Progress 10/01/13 to 03/06/18
Outputs
Progress Report Objectives (from AD-416): Objective 1: Develop and apply genomic and genetic tools to map and characterize the genetic bases of the key cranberry traits that determine yield. Objective 2: Based on horticultural, genetic, and genomic information, formulate and apply breeding approaches for genetically improving cranberry yield. Objective 3: Determine the development thresholds of key arthropod pests (cranberry fruitworm and Sparganothis fruitworm) to better predict the developmental status of populations in the field. Objective 4: Develop novel, innovative IPM strategies to reduce pesticide use and sustain cranberry yield, quality, and profitability. Objective 5: Develop alternative cranberry production practices that improve water conservation and decrease plant disease. Approach (from AD-416): Objective 1: Next-generation sequencing technology will be used to characterize the cranberry genome. The resultant data will be used to discover and mine molecular markers such as SSRs and SNPs. We will then develop high-resolution genetic maps using the developed markers based on several available half-sib F1 mapping populations. Phenotyping will involve collecting data on yield-related traits and other horticultural measurements, including total fruit weight, percent rotten fruit, average berry weight, and fruit quality parameters. These traits will be localized in the linkage map described above. Information derived from the high resolution cranberry linkage map with yield-related will be used to plan strategic crosses. Objective 2: Prior to creating cranberry hybrids, horticultural, genetic, and genomic information will be carefully considered to ensure that strategic crosses are accomplished. A microsatellite marker based fingerprinting assay will be developed for the true-to-type verification of the cranberry cultivars. We will also characterize known cranberry diversity from the breeding programs and collections and samples sent in by growers. Pedigree information will be evaluated in the light of marker information to determine the most likely genotypes or genetic pools associated with each named cultivar and their associated horticultural performance. A series of cranberry hybrids with complementary genetic pools will be created and evaluated. Objective 3: The temperature-specific development rates and degree-day (DD) accumulations associated with cranberry fruitworm (CFW) and Sparganothis fruitworm (SFW) will be determined. Larval growth rates will be measured over a wide range of controlled temperatures. Growth rates will be plotted against temperature, and models will be fit to the dynamic. From these models, the lower and upper development thresholds will be isolated. The thresholds will then be used to generate degree-day (DD) accumulations that can be linked to discrete biological events, such as flight initiation in the field, adult lifespan, ovipositional period, and egg-hatch periods. DD accumulations represent key developmental benchmarks, helping to optimize pest management in the cranberry system. Objective 4: novel insect pest management approaches will be investigated. Two primary tactics will be explored within the cranberry system: pheromone-based mating disruption and trophic position measurement. In partnership with private industry, as well as Wisconsin cranberry growers, the first ever 3-species mating disruption program will be deployed at large scales within commercial marshes. Population suppression of the target pests will be assayed and compared with conventional pest management approaches. Studies of arthropod trophic position will be conducted using stable isotopic analysis of amino acids. Trophic position estimation will reveal the lifetime trophic tendencies of carnivorous species, thereby providing empirical evidence as to which species are actually beneficial for cranberry production. This is the final report, project terminated March 6, 2018. This progress report relates to Objectives 1 and 2. We studied yield-related traits in cranberry using traditional data collection methods. We also developed high-throughput molecular and trait data collection and visualization software. We applied the software to collect and understand massive amounts of data. We developed thousands of molecular markers, eight high- density molecular maps, and a concomitant composite map, all of which are being used to study, identify, and map genes found to control cranberry traits (mainly yield-related), quality, and other traits of economic importance. We transferred molecular data from cranberry to blueberry and created molecular genetic maps in both species for comparative purposes of the genetic architecture of horticulturally important traits. In the future, these efforts will help breed improved cranberry cultivars and the transfer of genetic information among closely related species such as cranberry and blueberry will increase breeding efficiency and the implementation of marker-assisted breeding. The construction of our composite high-resolution molecular map with trait-makers associations is one of the most important accomplishments in ~200 years of cranberry domestication, breeding, and genetics work. This progress relates to Objectives 3 and 4. The ARS continues to advance the practice of integrated pest management (IPM) in United States cranberries by investigating explicitly the intersection between crop production technology, arthropod biology, and agroecology. Now in its 7th year of research and development, the multi-species pheromone-based mating disruption program in U.S. cranberries has shown that large-scale deployment can be tailored to the Wisconsin cranberry production system. In the process, this work has also revealed a novel mechanism by which insect pheromones protect crops. Specifically, the cranberry plant is able to invoke strong defensive responses when exposed to insect pheromones, and current work is examining how this response can be exploited to further defend the plant from insect attack. Other ARS studies are building on the discovery of two native nematode species in Wisconsin that are highly virulent bio-control agents against cranberry pests. A bio-insecticide has been formulated via mass-propagation of these nematodes and modified field-application systems. Finally, ARS work into bee-microbe interactions has shown that social and non-social bees consume significant microbial protein during larval development. Further, recent findings have revealed that when the microbes are removed from fermenting pollen, the larval bees die; collectively, this suggests that bees are reliant on pollen-borne microbes during development. Accomplishments 01 Cranberry and blueberry are closely related and recently domesticated fruit crops. Both species are presumed to have a North American origin and likely evolved from a common ancestor, but their evolution is little understood. ARS scientists in Madison, Wisconsin conducted comparative genetic mapping studies between cranberry and blueberry to examine the genetic similarity and to better understand the evolutionary relationships between the two species. A set of common molecular markers was identified, added to existing cranberry and blueberry marker datasets, and used to construct genetic maps for cranberry and blueberry. The two species possessed an exceptionally high degree of genetic similarity based on the shared markers in the developed genetic maps. This high genetic similarity was unexpected since the two species are observably very different, yet approximately 93% of the blueberry genetic map was aligned perfectly to the cranberry map. Thus, this research is important because it indicates that sequencing information and other genetic research will be highly transferable between these two species. Moreover, researchers working on genetics and breeding projects in cranberry and blueberry should work together to make work more transferrable and efficient in both species. The set of 323 universal cranberry/blueberry markers is a unique resource for the research community, and the molecular maps developed will enable future comparative genetic mapping studies, the identification and transfer of genes between studies and species, future studies exploring evolutionary relationships, and conventional/ molecular breeding efforts based on shared information. 02 Arthropod fauna of cranberries. Insects represent the most consistent and significant pests of Wisconsin cranberries. ARS scientists in Madison, Wisconsin, have conducted foundational surveys of the arthropod fauna associated with cranberries in both cultivated and wild systems have been described. This reveals the identities of the most significant pest threats (and beneficial species) to cranberries in Wisconsin, which will inform biological control efforts in U.S. cranberries. The diversity of spider fauna is particularly important given the abundance of spiders in cultivated cranberry beds. 03 Conservation bio-control in cranberries. Insects represent the most significant, consistent threat to U.S. cranberries, and most of these pests are suppressed by a diversity of predaceous insects. Conservation of predator populations�particularly spider populations�during springtime flooding has been demonstrated by ARS scientists in Madison, Wisconsin. These conserved bio-control agents were associated with reduced pest numbers, and given that insects tend to be the greatest threat to the cranberry harvest, carnivorous insects help to mitigate the threat. Thus, flooding not only reduces pest populations by directly removing the herbivores, but also allows the carnivores to survive, re-colonize, and suppress pest numbers. Such findings reveal how certain grower practices promote biological control, thereby advancing sustainable farming. 04 Pollinator-microbe symbioses. Pollinators are critical components of cranberry production. Bee larvae (bumble bees and blue orchard bees) appear to require certain pollen-borne microbes, and, when absent, the larvae die. Pollen-borne microbial communities experience major shifts in abundance depending on whether fungicide residues are present or not. ARS scientists in Madison, Wisconsin have further illuminated the relationships between pollen-borne microbes and pollinator populations. Altogether, this suggests that bee larvae require certain microbes within their fermenting pollen provisions and that fungicide residues may alter these microbial communities. Conserving the important microbial symbionts of bees translates into increased survivorship of the single most important pollinators of cranberries.
