., Emendack, Y., Boyles, R., Dalberg, J., Klein, R.R., Klein, P., Rooney, W. 2024. Registration of sorghum [sorghum bicolor (l.) moench] backcross-nested association mapping (BC-NAM) populations in BTx623 and RTx436 backgrounds . Journal of Plant Registrations. 18(1):204-219. https://doi.org/10.1002/plr2.20286.
Kent, M.A., Fonseca, J.M., Klein, P.E., Klein, R.R., Hayes, C.M., Rooney, W.L. 2023. Use of genomic prediction to screen sorghum B-lines in hybrid test crosses. The Plant Genome. Article e20369. https://doi.org/10.1002/tpg2.20369.
Jiao, Y., Singh, D., Barry, K., Daum, C., Yoshinaga, Y., Khan, A., Lu, Z., Wang, X., Wei, X., Tello-Ruiz, M.K., Burow, G.B., Hayes, C.M., Chen, J., Mortimer, J., Ware, D., Xin, Z. 2023. A large sequenced mutant library- valuable reverse genetic resource that covers 98% of the genes in a Sorghum genome. Plant Journal. 117(5):1543-1557. https://doi.org/10.1111/tpj.16582.