Location: Vegetable Crops Research2016 Annual Report
1a. 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.
1b. 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.
3. Progress Report:
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.
1. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
5. Significant Activities that Support Special Target Populations:
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. 64(3):451-466. 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.