Impacts
(N/A)
Publications
- Steffan, S.A., Singleton, M.E., Draney, M.L., Chasen, E.M., Johnson, K.E., Zalapa, J.E. 2017. Arthropod fauna associated with wild and cultivated cranberries in Wisconsin. Great Lakes Entomologist.
- Steffan, S.A., Dharampal, P.S., Diaz-Garcia, L., Currie, C.R., Zalapa, J.E. , Hittinger, C.T. 2017. Empirical, metagenomic, and computational techniques illuminate the mechanisms by which fungicides compromise bee health. Journal of Visualized Experiments.
- Schlautman, B., Diaz-Garcia, L., Covarrubias-Pazaran, G., Schlautman, N., Vorsa, N., Polashock, J.J., Ogden, E.L., Brown, A., Lin, Y., Bassil, N.V., Buck, E.J., Wiedow, C., McCallum, S., Graham, J., Iorizzo, M., Rowland, L. J., Zalapa, J.E. 2017. Comparative genetic mapping reveals synteny and collinearity between the American cranberry and diploid blueberry genomes. Molecular Breeding. 38:9.
- Van Zoeren, J., Guedot, C., Steffan, S.A. 2018. Conserving carnivorous arthropods: an example from early-season cranberry (Ericaceae) flooding. The Canadian Entomologist. 1-9.
- Crossley, M.S., Steffan, S.A., Voegtlin, D.J., Hamilton, K.L., Hogg, D.B. 2017. Variable isotopic compositions of host plant populations preclude assessment of aphid overwintering sites. Insects. 8(4):128.
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Progress 10/01/16 to 09/30/17
Outputs
Progress Report Objectives (from AD-416): Objective 1: Develop and apply genomic and genetic tools to map and characterize the genetic bases of the key cranberry traits that determine yield. Objective 2: Based on horticultural, genetic, and genomic information, formulate and apply breeding approaches for genetically improving cranberry yield. Objective 3: Determine the development thresholds of key arthropod pests (cranberry fruitworm and Sparganothis fruitworm) to better predict the developmental status of populations in the field. Objective 4: Develop novel, innovative IPM strategies to reduce pesticide use and sustain cranberry yield, quality, and profitability. Objective 5: Develop alternative cranberry production practices that improve water conservation and decrease plant disease. Approach (from AD-416): Objective 1: Next-generation sequencing technology will be used to characterize the cranberry genome. The resultant data will be used to discover and mine molecular markers such as SSRs and SNPs. We will then develop high-resolution genetic maps using the developed markers based on several available half-sib F1 mapping populations. Phenotyping will involve collecting data on yield-related traits and other horticultural measurements, including total fruit weight, percent rotten fruit, average berry weight, and fruit quality parameters. These traits will be localized in the linkage map described above. Information derived from the high resolution cranberry linkage map with yield-related will be used to plan strategic crosses. Objective 2: Prior to creating cranberry hybrids, horticultural, genetic, and genomic information will be carefully considered to ensure that strategic crosses are accomplished. A microsatellite marker based fingerprinting assay will be developed for the true-to-type verification of the cranberry cultivars. We will also characterize known cranberry diversity from the breeding programs and collections and samples sent in by growers. Pedigree information will be evaluated in the light of marker information to determine the most likely genotypes or genetic pools associated with each named cultivar and their associated horticultural performance. A series of cranberry hybrids with complementary genetic pools will be created and evaluated. Objective 3: The temperature-specific development rates and degree-day (DD) accumulations associated with cranberry fruitworm (CFW) and Sparganothis fruitworm (SFW) will be determined. Larval growth rates will be measured over a wide range of controlled temperatures. Growth rates will be plotted against temperature, and models will be fit to the dynamic. From these models, the lower and upper development thresholds will be isolated. The thresholds will then be used to generate degree-day (DD) accumulations that can be linked to discrete biological events, such as flight initiation in the field, adult lifespan, ovipositional period, and egg-hatch periods. DD accumulations represent key developmental benchmarks, helping to optimize pest management in the cranberry system. Objective 4: novel insect pest management approaches will be investigated. Two primary tactics will be explored within the cranberry system: pheromone-based mating disruption and trophic position measurement. In partnership with private industry, as well as Wisconsin cranberry growers, the first ever 3-species mating disruption program will be deployed at large scales within commercial marshes. Population suppression of the target pests will be assayed and compared with conventional pest management approaches. Studies of arthropod trophic position will be conducted using stable isotopic analysis of amino acids. Trophic position estimation will reveal the lifetime trophic tendencies of carnivorous species, thereby providing empirical evidence as to which species are actually beneficial for cranberry production. The progress reported relates to Objectives 1 and 2. We are studying the yield traits in cranberry using traditional data collection methods. We are also developing high-throughput data collection and visualization software to massively collect and understand data. Molecular tools are being applied to study and identify cranberry genes by mapping those genes found to control important cranberry traits, mainly yield traits. We have developed several high density molecular maps and a concomitant composite map that will be used to map many traits of economic importance. In the future, these efforts will help breed high yielding cranberry cultivars more efficiently by allowing markers-assisted breeding. This progress relates to Objectives 3 and 4, and milestones 8-10. The ARS continues to advance the practice of integrated pest management (IPM) in United States cranberries by investigating explicitly the intersection between crop production technology, arthropod biology, and agroecology. Now in its 6th year of research and development, the multi-species pheromone-based mating disruption program in cranberries has shown that it significantly reduces berry infestation rates. Optimal deployment systems continue to be refined. After retrofitting drones to deliver the pheromone-loaded paraffin emulsion to cranberry beds, the deployment system is now focusing on emulsion extruding devices that are mounted to the boom-arms of Wisconsin spray equipment. Other ARS studies are building on the discovery of a new species of insect-eating nematode in Wisconsin. Field studies have shown that this native nematode can control flea beetle populations as well as the best commercial insecticides. Insect phenology models among the top cranberry pests are being used to generate pest emergence data across Wisconsin, and published in trade journals on a biweekly basis. Finally, ARS work continues to reveal the importance of bee-microbe symbioses among native pollinators of cranberries. Accomplishments 01 Cranberry carbohydrate management. Cranberry plants produce both low- growing branches and vertical branches, known as uprights. Uprights are either reproductive (fruiting) or vegetative (nonfruiting) in a given year. Vegetative uprights only produce leaves, whereas fruiting uprights can produce flowers and thus have the potential to contribute to next years crop. Previous research has demonstrated that individual cranberry uprights exhibit biennial (every other year) bearing tendencies. Specifically, reproductive uprights have a lower probability of developing and setting fruit the following year relative to vegetative uprights. This study evaluated and compared carbohydrate concentrations across cranberry cultivars that differ in biennial fruiting tendencies. Vegetative uprights generally had greater concentrations of carbohydrates relative to reproductive uprights, while roots had the lowest concentration across all cultivars. Concentrations of carbohydrates in cranberry reproductive uprights were lowest at late bloom/early fruit set and bud development. These findings support the explanation that carbohydrate limitation in reproductive uprights may contribute to biennial fruiting by reducing the potential for return bloom. This research contributes to developing better cultivars through breeding for resource allocation for increased return bloom. The return bloom characteristic has the potential to enhance yields by circumventing traditional biennial fruiting tendencies. 