Location: Corn Insects and Crop Genetics Research
2023 Annual Report
Objectives
Objective 1: Improve knowledge of the genetics, genomics, ecology, and behavior of key maize insect pests as they affect abundance and pest resistance to insecticidal agents, including those expressed in transgenic maize.
Sub-objective 1.A. Determine genomic architecture of phenotypic traits within and among reproductive and ecological variants of European corn borer.
Sub-objective 1.B. Determine how insect movement and genetics impact potential for development of resistance to GE insecticidal toxins.
Sub-objective 1.C. Develop genomic and computational resources for study of key maize pests.
Objective 2: Identify and functionally dissect contributions of maize alleles that confer host plant resistance to lepidopteran pests.
Sub-objective 2.A. Identify contributing alleles and specialized metabolites conferring resistance to silk-feeding by corn earworm.
Sub-objective 2.B. Characterize resistance and develop doubled haploid inbred lines of maize with leaf activity against fall armyworm.
Objective 3: Determine potential impacts of farming practices in maize agro-ecosystems on the ecology and management of both arthropod pests and non-pests such as monarch butterflies and bees.
Sub-objective 3.A. Develop a risk-based decision support tool for managing sporadic insect pests of seedling maize.
Sub-objective 3.B. Develop strategies for improving monarch butterfly and bee habitat in agricultural landscapes.
Approach
European corn borer, corn rootworm, and western bean cutworm are the most serious pests of maize in the Corn Belt, while corn earworm and fall armyworm are major pests in the southern half of the United States. Genetically-engineered (GE) maize is an important management tool for these insect pests, but they have evolved resistance to GE crops in many areas, seriously threatening their continued effectiveness. This project will take an integrated approach toward developing management strategies and tools to use against these insect pests with emphases on insect resistance management to GE maize, insect ecology, insect genetics and genomics, and native host plant resistance. We will address critical knowledge gaps including maize insect pest population genetic dynamics and genomic function, dispersal behavior, efficacy of insect resistance monitoring, and insect resistance management strategies, including ways to incorporate a diversity of pest suppression tactics. Native host plant resistance to control insect pests can serve the latter function, and provide a cost-efficient sustainable management tool for growers who choose not to use GE maize. This project will study native resistance in maize to insect pests, particularly corn earworm and fall armyworm, so that low-input control options can be developed. Given concerns on the indirect effects of farming practices on non-target arthropods, including bees and monarch butterflies, project scientists will work with stakeholders to develop strategies for increasing habitat for monarch butterflies to counter loss of milkweeds in maize and soybean fields. In addition, researchers will provide growers a decision support tool to allow realistic assessment of when the use of seeds coated with neonicotinoid insecticide is justified in their particular fields to control sporadic seedling pests and when it is not, reducing overall insecticide input. Collectively, this research will result in maize pest management systems that are stable and reliable, cost effective for producers, and safe for growers, consumers and the environment.
Progress Report
In support of Objective 1, research continued in understanding genetic and genomic aspects of key maize pests in relation to population and ecological dynamics, and subsequent impacts on the development and spread of resistance to control tactics. Farmers plant genetically engineered (GE) maize hybrids that express one or more Bacillus thuringiensis (Bt) pesticidal proteins to manage crop damage by corn earworm (CEW), European corn borer (ECB), western corn rootworm (WCR), and western bean cutworm (WBC). However, all these pests have developed resistance to one or more Bt proteins, resulting in economic losses and threatening the sustainability of GE maize.
ECB has been sub-divided into three races characterized by differences in the chemical sex-attractant (pheromone) emitted by females and the corresponding response by males, and in post-dormancy larval development time that determines number of annual reproductive generations (voltinism). The geographic ranges of the different races often overlap, and even though individuals tend to mate only with others of their own race, some hybridization between races does occur. Hybridization can result in exchange of some genes between races, and it is not clear how easily a resistance gene that developed in one race could spread into another. In support of Sub-Objectives 1A and 1B, we examined full-genome sequence assemblies of ECB and discovered that the pheromone, behavior, and voltinism genes responsible for maintaining race identity reside in a chromosomal inversion. The inverted part of the chromosome is prevented from recombining during sexual reproduction, which means the genes located in the inversion are inherited as a group in the resulting offspring. This suggests that genes conferring resistance to Bt proteins, and which are not located in the inversion, may more readily spread between races, and therefore more rapidly throughout ECB populations in general regardless of race.
