Location: Vegetable Crops Research2014 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.
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. 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.
1. 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).
2. 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.
3. 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.
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.
Polashock, J.J., Zelzion, U., Fajardo, D.A., Zalapa, J.E., Georgi, L., Bhattacharya, D., Vorsa, N. 2014. The American cranberry: first insights into the whole genome of a species adapted to bog habitat. Biomed Central (BMC) Plant Biology. 14:165.
Steffan, S.A., Chikaraishi, Y., Horton, D.R., Ohkouchi, N., Singleton, M., Hogg, D.B., Miliczky, E., Jones, V. 2013. Trophic hierarchies illuminated via amino acid isotopic analysis. PLoS One. 8(9):e76152. Available: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0076152.