02 New cranberry fingerprinting methods. Cranberry is in need of inexpensive high-throughput genetic fingerprinting methods for research and germplasm purity testing for agricultural purposes. In this study, we developed sixteen molecular marker panels, which can be used for high-throughput deoxyribonucleic acid (DNA) fingerprinting in cranberry. The panels contained a total of 61 molecular markers which easily separated important commercial cranberry cultivars. In addition, a subset of these panels were used to genotype (characterize with molecular markers) seedlings extracted from fruits in a cranberry bed planted with the cultivar Stevens. The seedlings were determined to be either self-pollinated or cross-pollinated using presence/absence of Stevens inherited molecular markers. This research provides the first quantitative evidence that the majority of seeds in commercial cranberries are self-pollinated. Therefore, the efficient and powerful DNA fingerprinting made possible by the presented molecular marker panels represents an important and applicable resource in the cranberry industry for assessing the purity of grower and licensed propagator cranberry vines, protecting intellectual property rights, assisting growers in determining genetic purity of existing beds, and for enabling genetic research and analysis of genetic diversity in cultivated, breeding and wild cranberry germplasm. 03 Development of a cranberry composite map. Cranberry is a recently domesticated, but economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genetic features and by enabling molecular-assisted breeding. To increase the availability of cranberry genomic resources, we used a sequencing approach to simultaneously discover thousands of molecular markers in the cranberry genetic code within three inter-related cranberry populations, whose pedigrees trace to seven wild cranberry selections that represent the genetic base of the commercial cranberry industry. Genetic maps were constructed for the three cranberry populations, which were merged to create the first high-density cranberry composite map containing 6073 markers in 12 chromosomes. Collectively, the results presented represent an important contribution to the current understanding of cranberry genetic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry. 04 Cranberry genetic data visualization. Visualization of data from any stage of genetic and genomic research is one of the most useful approaches for detecting potential errors, ensuring accuracy and reproducibility, and presentation of the resulting data. Therefore, we developed a software package for plotting a variety of genetic data types in a concise manner for data exploration and presentation. The program is very simple, requires minimal coding experience, even for complex figures that incorporate high-dimensional genetic information, and allows simultaneous analysis and visual exploration of genomic and genetic data. The program is also very flexible in formatting and configuration, automatable, and provides publication quality figures. This software tool is useful for any species and freely available for genetic and genomic researchers with little computational expertise. 05 Cranberry high-throughput phenotyping methods. In crop breeding programs, massive trait data collection is key for the efficient evaluation and selection of new cultivars and varieties. In these cases, multiple populations with numerous individuals are constantly being evaluated for traits requiring a considerable investment in time and money. The need for new approaches to massively acquire trait data will continue to increase in coming years. We developed a software, called GiNA, for image-based horticultural trait data collection such as shape and color data. The GiNA image analysis framework is highly accessible and freely available to scientists and groups working in major and minor crop research programs. The application and use of this software is simple, but very helpful in terms of the massive amount of high- quality measurements that can be generated. Although many image-based trait collection technologies are available, they are not easy-to-use and optimize, and they are not economically accessible for scientists that commonly face limitations related with massive trait data collection activities. Trait data collection using software such as GiNA can lead to an accelerated progress in crop improvement and a more efficient characterization of traits of interest for both science and industry. 06 Phenology models have been validated by field trapping of the respective moth flights. Specifically, the temperature-mediated development thresholds of the cranberry fruitworm, Acrobasis vaccinii, have allowed us to generate degree-day accruals based on current weather, and these are used to provide predictions for growers as to when the moth flights will start, as well as when it reaches its peak. This service has allowed growers to time their sprays and plan future control strategies. The degree-day accruals have also been calculated for sparganothis fruitworm. All degree-days are tabulated by pest species, along with their corresponding color-coded maps of Wisconsin (heat maps of pest development). All pest projection information has been published bi-weekly in trade journals widely available to growers. 07 There were two significant accomplishments in the USDA-ARS pheromone mating disruption program in Wisconsin cranberries: 1) a three-species mating disruption blend was applied to commercial acreage; 2) the mating disruption materials were applied via an unmanned aerial vehicle (UAV). The mating disruption system deployed in cranberries represents the first time for any crop that three different pest species were targeted with a single pheromone blend. Further, this work was the first use of fully autonomous UAVs to deploy pest control materials. Pest suppression was demonstrated for all three pest species; thus, the research program was successful in mechanizing the deployment of pheromones via UAVs, as well as demonstrating the potential impact that the top insect pests of cranberries could be controlled by disrupting mating, thereby decreasing fruit damage and increasing crop yields. 08 Newly discovered native nematode species were demonstrated to be highly virulent biological control agents against some of the most troublesome pests of cranberries (sparganothis fruitworm, cranberry fruitworm, and flea beetles). Field trials using large sods from commercial cranberry marshes revealed that Oscheius wisconsinensis (the most promising nematode among the recently discovered species) can effectively track down, subdue, and kill cranberry pests in the soil. The nematodes represent an effective �green� bio-insecticide that can reduce chemical use by growers.
Impacts
(N/A)
Publications
- DeVetter, L.W., Beaver, E., Colquhoun, J., Zalapa, J., Harbut, R. 2016. Comparison of nonstructural carbohydrates across cranberry cultivars. European Journal of Horticultural Science. 81(6):321-326. doi: 10.17660/ eJHS.2016/81.6.5.
- Schlautman, B., Bolivar-Medina, J., Hodapp, S., Zalapa, J. 2017. Cranberry SSR multiplexing panels for DNA horticultural fingerprinting and genetic studies. Scientia Horticulturae. 219:280-286. doi. 10.1016/j.scienta.2017. 03.005.
- Blanke, C.M., Chikaraishi, Y., Takizawa, Y., Steffan, S.A., Dharampal, P.S. , Vander Zanden, M.J. 2017. Comparing compound-specific and bulk stable nitrogen isotope trophic discrimination factors across multiple freshwater fish species and diets. Canadian Journal of Fisheries and Aquatic Sciences. 74(8):1291-1297. doi: 10.1139/cjfas-2016-0420.
- Takizawa, Y., Dharampal, P.S., Steffan, S.A., Takano, Y., Ohkouchi, N., Chikaraishi, Y. 2017. Intra-trophic isotopic discrimination of 15N/14N for amino acids in autotrophs: Implications for nitrogen dynamics in ecological studies. Ecology and Evolution. 7(9):2916-2924. doi: 10.1002/ ece3.2866.
- Schlautman, B., Covarrubias-Pazaran, G., Diaz-Garcia, L., Iorizzo, M., Polashock, J., Grygleski, E., Vorsa, N., Zalapa, J. 2017. Construction of a high-density American cranberry (Vaccinium macrocarpon Ait.) composite map using genotyping-by-sequencing for multi-pedigree linkage mapping. Genes, Genomes, and Genomics. 7(4):1177-1189. doi: 10.1534/g3.116.037556.
- Diaz-Garcia, L., Covarrubias-Pazaran, G., Schlautman, B., Zalapa, J. 2017. SOFIA: An R package for enhancing genetic visualization with Circos. Journal of Heredity. 108(4):443-448. doi: 10.1093/jhered/esx023.
- Steffan, S.A., Singleton, M.E., Sojka, J., Chasen, E.M., Deutsch, A.E., Zalapa, J.E., Guedot, C. 2017. Flight synchrony among the major moth pests of cranberries in the Upper Midwest, USA. Insects. 8(1):26. doi: 10.3390/ insects8010026.
- Pauli, J.N., Steffan, S.A., Newsome, S.D. 2015. Response to Pilaar Birch and Graham. Bioscience. 65(10):953-954. doi: 10.1093/biosci/biv134.