In much of the U.S. Corn Belt, ECB produces two generations of damaging larvae per summer. The first (or Spring) generation arises from eggs laid by female moths that overwintered as larvae in diapause, a state of suspended development (similar in principle to hibernation), Larvae of the Spring generation produce adults that emerge in mid-Summer. Moths producing this second (or Summer) generation do not pass through diapause but develop directly from egg to adult. Previous studies of ECB moth flight behavior were conducted with laboratory-reared moths maintained under conditions of direct development. In support of Sub-Objective 1B, we placed several cohorts of ECB larvae from the ARS laboratory colony into diapause for emergence several months later, in mid to late summer 2023. The resultant adults will be tested on flight mills to determine if flight behavior of adults that have passed through diapause is like that of moths which develop continuously. The experiments will help clarify if adults of the two generations in the field behave similarly when dispersing in the agricultural landscape.
In support of Sub-Objective 1C, a draft WCR genome assembly was completed and published. This was a long-term project funded by a USDA National Institute of Agriculture (NIFA) Sustainable Bioenergy Grant (award# 2010–04160). This work includes annotation of gene families often involved in Bt and chemical insecticide resistance, and in chemosensory perception. This work also included predictions of genes whose activity changes when larvae were fed maize roots compared to those fed an alternative host plant, a marginal host, and a poor host, as well as those that were starved. The fewest changes in gene activity were observed between maize and the alternate host, Miscanthus, suggesting that WCR may become a pest of this potential biofuel crop. A second WCR genome assembly was generated in cooperation with the ARS Ag100Pest initiative. Analyses involving this new assembly as part of a USDA-NIFA, Biotechnology Risk Assessment Grant (award# 2012-33522-20010) with collaborators at Iowa State University (ISU), revealed two genes putatively contributing to Cry3Bb1 resistance, based on pedigree and population genome resequencing data. The genome assembly of a Bt Cry1Ac resistant strain of CEW was completed through the ARS Ag100Pest initiative and published. To investigate the genomic basis of Cry1A resistance in CEW, genome and transcript sequence data were generated from the resistant strain and a recurrent backcross strain, where resistant CEW were backcrossed multiple times to susceptible CEW to isolate the resistance genes. These genome assemblies are key resources being used to identify and validate the genes that cause Bt resistance.
Also, in support of Sub-Objective 1C, research funded by a USDA-NIFA Crop Protection and Pest Management grant (award# 2020-70006-33018) was conducted in collaboration with Iowa State University scientists. This research successfully validated that mutations in a gene active in the nervous system of insects cause resistance to pyrethroid insecticides. In addition, this collaborative project yielded high-throughput genetic markers for detection of resistant individuals in field populations.
In support of Objective 2, research continued examining the use of host plant resistance to control fall armyworm in maize. Field work was conducted in 2022 to validate fall armyworm leaf feeding resistance in inbred lines derived from maize population BS39 and partial inbred line GEMN-0095. A derived line from BS39 (BS39:0043) was tested in the greenhouse and was more resistant than resistant check Mp708 at maize stages V5 and V6. BS39, and the founding landraces used to develop this population, were tested for resistance to leaf-feeding fall armyworm. Plants grown in the field and artificially infested at the seven or eight-leaf stage were visually scored for leaf-feeding damage at 7 and 14 days post infestation. All founders (i.e., NSL 283507, PI 498583, PI 583912, and PI 674097) were more resistant than the susceptible check, GEMN-0131. BS39 was variable in response to leaf feeding by fall armyworm with individual plants showing resistance or susceptibility at 14 days across both years of testing. This variability is currently being used to select for greater levels of resistance to leaf feeding fall armyworm.
