Location: Corn Insects and Crop Genetics Research
2016 Annual Report
Objectives
Objective 1: Improve knowledge of the ecology, genetics, and behavior of key corn pests, especially corn rootworm and lepidopteran species, such as European corn borer, corn earworm and western bean cutworm, in relation to pest abundance and insect resistance to transgenic corn.
Sub-objective 1.A. Correlate genetic markers with phenotypic traits of interest in European corn borer, western corn rootworm and western bean cutworm.
Sub-objective 1.B. Determine how larval movement and adult dispersal influence insect resistance to transgenic corn.
Objective 2: For corn agro-ecosystems, determine potential impacts of changing farming practices on the demographics and ecology of pest and non-pest arthropods, such as the monarch butterfly.
Sub-objective 2.A. Assess the potential value of neonicotinoid insecticide seed treatments to growers of major row crops under different agronomic conditions.
Sub-objective 2.B. Develop strategies for improving monarch butterfly habitat in modern farm landscapes.
Objective 3: Characterize genetic and biochemical responses associated with corn defenses to rootworm and lepidopteran caterpillar pest injury to enhance conventional and transgenic crop protection strategies.
Sub-objective 3.A. Develop genetic markers and genomic tools for western corn rootworm, European corn borer, western bean cutworm, and other pests of corn.
Sub-objective 3.B. Characterize genetic regulation of surface lipids on corn silks and assess protective capacity of these lipids on corn earworm feeding.
Approach
Field-resistance in western corn rootworm (WCR) to Cry3Bb1 Bt toxins and in European corn borer (ECB) to Cry1Fa and Cry1Ab toxins will be mapped by using genotyping-by-sequencing (GBS) protocols and single nucleotide polymorphism (SNP) markers. Pedigrees will be constructed from Bt resistant and susceptible individuals of both species. GBS will be performed by constructing genomic DNA libraries from non-size-selected fragments, to which adapters with a unique barcode are ligated. A population mapping approach using a high density of SNP markers will be taken to identify loci that differ significantly between E- and Z-race ECB. The premise of population mapping is similar to quantitative trait loci (QTL) mapping, but SNPs with skewed frequencies between races are assumed to result from either selection for race-specific adaptations or genetic drift facilitated by restricted gene flow. GBS-derived SNP markers will be used to estimate gene flow among WCR populations. The strategy will be to estimate Wright's neighborhood area for WCR, the radius of which constitutes a measure of the typical distance genes move per generation. Dispersal and survival rates of fall armyworm (FAW) will be measured in field plot trials. FAW egg masses will be placed in the whorl of vegetative-stage corn plants surrounded by uninfested plants. Living and dead larvae on plants will be counted periodically using destructive sampling. Planting arrangements will include various combinations of Bt and non-Bt isoline plants. Flight behavior and capacity of WCR will be characterized and compared across three Cry3Bb1-resistant and two susceptible strains using flight mills to determine the degree to which resistance affects dispersal. In collaboration with other ARS laboratories and as a NP304 effort, a comprehensive review of the literature will be conducted to provide information on the usefulness of seed treatment with neonicotinoid insecticide in controlling target pests and protecting crops from yield loss. A series of studies will be conducted related to milkweed species selection (larval performance and oviposition preference), and milkweed plant establishment (determining patch sizes and maximizing sustainability of milkweeds). Initially, studies will focus on four Asclepias species found in Iowa: common milkweed, A. syriaca, swamp milkweed, A. incarnata, butterfly weed, A. tuberosa, and whorled milkweed, A. verticillata. Also, studies will be conducted to determine how to maintain these plants in the landscape while avoiding loss from plant competition. This will require identifying the best companion plants for the targeted milkweed species. Two sources of corn germplasm will be used to screen for silk activity against corn earworm (CEW). These corn lines and CEW resistant checks will be grown in the field. Emerged silks will be harvested, immediately frozen in liquid nitrogen, lyophilized, and ground to a powder using a knife mill. One cohort of powdered silks will be used for surface lipid metabolic analysis, while another will be used for CEW bioassays, allowing the metabolomic analysis and CEW feeding studies to be conducted in parallel.