- Hirsch, H., Brunet, J., Zalapa, J.E., von Wehrden, H., Hartmann, M., Kleindienst, C., Schlautman, B., Kosman, E., Wesche, K., Renison, D., Hensen, I. 2017. Intra- and interspecific hybridization in invasive Siberian elm. Biological Invasions. 19(6):1889-1904. doi: 10.1007/s10530- 017-1404-6.
- Diaz-Garcia, L., Covarrubias-Pazaran, G., Schlautman, B., Zalapa, J. 2016. GiNA, an efficient and high-throughput software for horticultural phenotyping. PLoS One. 11(8). doi: 10.1371/journal.pone.0160439.
- Steffan, S.A., Chasen, E.M., Deutsch, A.E., Mafra-Neto, A. 2017. Multi- species mating disruption in cranberries (Ericales:Ericaceae): Early evidence using a flowable emulsion. Journal of Insect Science. 17(2):54. doi: 10.1093/jisesa/iex025.
- Pauli, J.N., Newsome, S.D., Cook, J.A., Harrod, C., Steffan, S.A., Baker, C.J. O., Ben-David, M., Bloom, D., Bowen, G.J., Cerling, T.E., Cicero, C., et al. 2017. Why we need a centralized repository for isotopic data. Proceedings of the National Academy of Sciences. 114(12):2997-3001. doi: 10.1073/pnas.1701742114.
- Steffan, S.A., Chikaraishi, Y., Dharampal, P.S., Pauli, J.N., Guedot, C., Ohkouchi, N. 2017. Unpacking brown food-webs: Animal trophic identity reflects rampant microbivory. Ecology and Evolution. 7(10):3532-3541. doi: 10.1002/ece3.2951.
- McMahan, E.E., Steffan, S.A., Guedot, C. 2017. Population densities of lepidopteran pests in selected cranberry cultivars in Wisconsin. Journal of Economic Entomology. 110(3):1113-1119. doi: 10.1093/jee/tow274.
- Daverdin, G., Johnson-Cicalese, J., Zalapa, J.E., Vorsa, N., Polashock, J. J. 2017. Mapping and identification of fruit rot resistance QTL in American cranberry using GBS. Molecular Breeding. doi: 10.1007/s11032-017- 0639-3.
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Progress 10/01/15 to 09/30/16
Outputs
Progress Report Objectives (from AD-416): Objective 1: Develop and apply genomic and genetic tools to map and characterize the genetic bases of the key cranberry traits that determine yield. Objective 2: Based on horticultural, genetic, and genomic information, formulate and apply breeding approaches for genetically improving cranberry yield. Objective 3: Determine the development thresholds of key arthropod pests (cranberry fruitworm and Sparganothis fruitworm) to better predict the developmental status of populations in the field. Objective 4: Develop novel, innovative IPM strategies to reduce pesticide use and sustain cranberry yield, quality, and profitability. Objective 5: Develop alternative cranberry production practices that improve water conservation and decrease plant disease. Approach (from AD-416): Objective 1: Next-generation sequencing technology will be used to characterize the cranberry genome. The resultant data will be used to discover and mine molecular markers such as SSRs and SNPs. We will then develop high-resolution genetic maps using the developed markers based on several available half-sib F1 mapping populations. Phenotyping will involve collecting data on yield-related traits and other horticultural measurements, including total fruit weight, percent rotten fruit, average berry weight, and fruit quality parameters. These traits will be localized in the linkage map described above. Information derived from the high resolution cranberry linkage map with yield-related will be used to plan strategic crosses. Objective 2: Prior to creating cranberry hybrids, horticultural, genetic, and genomic information will be carefully considered to ensure that strategic crosses are accomplished. A microsatellite marker based fingerprinting assay will be developed for the true-to-type verification of the cranberry cultivars. We will also characterize known cranberry diversity from the breeding programs and collections and samples sent in by growers. Pedigree information will be evaluated in the light of marker information to determine the most likely genotypes or genetic pools associated with each named cultivar and their associated horticultural performance. A series of cranberry hybrids with complementary genetic pools will be created and evaluated. Objective 3: The temperature-specific development rates and degree-day (DD) accumulations associated with cranberry fruitworm (CFW) and Sparganothis fruitworm (SFW) will be determined. Larval growth rates will be measured over a wide range of controlled temperatures. Growth rates will be plotted against temperature, and models will be fit to the dynamic. From these models, the lower and upper development thresholds will be isolated. The thresholds will then be used to generate degree-day (DD) accumulations that can be linked to discrete biological events, such as flight initiation in the field, adult lifespan, ovipositional period, and egg-hatch periods. DD accumulations represent key developmental benchmarks, helping to optimize pest management in the cranberry system. Objective 4: novel insect pest management approaches will be investigated. Two primary tactics will be explored within the cranberry system: pheromone-based mating disruption and trophic position measurement. In partnership with private industry, as well as Wisconsin cranberry growers, the first ever 3-species mating disruption program will be deployed at large scales within commercial marshes. Population suppression of the target pests will be assayed and compared with conventional pest management approaches. Studies of arthropod trophic position will be conducted using stable isotopic analysis of amino acids. Trophic position estimation will reveal the lifetime trophic tendencies of carnivorous species, thereby providing empirical evidence as to which species are actually beneficial for cranberry production. The progress reported relates to Objectives 1 and 2. We are continuing to develop molecular tools useful for breeding and genetics studies in cranberry using sequencing data from next-generation sequencing. We continue to apply these molecular tools to study the genetic diversity of cranberry germplasm and related species. We are also investigating cranberry genes using the molecular data we are generating and mapping those genes found to control important cranberry traits, mainly yield and quality traits, to be integrated with current phenotypic selection methods and emerging molecular technologies. Several high density molecular maps with information about traits of economic importance are also being developed that will help breed high yielding cranberry cultivars more efficiently. We currently have collected three years of cranberry phenotypic data on yield and other traits on several mapping populations and continue to collect data that will be further integrated in our gene mapping efforts. This progress relates to Objectives 3 and 4, and milestones 8-10. The ARS continues to advance the practice of integrated pest management (IPM) in United States cranberries by investigating explicitly the intersection between crop production technology, arthropod biology, and agroecology. Now in its 5th year of research and development, the multi-species pheromone-based mating disruption program in cranberries has been shown to be highly successful, reducing black-headed fireworm and cranberry fruitworm populations significantly. We have mechanized the deployment of the paraffin emulsion carrier of insect pheromones by retrofitting drones that fly over cranberry marshes, delivering the paraffin emulsion to the cranberry beds. To improve control of the top pest of cranberries (the cranberry fruitworm), we have isolated the temperature-based developmental thresholds of this insect. This allows us to use models of temperature-mediated growth to estimate pest development in the field, refining how growers time their management efforts, a key pillar of IPM. Notably, we have discovered at least one new species of insect-eating nematode here in Wisconsin. Based on virulence screening, these nematodes represent promising new bio-control agents for United States cranberries. Accomplishments 01 Cranberry molecular tool development. Reading deoxyribonucleic acid (DNA) fragment types is an important initial component of many genetic studies. We developed a computer software package called Fragman to serve as a freely available resource for automatic scoring of DNA fragment lengths useful for genetic studies. We used a unique set of cranberry genotypes based on molecular markers to highlight the capabilities of Fragman. The software is a valuable new tool for genetic analysis and is currently being adopted by the scientific community. The package produces equivalent results to other popular paid software for fragment analysis while possessing unique advantages and the possibility of automation for high-throughput experiments. 