In support of Objective 3, the results of research on breeding monarch butterfly movement ecology and toxicology conducted over the last few years by a collaborative team of ARS and Iowa State University scientists were synthesized and used in a model to predict population outcomes under possible scenarios of milkweed habitat conservation. The scenarios tested were maintenance of current milkweed density, moderate levels of new milkweed habitat establishment, and maximum levels of new milkweed habitat establishment. The synthesis and modeling outcome were published as a major review article.
Accomplishments
1. Elevated stress responses contribute to larval western corn rootworm (WCR) adaptations to feeding of different crop plants. WCR larvae feed on the roots of a narrow range of grasses including maize and the cellulosic biofuel crop, Miscanthus. This damage results in significant yield loss for farmers in the United States. Farmers manage WCR damage by growing maize hybrids that express one or more insecticidal Bacillus thuringiensis proteins, applying chemical insecticides, or by rotating crops grown annually in the same field to include plants that are not viable hosts for WCR larvae. Each of these management practices are threatened by development of resistance, which has developed multiple times in various WCR populations in North America. The capacity for WCR to adapt to crop rotations between maize and cellulosic biofuel crops remains unknown. ARS researchers in Ames, Iowa, and an international team of collaborators investigated the changes in gene expression among WCR larvae that fed on roots of maize, the biofuel crops Miscanthus and switchgrass, or sorghum (non-host). A control group was starved for comparison. The fewest number of significant changes in gene expression were observed for larvae that fed on maize compared to Miscanthus, suggesting many of the same genes are involved in adaptation to these host plants. The greater number of differentially expressed genes between maize and other host plants, including the switchgrass biofuel crop, were predicted to function mostly in cell stress response mechanisms. Elevated stress response was interpreted to indicate WCR larvae are less-well adapted for feeding on non-maize and non-Miscanthus crops. This information will help identify target genes for improved host plant resistance breeding in maize, and guide other research of university, government, and industry scientists for evaluating and improving management of WCR on maize and other cellulosic biofuel crops.
2. High mobility of monarch butterflies is predicted to largely offset negative impacts of pesticide exposure and habitat fragmentation on population growth in agricultural landscapes. The North American monarch butterfly (Danaus plexippus) is a candidate species for listing under the Endangered Species Act. Multiple factors are associated with the decline in the eastern population, including the loss of breeding and foraging habitat and pesticide use. Establishing breeding habitat in agricultural landscapes of the North Central region of the United States is critical to increasing reproduction during the summer. ARS researchers from Ames, Iowa, in collaboration with Iowa State University integrated spatially explicit modeling with results from empirical movement ecology and pesticide toxicology studies to simulate population outcomes for different habitat establishment scenarios. Because of their mobility, they conclude that breeding monarchs in the North Central states should be resilient to pesticide use and habitat fragmentation. Consequently, the team predicts that adult monarch recruitment through reproduction can be enhanced even if new habitat is established near pesticide-treated crop fields and even if habitat patches are not of perfect size or closeness. The team's research over the last few years has improved the understanding of monarch population dynamics at the landscape scale by examining the interactions among monarch movement ecology, habitat fragmentation, and pesticide use. This information will be used by government regulators, scientists, and environmental conservation organizations planning monarch habitat restoration in agriculture-dominated landscapes.
3. Construction of a genome assembly for a strain of corn earworm (CEW) that has developed resistance to a Bacillus thuringiensis (Bt) protein meant to control this pest. CEW larvae feed on kernels of maize in the ear, sometimes causing economic damage. Ear feeding by insects such as CEW is also the most common way for aflatoxin producing pathogens to enter the grain. Aflatoxins are toxic to livestock and humans. Farmers plant maize hybrids that express one or more insecticidal Bt proteins to control CEW, but this pest insect has developed resistance to several Bt proteins in hybrid maize. This resistance is widespread across the United States, making prevention of ear damage in maize increasingly difficult. An ARS researcher in Ames, Iowa, in collaboration with a team of other researchers participating in the ARS Ag100Pest Initiative, assembled the genome from a strain of CEW resistant to the Bt protein Cry1Ac. This genome assembly is comprised of intact chromosomes and is at a level of completeness not currently common for insect pests. Gene coding regions predicted for this CEW genome are the most complete reported to date. These genomic resources generated by the Ag100Pest Initiative will provide university, government, and industry scientists with a powerful and dynamic tool for evaluating genomic changes that contribute to development of Bt resistance in pest insect populations.