Progress Report
Resistance of western corn rootworm (WCR) to transgenic Bt-corn has been increasing in the Corn Belt, emphasizing the urgent need for better understanding of this pest's dispersal behavior, which strongly influences rate of resistance development and the rate at which resistance spreads after it develops. Genotyping-by-sequencing is underway of adults collected in 60 fields across two 120-mile transects in the species' native home range of eastern Colorado and western Kansas for both 2014 and 2016. Preliminary analyses of part of the 2014 samples indicate an average lifetime dispersal of approx. 0.28 km of about 7/8 of a rootworm population, but that the other 1/8 migrating out of the natal field can and do go a long way, up to 200 km or further. Comparison of DNA profiles from the same locations between 2014 and 2016 will provide an independent temporal estimate of dispersal distances. Novel viruses that infect western corn rootworm were discovered using next generation sequence (NGS) data generated at ARS Scientists at Ames, IA and may provide an opportunity for developing management options.
Comparison of viruses in collections of rootworm from several locations in 2015 including Iowa, eastern Colorado, and Pennsylvania with earlier collections in 2013 and 2014 indicate large variability in virus prevalence from year to year within a location. Serious questions have arisen about the safety of neonicotinoid seed treatments of corn, soybean, cotton, and wheat to pollinators, especially honey bees, yet their use on seed is very widespread. Farmers tend to rely on them as "insurance" treatments against sporadic minor pests, but the actual benefit derived is unclear. A major collaborative effort led by an ARS scientist in Ames is underway to review the vast literature on the prevalence and risk posed by these pests, and data are being collected from other scientists and the literature to perform a meta-analysis on the value of neonicotinoid seed treatments to the farmer based on pest pressure and region of the country. A set of annotated transcriptome sequences representing all genes expressed in the European corn borer (ECB) midgut was constructed from RNA sequencing (RNA-seq) data.
Analyses of RNA-seq data from Cry1F resistant and susceptible strains of ECB on non-Cry1F control and Cry1F toxin diet treatments demonstrated that a high number of genes are differentially expressed between ECB strains and treatments. Compared to the susceptible strain, Cry1F resistant larvae showed nominal changes in gene expression between Cry1F and control treatments, suggesting that toxin exposure evokes no cellular response. These data are important for understanding the evolution of resistance by signal transduction presented in an invited review article, as well as support an ARS-wide initiative to advance the capabilities of genomic data analysis within the agency.
WCR resistance to chemical insecticides remains problematic for growers and agrochemical companies. High-throughput genotyping data was used to identify a single genetic locus that strongly influences the inheritance of resistance to organophosphate insecticides. These genetic data were paired with gene expression data to show that the increased expression of a single esterase gene is linked to the increase in WCR resistance. These results are important in ongoing efforts to develop rapid molecular genetic-based diagnostic marker for monitoring of pest insect resistance trait in the field.
The western bean cutworm (WBC) is a pest of corn that has developed a high level of resistance to Cry1F toxin in several regions of the United States. In efforts to develop maternally-inherited markers for population genetic analyses, the entire WBC mitochondrial genome was sequenced assembled using NGS data, and variable sites were identified. Field samples were collected and a laboratory colony was started for selection of Cry1F resistant individuals.
Research has begun to develop strategies for increasing habitat for monarch butterflies to counter loss of milkweeds in corn and soybeans. Collaborations with grower groups has been facilitated by partnering with the Iowa Monarch Conservation Consortium. Experiments have investigated monarch utilization of different milkweed species and milkweed patch stem densities. One project compares how monarch larvae survive and grow on nine different milkweed species with overlapping ranges. Monarch butterfly oviposition preferences on these nine milkweed species also are being examined. Another study is investigating effects of common and swamp milkweed densities on monarch oviposition. Several non-crop areas have been identified for planting habitat seed mixes in the fall or winter.
Accomplishments
1. ARS capacity to conduct genomic analyses was evaluated with National Program Leaders and scientists from all Areas. The Arthropod Genomic Research workshop (July 26-28, 2016) was planned and conducted by a scientist from Ames, Iowa. This workshop produced a set of recommendations for facilitating genomic analyses that are being adopted by ONP and the ARS Chief Information Officer (CIO). Furthermore, these recommendations are in clear and direct support of the ARS Big Data initiative and allow scientists to access ARS high performance compute (HPC) nodes (Ceres), and the Science Gateway infrastructure. This accomplishment of developing application pipelines to computational resources allows ARS researchers to more efficiently analyze genomics data and impacts the future course of ARS genomics research.