02 Cranberry gene homology. The yield and quality of many crops is affected by premature fruit detachment and concomitant loss of yield. Environmental stresses often hasten or alter the fruit premature detachment process. Thus, understanding this process can not only lead to genetic improvement, but also changes in cultural practices and management that will contribute to higher yields, improved quality, and greater sustainability. We identified fifteen cranberry genes related to the premature fruit detachment process based on other plant species. In general, the high similarity of both cranberry and grape to know fruit detachment genes suggests that there may be shared functions and similar processes. Ultimately, improving our understanding of both early and late fruit detachment in fruit crops using molecular tools combined with traditional breeding, morphological and physiological studies will lead to better management practices and improved quality and greater yields. 03 Cranberry molecular and trait mapping. We developed two high- resolution genetic maps of cranberry that will facilitate other genetic studies, e.g. identification of relevant genes controlling traits and allow marker assisted selection (MAS) which will facilitate genetic gain through breeding and increasing cranberry breeding efficiency. A saturated genetic map was developed containing 541 markers representing all 12 cranberry chromosomes. The genetic map was developed using a cross between horticulturally elite cultivars Mullica Queen [(Howes x Searles) x LeMunyon)] and Crimson Queen (Stevens x BenLear). This particular population was analyzed for a three-year period for horticultural traits including total yield, mean fruit weight, and fruit cycling. We identified several positions in map (�markers-trait associations�), controlling fruit weight, yield, cycling in cranberry. Additionally, we developed another map for a second elite cranberry population, BGBLNL x GH1 (Grygleski). We mapped 5154 molecular markers and studied the genetic features of each of the 12 cranberry chromosomes. Based on these two cranberry molecular maps, we compared the order of cranberry sequences to other crops such as kiwifruit, grape, and coffee genomes. These efforts and first yield study represent a substantial addition in cranberry that will allow breeders to develop new molecular breeding schemes to produce improved varieties for growers and consumers. 04 Wild diversity in cranberry and other Vacciniums. We developed new molecular markers in cranberry to serve as an efficient, cost-effective means for characterizing the basic molecular relationships in the cranberry family. Additionally, we investigated the genetic relationships among cranberry�s closest wild relative species. We collected samples of the cranberry wild relative species in a 1000 km transect in eastern Canada. We determined chromosome numbers, completed a trait analysis of flowering stems, and assessed genetic diversity. We confirmed that there are at least two distinct types in the wild relative species. Our data also indicates that both types co- occur much more frequently than previously recognized. Increased understanding of genetic relationships among cranberry-related species will facilitate breeding strategies among the different species to improve economically important traits of commercial crops. 05 Isotope ecology illuminates carnivore roles in crop protection. ARS researchers in Madison, Wisconsin, are leading an international team of entomologists and geochemists, illuminating the �black box� of brown food webs. Brown food-webs represent detrital pathways (decaying plant matter), which are the dominant �flows� of matter on Earth. Because brown and green food webs are often conjoined among higher-order consumer groups, it is paramount to understand the trophic identities of the microbes in the detrital pathways because these microbes shape the trophic identities of almost all higher-order carnivores. Such carnivores are relied upon for crop protection. For the first time, integration of the microbiome into traditional food-webs is allowing researchers to accurately interpret the trophic roles of beneficial carnivore populations. ARS scientists are able to characterize which carnivores are contributing to pest control, and which are not. This cuts to the core of any bio-control program: isolating and enhancing the activities of key natural enemies. The implications of these findings are that we can begin to wisely and defensibly advise growers and/or pest management professionals on which carnivore populations warrant conservation efforts, thereby enhancing bio-control on the farm. 06 Pollinator health in cranberries. Bees are widely known to rely on microbial symbionts, both outside their gut, as well as within. Outside the gut, microbes flourish within bee pollen, and tend to be dominated by fungi. ARS researchers in Madison, Wisconsin, in collaboration with University of Wisconsin-Madison microbiologists and geneticists, have been investigating the importance of fungi in bee pollen for larval nutrition, as mediated by the presence of fungicide residue in the pollen. Our studies diverged from past work in that we focused on the larvae (as opposed to adults) of native bee species. We have shown that the microbial communities of pollen are primarily fungi (in terms of biomass). We generated the first evidence that fungicide residues on pollen are potentially harmful to larval bees. We also have data showing that a significant portion of the protein consumed by bee larvae is actually fungi (mostly yeasts). What does this mean? Bees are fungivores, and it appears that virtually all bees are �yeast- farmers.� We have documented that fungicide residues in pollen can cause dramatic losses among bumble bee colonies, which has increased researcher, grower, industry stakeholder, and public understanding of the relationship between bees, fungicides, and the pollen microbiome. In the near-term, this work has changed how many view the impacts of fungicides on native pollinators (based on readership and citation metrics), and in the long-term, it is expected that our findings will add to the growing body of literature that informs pesticide policy in the US. 07 Physiology and seasonality of cranberry arthropod pests. The top pest threats to Wisconsin cranberry production are insects, and among these the worst is the cranberry fruitworm, Acrobasis vaccinii. To improve management efforts of this pest, ARS researchers in Madison, Wisconsin, measured larval growth rates as a function of temperature. Then, growth rates were modeled across a broad temperature range to isolate the upper and lower temperature thresholds. These thresholds represent the basis for future work in which degree-day accumulations are generated, based on local weather data. Such degree-day accumulations can then be linked to discrete biological events in the insect�s life cycle, so that growers can better estimate optimal spray timings using their local weather reports.
Impacts
(N/A)
Publications
- Jones, V.P., Mills, N.J., Brunner, J.F., Horton, D.R., Beers, E.H., Unruh, T.R., Shearer, P.W., Goldberger, J.R., Castagnoli, S., Lehrer, N., Miliczky, E., Steffan, S.A., Amarasakare, K.G., Chambers, U., et al. 2016. From planning to execution to the future: An overview of a concerted effort to enhance biological control in apple, pear, and walnut orchards in the western U.S. Biological Control. 102:1-6. doi: 10.1016/j.biocontrol. 2016.03.013.
- Steffan, S.A., Chikaraishi, Y., Currie, C.R., Horn, H., Gaines Day, H.R., Pauli, J.N., Zalapa, J.E., Ohkouchi, N. 2015. Microbes are trophic analogs of animals. Proceedings of the National Academy of Sciences. 112(49):15119- 15124. doi: 10.1073/pnas.1508782112.
- Steffan, S.A., Chikaraishi, Y., Horton, D.R., Miliczky, E., Zalapa, J.E., Jones, V.P., Ohkouchi, N. 2015. Beneficial or not? Decoding carnivore roles in plant protection. Biological Control. 91:34-41. doi: 10.1016/j. biocontrol.2015.07.002.
- Brunet, J., Zalapa, J., Guries, R. 2016. Conservation of genetic diversity in slippery elm (Ulmus rubra) in Wisconsin despite the devastating impact of Dutch elm disease. Conservation Genetics. 17(5):1001-1010. doi: 10.1007/ s10592-016-0838-1.
- Schlautman, B., Covarrubias-Pazaran, G., Diaz-Garcia, L.A., Johnson- Cicalese, J., Iorrizo, M., Rodriguez-Bonilla, L., Bougie, T., Bougie, T., Wiesman, E., Steffan, S., Polashock, J., Vorsa, N., Zalapa, J. 2015. Development of a high-density cranberry SSR linkage map for comparative genetic analysis and trait detection. Molecular Breeding. 35(8):177. doi: 10.1007/s11032-015-0367-5.
- Schlautman, B., Covarrubias-Pazaran, G., Fajardo, D., Steffan, S., Zalapa, J. 2016. Discriminating power of microsatellites in cranberry organelles for taxonomic studies in Vaccinium and Ericaceae. Genetic Resources and Crop Evolution. doi: 10.1007/s10722-016-0371-6.
- Ecker, G., Zalapa, J., Auer, C. 2015. Switchgrass (Panicum virgatum L.) genotypes differ between coastal sites and inland road corridors in the Northeastern US. PLoS One. 10(6). doi: 10.1371/journal.pone.0130414.