Review Publications
Tong, D., Zhang, L., Wu, N., Xie, D., Fang, G., Coates, B.S., Sappington, T.W., Liu, Y., Cheng, Y., Xia, J., Jiang, X., Zhan, S. 2022. The oriental armyworm genome yields insights into the long-distance migration of noctuid moths. Cell Reports. 41(12). Article 111843. https://doi.org/10.1016/j.celrep.2022.111843.
Feng, M., Zhang, Y., Coates, B.S., Du, Q., Gao, Y., Li, L., Yuan, H., Sun, W., Chang, X., Zhou, S., Wang, Y. 2023. Assessment of Beauveria bassiana for the biological control of corn borer, Ostrinia furnacalis, in sweet maize by irrigation application. BioControl. 68: 49-60. https://doi.org/10.1007/s10526-022-10175-1.
Coates, B.S., Walden, K.O., Lata, D., Vellichirammal, N.N., Mitchell, R.F., Andersson, M.N., Mckay, R., Lorenzen, M.D., Grubbs, N., Wang, Y., Han, J., Xuan, J., Willadsen, P., Wang, H., French, B.W., Bansal, R., Sedky, S.F., Souza, D., Bunn, D., Meinke, L.J., Miller, N.J., Siegfried, B.D., Sappington, T.W., Robertson, H.M. 2023. A draft Diabrotica virgifera virgifera genome: insights into control and host plant adaption by a major maize pest insect. BMC Genomics. 24. Article 19. https://doi.org/10.1186/s12864-022-08990-y.
Stahlke, A.R., Chen, J., Tembrock, L.R., Sim, S.B., Chudalayandi, S., Geib, S.M., Scheffler, B.E., Perera, O.P., Gilligan, T.M., Childers, A.K., Hackett, K.J., Coates, B.S. 2022. A chromosome-scale genome assembly of a Helicoverpa zea strain resistant to Bacillus thuringiensis Cry1Ac insecticidal protein. Genome Biology and Evolution. 15(3). Article evac131. https://doi.org/10.1093/gbe/evac131.
Valmorbida, I., Hohenstein, J.D., Coates, B.S., Bevilaqua, J.G., Menger, J., Hodgson, E.W., Koch, R.L., O'Neal, M.E. 2022. Association of voltage-gated sodium channel mutations with field-evolved pyrethroid resistant phenotypes in soybean aphid and genetic markers for their detection. Scientific Reports. 12.Article 12020. https://doi.org/10.1038/s41598-022-16366-1.
Abel, C.A., Williams, W.P. 2022. Evaluation of twenty maize germplasms from Belize, French Guiana, Guyana, and Suriname for resistance to leaf-feeding Spodoptera frugiperda. Southwestern Entomologist. 47(3):559-564. https://doi.org/10.3958/059.047.0303.
Blanco, C., Conover, K., Hernandez, G., Valentini, G., Portilla, M., Abel, C.A., Williams, W.P., Nava-Camberos, U., Huschison, W., Dively, G. 2022. Grain yield is not impacted by early defoliation of maize: implications for Fall armyworm action thresholds. Southwestern Entomologist. 47(2):335-344. https://doi.org/10.3958/059.047.0209.
Abel, C.A., Frei, U.K., Woolfolk, S.W. 2023. Evaluating founding landraces of maize population PI 674097 for resistance to leaf-feeding Spodoptera frugiperda. Southwestern Entomologist. 48(1):83-88. https://doi.org/10.3958/059.048.0108.
Grant, T.J., Fisher, K.E., Krishnan, N., Mullins, A.N., Hellmich II, R.L., Sappington, T.W., Adelman, J.S., Coats, J.R., Hartzler, R.G., Pleasants, J.M., Bradbury, S.P. 2022. Monarch butterfly ecology, behavior, and vulnerabilities in North Central United States agricultural landscapes. Bioscience. 72(12):1176-1203. https://doi.org/10.1093/biosci/biac094.