None
Review Publications
Tang, J., Cheng, Y., Sappington, T.W., Jiang, X., Zhang, L., Luo, L. 2016. Egg hatch and survival and development of beet webworm (Lepidoptera: Crambidae) larvae at different combinations of temperature and relative humidity. Journal of Economic Entomology. 109(4):1603-1611. doi:10.1093/jee/tow106.
Vellichirammal, N.N., Wang, H., Eyun, S., Moriyama, E.N., Coates, B.S., Miller, N.J., Siegfried, B.D. 2015. Transcriptional analysis of susceptible and resistant European corn borer strains and their response to Cry1F protoxin. Biomed Central (BMC) Genomics. 16:558. doi: 10.1186/s12864-015-1751-6.
Coates, B.S., Poelchau, M.F., Childers, C., Evans, J.D., Handler, A.M., Guerrero, F., Skoda, S.R., Hopper, K.R., Wintermantel, W.M., Ling, K., Hunter, W.B., Oppert, B.S., Perez De Leon, A.A., Hackett, K.J., Shoemaker, D.D. 2015. Arthropod genomics research in the United States Department of Agriculture-Agricultural Research Service: Current impacts and future prospects. Trends in Entomology. 11(1):1-27.
Coates, B.S., Alvez, A., Wang, H., Zhou, Z., Nowastski, T., Chen, H., Rangasamy, M., Robertson, H.M., Whitfield, C.W., Walden, K.K., Kachman, S.D., French, B.W., Meinke, L.J., Hawthorne, D., Abel, C.A., Sappington, T.W., Siegfried, B.D., Miller, N.J. 2016. Quantitative trait locus mapping and functional genomics of an organophosphate resistance trait in the western corn rootworm, Diabrotica virgifera virgifera. Insect Molecular Biology. 25(1):1-15. doi: 10.1111/imb.12194.
Coates, B.S. 2016. Bacillus thuringiensis toxin resistance mechanisms among Lepidoptera: progress on genomic approaches to uncover causal mutations in the European corn borer, Ostrinia nubilalis. Current Opinion in Insect Science. 15:70-77. doi: 10.1016/j.cois.2016.04.003.
Coates, B.S., Abel, C.A. 2016. The mitochondrial genome of the western bean cutworm, Striacosta albicosta (Lepidoptera: Noctuidae). Mitochondrial DNA. 1(1):487-488. doi: 10.1080/23802359.2016.1192499.
Jiang, X., Zang, L., Yang, H., Sappington, T.W., Cheng, Y., Luo, L. 2016. Biocontrol of the oriental armyworm, Mythimna separata, by the tachinid fly, Exorista civilis, is synergized by Cry1Ab protoxin. Scientific Reports. 6:26873. doi:10.1038/srep26873.
Poelchau, M.F., Coates, B.S., Childers, C., Evans, J.D., Hackett, K.J., Shoemaker, D.D. 2016. Agricultural applications of insect ecological genomics. Current Opinion in Insect Science. 13:61-69. doi:10.1016/j.cois.2015.12.002.
Seymour, M., Perera, O.P., Fescemyer, H.W., Jackson, R.E., Fleischer, S.J., Abel, C.A. 2016. Peripheral genetic structure of Helicoverpa zea indicates asymmetrical panmixia. Ecology and Evolution. 6(10):3198-3207. doi: 10.1002/ece3.2106.
Guo, J., He, K., Hellmich II, R.L., Bai, S., Zhang, T., Liu, Y., Ahmed, T., Wang, Z. 2016. Field trials to evaluate the effects of transgenic cry1le maize on the community characteristics of arthropod natural enemies. Scientific Reports. 6:22102. doi: 10.1038/srep22102.
Albright, V.C., Hellmich II, R.L., Coats, J.R. 2016. Enzyme-linked immunosorbent assay detection and bioactivity of Cry1Ab protein fragments. Environmental Toxicology and Chemistry. doi: 10.1002/etc.3497.
Wach, M., Hellmich II, R.L., Layton, R., Romeis, J., Gadalete, P. 2016. Dynamic role and importance of surrogate species for assessing potential adverse environmental impacts of genetically engineered insect-resistant plants on non-target organisms. Transgenic Research. 25(4):499-505. doi:10.1007/s11248-016-9945-5.