- Smith, T.W., Walinga, C., Wang, S., Kron, P., Suda, J., Zalapa, J. 2015. Evaluating the relationship between diploid and tetraploid Vaccinium oxycoccos (Ericaceae) in eastern Canada. Botany. 93(10):623-636. doi: 10. 1139/cjb-2014-0223.
- Covarrubias-Pazaran, G., Diaz-Garcia, L., Schlautman, B., Salazar, W., Zalapa, J. 2016. Fragman: an R package for fragment analysis. BioMed Central (BMC) Genetics. 17(1):62. doi: 10.1186/s12863-016-0365-6.
- Chasen, E.M., Steffan, S.A. 2016. Temperature-mediated growth thresholds of Acrobasis vaccinii (Lepidoptera: Pyralidae). Environmental Entomology. 45(3):732-736. doi: 10.1093/ee/nvw053.
- Mills, N.J., Jones, V.P., Baker, C.C., Melton, T.D., Steffan, S.A., Unruh, T.R., Horton, D.R., Shearer, P.W., Amarasekare, K.G., Miliczky, E. 2016. Using plant volatile traps to estimate the diversity of natural enemy communities in orchard ecosystems. Biological Control. 102:66-76. doi: 10. 1016/j.biocontrol.2016.05.001.
- Covarrubias-Pazaran, G., Diaz-Garcia, L., Schlautman, B., Deutsch, J., Salazar, W., Hernandez-Ochoa, M., Grygleski, E., Steffan, S., Iorizzo, M., Polashock, J.J., Vorsa, N., Zalapa, J. 2016. Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping. Biomed Central (BMC) Genomics. 17(1) :451. doi: 10.1186/s12864-016-2802-3.
- Patterson, S.E., Bolivar-Medina, J.L., Falbel, T.G., Hedtcke, J.L., Nevarez-McBride, D., Maule, A.F., Zalapa, J.E. 2016. Are we on the right track: Can our understanding of abscission in model systems promote or derail making improvements in less studied crops? Frontiers in Plant Science. 6(1268). doi: 10.3389/fpls.2015.01268.
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Progress 10/01/14 to 09/30/15
Outputs
Progress Report Objectives (from AD-416): Objective 1: Develop and apply genomic and genetic tools to map and characterize the genetic bases of the key cranberry traits that determine yield. Objective 2: Based on horticultural, genetic, and genomic information, formulate and apply breeding approaches for genetically improving cranberry yield. Objective 3: Determine the development thresholds of key arthropod pests (cranberry fruitworm and Sparganothis fruitworm) to better predict the developmental status of populations in the field. Objective 4: Develop novel, innovative IPM strategies to reduce pesticide use and sustain cranberry yield, quality, and profitability. Approach (from AD-416): Objective 1: Next-generation sequencing technology will be used to characterize the cranberry genome. The resultant data will be used to discover and mine molecular markers such as SSRs and SNPs. We will then develop high-resolution genetic maps using the developed markers based on several available half-sib F1 mapping populations. Phenotyping will involve collecting data on yield-related traits and other horticultural measurements, including total fruit weight, percent rotten fruit, average berry weight, and fruit quality parameters. These traits will be localized in the linkage map described above. Information derived from the high resolution cranberry linkage map with yield-related will be used to plan strategic crosses. Objective 2: Prior to creating cranberry hybrids, horticultural, genetic, and genomic information will be carefully considered to ensure that strategic crosses are accomplished. A microsatellite marker based fingerprinting assay will be developed for the true-to-type verification of the cranberry cultivars. We will also characterize known cranberry diversity from the breeding programs and collections and samples sent in by growers. Pedigree information will be evaluated in the light of marker information to determine the most likely genotypes or genetic pools associated with each named cultivar and their associated horticultural performance. A series of cranberry hybrids with complementary genetic pools will be created and evaluated. Objective 3: The temperature-specific development rates and degree-day (DD) accumulations associated with cranberry fruitworm (CFW) and Sparganothis fruitworm (SFW) will be determined. Larval growth rates will be measured over a wide range of controlled temperatures. Growth rates will be plotted against temperature, and models will be fit to the dynamic. From these models, the lower and upper development thresholds will be isolated. The thresholds will then be used to generate degree-day (DD) accumulations that can be linked to discrete biological events, such as flight initiation in the field, adult lifespan, ovipositional period, and egg-hatch periods. DD accumulations represent key developmental benchmarks, helping to optimize pest management in the cranberry system. Objective 4: novel insect pest management approaches will be investigated. Two primary tactics will be explored within the cranberry system: pheromone-based mating disruption and trophic position measurement. In partnership with private industry, as well as Wisconsin cranberry growers, the first ever 3-species mating disruption program will be deployed at large scales within commercial marshes. Population suppression of the target pests will be assayed and compared with conventional pest management approaches. Studies of arthropod trophic position will be conducted using stable isotopic analysis of amino acids. Trophic position estimation will reveal the lifetime trophic tendencies of carnivorous species, thereby providing empirical evidence as to which species are actually beneficial for cranberry production. This progress relates to Objectives 1 and 2. We are developing molecular tools useful for breeding and genetics studies in cranberry using nuclear and organellear sequencing data from next-generation sequencing. Another area of emphasis has been the application of molecular tools to study the genetic diversity of cranberry germplasm. We are also generating critical applied and basic knowledge about cranberry traits, mainly yield and quality traits, to be integrated with current phenotypic selection methods and emerging molecular technology. A high density molecular map with information about traits of economic importance is also being developed that will help breed high yielding cranberry cultivars more efficiently. We currently have collected three years of cranberry phenotypic data on yield and other traits on two mapping populations. This progress relates to Objectives 3 and 4, and milestones 8-10. The ARS continues to advance the practice of integrated pest management (IPM) in United States cranberries by illuminating key elements of arthropod biology and ecology. Now in its fourth year of research and development, the multi-species pheromone-based mating disruption program in cranberries has been shown to be highly successful, reducing black-headed fireworm and cranberry fruitworm populations significantly. We are now scaling up the deployment of this technology to whole-marsh and regional applications using unmanned aerial vehicles (UAVs). To improve cranberry IPM programs, the development thresholds and degree-day benchmarks for cranberry fruitworm, Acrobasis vaccinii, are being pursued. This moth is the top pest of Wisconsin cranberries, thus effective control tactics are critical to crop protection objectives. Accomplishments 01 Polymorphic cranberry molecular markers. A lack of abundant, genome- wide molecular markers has limited the adoption of modern molecular assisted selection approaches in cranberry breeding programs. To increase the number of available markers in the species, ARS scientists in Madison, WI identified, tested, and validated microsatellite markers from existing deoxyribonucleic acid (DNA) sequencing data. In total, 979 DNA markers were designed, synthesized, and tested; 697 of the markers were found to be variable in four cranberry plants. Of the 697 variable markers, 507 were selected for additional genetic diversity and segregation analyses in 29 cranberry plants. More than 95% of the 507 markers did not display segregation distortion and contained moderate to high levels of diversity. This comprehensive collection of developed and validated DNA markers represents a substantial addition to the molecular tools available for geneticists and genomicists in cranberry and Vaccinium that will allow breeders to development of new molecular breeding schemes to produce improved varieties for growers and consumers. 02 Wild diversity in cranberry. The natural populations of American cranberry (Vaccinium. macrocarpon) and small cranberry (V. oxycoccos) were characterized by ARS scientists from Madison, WI, using microsatellite markers. The data collected offers insight into natural cranberry diversity and differentiation among two closely related species and will be useful for future studies about natural cranberry diversity and natural population characteristics as well as other cranberry breeding and genetics studies. Unique cranberry types can be generated by the hybridization of V. macrocarpon and V. oxycoccos populations. Therefore, a genetic fingerprint allowing the differentiation of each species will aid further studies of genetic diversity and pedigree analysis of natural and breeding populations. 03 Cranberry iron nutrition. Cranberry is naturally adapted to environments with high concentrations of soluble iron. Yet, there is a need to further explore iron nutrition in cranberry given concerns of toxicity problems from irrigation with iron-rich water. ARS scientists from Madison, WI, investigated the threat of iron toxicity by evaluating chelated iron effects on cranberry plant growth. Shoot growth was reduced with increasing chelated iron concentrations and plant symptoms included leaf drop, necrosis, mortality in the higher concentration treatments, and increasing amounts of iron with increasing chelated iron dosages. However, iron tissue levels were within the normal range found in healthy field plants in all treatments. We hypothesized that the toxicity symptoms observed in cranberry plants treated with chelated iron is likely due to a specific toxicity of cranberry to the chelators not the iron. Elucidating the benefits or risks to particular accumulations of iron and other micronutrients are needed in order to establish sufficiency ranges, thresholds, and help growers better understand toxicity risks. 04 Cranberry yield studies. Improved methods of yield prediction are essential to develop early crop pricing forecasts for the cranberry industry. However, yield is a complex trait that is influenced by multiple interacting factors involving crop genetics, plant physiology, and the environment. The fact that each factor is poorly understood and the interaction between factors complicate yield prediction. ARS scientists from Madison, WI, improved the current understanding of yield by measuring the effects of genetic, physiological, and environmental variables on yield. Sixty-six variables representing several commercial cultivars were studied for two years. Yield in cranberry was strongly influenced by fruit number and size. However, fruit traits are not as useful for early prediction of yield. Although early crop forecasting in cranberry may be difficult, this study suggests that managing environmental and genetic variability while maintaining consistency in yield may be crucial in the development of more accurate methods of yield prediction. 05 Physiology and seasonality of cranberry arthropod pests. Insects are consistently ranked as the top pest threats to Wisconsin cranberry production. To improve insect management efforts, ARS researchers in Madison, WI, measured larval growth rates of a major pest, the Sparganothis fruitworm, as a function of temperature. Then, growth rates were modeled across a broad temperature range to isolate the temperature thresholds demarcating maximal and minimal growth. Finally, growth thresholds were used to generate degree-day accumulations based on local weather data, and these accumulations were linked with discrete biological events (�degree-day benchmarks�) in the insect�s life cycle, so that growers can better estimate optimal spray timings using their local weather reports. 06 High-resolution food web studies. In collaboration with researchers in Yokosuka, Japan, the University of Wisconsin, and the University of New Mexico, ARS researchers in Madison, WI, have examined food-chains in both natural and managed ecosystems (farms). This study represents the largest assessment of consumer trophic position (i.e., place in the food-chain), using amino acid isotopic analysis. We provide the first definitive evidence that omnivory is the dominant paradigm of food web ecology. This means that many populations in agricultural fields are not neatly compartmentalized into functional �roles,� but rather indulge in a high degree of trophic opportunism, that often involves cannibalism and/or attacking beneficial insects, which undermines crop protection objectives. A nationwide conversation on the establishment of IsoBank, an indexed, searchable archive for isotopic data, modeled after GenBank have been started. These kinds of archives further the advancement of science by facilitating massive data sharing and providing bases for biological pest management programs. 07 Pollinator health in cranberries. Fungicides are often sprayed on flowering cranberry beds, sometimes 2-3 times during bloom. Given that cranberries are a native plant, native pollinator species (180+ species) commonly visit commercial marshes, resulting in exposure to fungicides. University of Wisconsin and ARS researchers in Madison, WI, examined how colonies of a native bumble bee species, Bombus impatiens, performed following exposure to fungicide residues. We report the first evidence that fungicides, once widely considered �bee-safe,� may be detrimental to native bee health. This establishes a basis to re- examine the wisdom of applying fungicides to flowering crops, whether pollinated by managed or wild bees.
Impacts
(N/A)
Publications
- Deutsch, A.E., Rodriguez-Saona, C.R., Zalapa, J.E., Steffan, S.A. 2015. Temperature-mediated development thresholds of Sparganothis sulfureana (Lepidoptera: Tortricidae) in cranberries. Environmental Entomology. 44(2) :400-405.
- Zalapa, J.E., Bougie, T.C., Bougie, T.A., Schlautman, B.J., Wiesman, E., Guzman, A., Fajardo, D.A., Steffan, S., Smith, T. 2014. Clonal diversity and genetic differentiation revealed by SSR markers in wild Vaccinium macrocarpon and Vaccinium oxycoccos. Annals of Applied Biology. 166(2):196- 207.
- Deutsch, A.E., Rodriguez-Saona, C.R, Kyryczenko-Roth, V., Sojka, J., Zalapa, J.E., Steffan, S.A. 2014. Degree-day benchmarks for Sparganothis sulfureana (Lepidoptera: Tortricidae) development in cranberries. Journal of Economic Entomology. 107(6):2130-2136.
- Chikaraishi, Y., Steffan, S.A., Ogawa, N.O., Ishikawa, N.F., Sasaki, Y., Tsuchiya, M., Ohkouchi, N. 2014. High-resolution food webs based on nitrogen isotopic composition of amino acids. Ecology and Evolution. 4(12) :2423-2449.
- DeVetter, L., Colquhoun, J., Zalapa, J., Harbut, R. 2015. Yield estimation in commercial cranberry systems using physiological, environmental, and genetic variables. Scientia Horticulturae. 190(1):83-93.
- Schlautman, B., Fajardo, D., Bougie, T., Wiesman, E., Polashock, J., Vorsa, N., Steffan, S., Zalapa, J. 2015. Development and validation of 697 novel polymorphic genomic and EST-SSR Markers in the American cranberry (Vaccinium macrocarpon Ait.). Molecules. 20(2):2001-2013.
- Jones, V.P., Horton, D.R., Mills, N.J., Unruh, T.R., Baker, C.C., Melton, T.D., Miliczky, E., Steffan, S.A., Shearer, P.W., Amarasekare, K.G. 2015. Evaluating plant volatiles for monitoring natural enemies in apple, pear and walnut orchards. Biological Control. Available:
- Pauli, J.N., Steffan, S.A., Newsome, S.D. 2015. It is time for IsoBank. Bioscience. 65(3):229-230.
- Chikaraishi, Y., Steffan, S.A., Takano, Y., Ohkouchi, N. 2015. Diet quality influences isotopic discrimination among amino acids in an aquatic vertebrate. Ecology and Evolution. 5(10):2048-2059.
- Bernauer, O.M., Gaines-Day, H.R., Steffan, S.A. 2015. Colonies of bumble bees (Bombus impatiens) produce fewer workers, less bee biomass, and have smaller mother queens following fungicide exposure. Insects. 6(2):478-488.
- Siebach, S., Zalapa, J., Covarrubias-Pazaran, G., Harbut, R., Workmaster, B., Wasko DeVetter, L., Steffan, S., Guedot, C., Atucha, A. 2015. Toxicity of chelated iron (Fe-DTPA) in American cranberry. Journal of Horticulture. 2:129. DOI:10.4172/2376-0354.1000128.
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Progress 10/01/13 to 09/30/14
Outputs
Progress Report Objectives (from AD-416): Objective 1: Develop and apply genomic and genetic tools to map and characterize the genetic bases of the key cranberry traits that determine yield. Objective 2: Based on horticultural, genetic, and genomic information, formulate and apply breeding approaches for genetically improving cranberry yield. Objective 3: Determine the development thresholds of key arthropod pests (cranberry fruitworm and Sparganothis fruitworm) to better predict the developmental status of populations in the field. Objective 4: Develop novel, innovative IPM strategies to reduce pesticide use and sustain cranberry yield, quality, and profitability. Approach (from AD-416): Objective 1: Next-generation sequencing technology will be used to characterize the cranberry genome. The resultant data will be used to discover and mine molecular markers such as SSRs and SNPs. We will then develop high-resolution genetic maps using the developed markers based on several available half-sib F1 mapping populations. Phenotyping will involve collecting data on yield-related traits and other horticultural measurements, including total fruit weight, percent rotten fruit, average berry weight, and fruit quality parameters. These traits will be localized in the linkage map described above. Information derived from the high resolution cranberry linkage map with yield-related will be used to plan strategic crosses. Objective 2: Prior to creating cranberry hybrids, horticultural, genetic, and genomic information will be carefully considered to ensure that strategic crosses are accomplished. A microsatellite marker based fingerprinting assay will be developed for the true-to-type verification of the cranberry cultivars. We will also characterize known cranberry diversity from the breeding programs and collections and samples sent in by growers. Pedigree information will be evaluated in the light of marker information to determine the most likely genotypes or genetic pools associated with each named cultivar and their associated horticultural performance. A series of cranberry hybrids with complementary genetic pools will be created and evaluated. Objective 3: The temperature-specific development rates and degree-day (DD) accumulations associated with cranberry fruitworm (CFW) and Sparganothis fruitworm (SFW) will be determined. Larval growth rates will be measured over a wide range of controlled temperatures. Growth rates will be plotted against temperature, and models will be fit to the dynamic. From these models, the lower and upper development thresholds will be isolated. The thresholds will then be used to generate degree-day (DD) accumulations that can be linked to discrete biological events, such as flight initiation in the field, adult lifespan, ovipositional period, and egg-hatch periods. DD accumulations represent key developmental benchmarks, helping to optimize pest management in the cranberry system. Objective 4: novel insect pest management approaches will be investigated. Two primary tactics will be explored within the cranberry system: pheromone-based mating disruption and trophic position measurement. In partnership with private industry, as well as Wisconsin cranberry growers, the first ever 3-species mating disruption program will be deployed at large scales within commercial marshes. Population suppression of the target pests will be assayed and compared with conventional pest management approaches. Studies of arthropod trophic position will be conducted using stable isotopic analysis of amino acids. Trophic position estimation will reveal the lifetime trophic tendencies of carnivorous species, thereby providing empirical evidence as to which species are actually beneficial for cranberry production. The progress reported relates to Objectives 1 and 2. ARS continues to develop molecular tools useful for breeding and genetics studies in Vaccinium. We have sequenced, reconstructed, and annotated the cranberry nuclear genome and the plastid and mitochondrial genomes using next- generation sequencing and bioinformatics approaches. We continue to develop molecular markers for genetic diversity studies of cultivated and natural germplasm. Additionally, we are working on the discovery of polymorphic microsatellite and single nucleotide polymorphism markers for molecular mapping studies. A high resolution molecular map with information about traits of economic importance is also being developed that will help breed high yielding cranberry cultivars more efficiently. We currently have collected three years of cranberry phenotypic data on yield and other traits on two mapping populations. The progress reported relates to Objectives 3 and 4. ARS is advancing the practice of integrated pest management (IPM) in US cranberries, and continues to investigate how pest control professionals can exploit arthropod biology to more wisely control pests. We are refining a pheromone-based mating disruption system for US cranberries. Now in year- 3, this work is delivering a multi-species mating disruption program to the cranberry industry. ARS continues to focus on three main projects: 1) the temperature-specific growth and development of Sparganothis fruitworm, 2) the trophic structure of the cranberry system, and 3) flea beetle overwintering biology. The Sparganothis studies provide information integral to the creation of phenology models of this pest, which lend greater predictability to pest forecasting. In studies of trophic structure, we are using compound-specific isotopic methods to illuminate, for the first time, whether carnivorous arthropods contribute significantly to crop protection. Using isotopic techniques and analyses of flea beetle emergence patterns, we continue to investigate how deep their larvae feed, to better target them with a single soil drench bio- insecticide. Accomplishments 01 Next-generation sequencing of organellar genomes in cranberry. Little genetic information exists in cranberry for breeding and genetic studies. We have used next-generation sequencing technology to sequence the genetic code cranberry, which is an understudied, but economically important crop species. State-of-the-art molecular methods and computer-based approaches were used to reconstruct the cranberry plastid and mitochondrial (organellar) genetic codes. These organellar genetic codes are involved in energy formation (photosynthesis) and utilization (respiration) in cranberry. We investigated the cranberry organellar genetic code size, organization, gene content, and variation. This research is important because it will allow us to study photosynthesis and respiration in cranberry, which are key processes for the formation of fruit and ultimately determine cranberry yield. The cranberry organellar genetic codes deciphered through this research are the first and only available in the entire cranberry family (Ericaceae), which comprise thousands of species without previous information. This research will allow us to characterize and compare the energy production/utilization machinery of cranberry and other closely and distantly related species. Ultimately, all the genetic information about energy production/utilization systems will allow us to breed more energy efficient cranberries while transferring and utilizing information to and from other sister species such as blueberry and lingonberry (Vaccinium genus). 02 Sequencing of the cranberry nuclear genome. In terms of taxonomy, cranberries are in the core Ericales, an order for which genome sequence data are currently lacking. Therefore, we used next- generation sequencing technology to identify candidate genes useful to further study important biochemical pathways and cellular processes and to use for marker development for breeding and the study of horticultural characteristics, such as yield and quality traits and disease and insect resistances. This is the first available nuclear genome of the American cranberry, and the only in Vaccinium, which includes several widely cultivated fruit crops native to North America such as blueberry. This research will be invaluable for cranberry breeding and genetic studies regarding yield, quality, and disease and pest resistance. Further, we identified genes controlling many cranberry phytochemical compounds, some of which are beneficial to human health, which can be used to breed more healthy cranberries for the US public. 03 Multi-species mating disruption system. ARS in collaboration with private industry, has created a multi-species mating disruption system that preempts the successful reproduction of the major cranberry pests. This mating disruption system works for two moth species, and is being integrated with current production practices on commercial marshes in Wisconsin. ARS research has also focused on the biology and phenology of Sparganothis fruitworm. Building on our past findings (temperature- mediated development thresholds) we have linked degree-day accumulations to discrete biological stages of the fruitworm, allowing growers to monitor its development using only weather data. Our data lend precision to cranberry integrated pest management (IPM) and are already being used by pest management consultants. Following our controlled-feeding study using the stable isotope, 15N, we developed this method into a significant new tool to quantify how an arthropod feeds within its �food chain.� This reveals whether predaceous insects are actually beneficial for crop protection, because it tells us whether a given predator population is eating pests of the crop.
Impacts
(N/A)
Publications
- Pauli, J., Mendoza, J., Steffan, S.A., Carey, C.C., Weimer, P.J., Peery, Z. 2014. A syndrome of mutualism reinforces the lifestyle of a sloth. Proceedings of the Royal Society B. 281:20133006.
- Fajardo, D., Schlautman, B., Steffan, S.A., Polashock, J.J., Vorsa, N., Zalapa, J.E. 2014. The American cranberry mitochondrial genome reveals the presence of selenocysteine (tRNA-Sec and SECIS) insertion machinery in land plants. Gene. 536(2):336-343.
- Steffan, S.A., Lee, J.C., Singleton, M., Vilaire, A., Walsh, D., Lavine, L. , Patten, K. 2013. Susceptibility of cranberries to Drosophila suzukii (Diptera: Drosophilidae). Journal of Economic Entomology. 106(6):2424-2427.
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