Research Project: Cranberry Genetics and Insect Management

Location: Vegetable Crops Research

2020 Annual Report

Objectives
Objective 1: Map and identify genes that underlie cranberry yield and quality traits, and explain the phenotypic differences between selected genotypes using genetic, genomic, and molecular approaches. Objective 2: Develop new enhanced cranberry germplasm and cultivars by integrating genetic and genomic breeding approaches with conventional cranberry breeding. Objective 3: Develop tools for the early detection and prevention of new, emerging cranberry pests (insects and mites). Sub-objective 3. Develop bio-insecticides using newly discovered, native nematode species. Objective 4: Develop new integrated pest management technologies for pest management and sustainable production of cranberry. Sub-objective 4.A. Develop a multi-species mating disruption program for the major moth pests of U.S. cranberries. Sub-objective 4.B. Investigate the biology and ecology of native pollinators to ensure the sustainable production of cranberries. Objective 5: Develop alternative cranberry production practices that improve water conservation and decrease plant disease. [NP301 C1 PS1B C2 PS2A] Expected benefits include a systems approach to cranberry production that includes genetic improvement, genomics, disease and pest mitigation, and water conservation.

Approach
Objective 1: A multi-pedigree QTL mapping approach will be used to map cranberry yield and fruit quality traits. Phenotypic trait data collection will include traditional and newly developed high-throughput methodologies to measure yield and fruit quality related traits and other horticultural measurements, including total fruit weight, percent rotten fruit, average berry weight, and other fruit quality parameters such as TAcy and firmness. A composite SSR/SNP high-resolution cranberry genetic map developed based on three half-sibling populations will be used for QTL analysis. Objective 2: This research will collaborate with cranberry growers to establish a cranberry research station in Wisconsin and to establish various sized research plots to test the horticultural needs and performance of a selection of important cranberry cultivars. Phenotypic information that will be collected will be determined based on previous research to include the best traits to measure yield and quality. Additionally, a classic inbred-hybrid system will be used based on the best performing cranberry cultivars in the industry to develop improved cranberry lines and varieties in terms of yield and quality. Prior to creating cranberry inbreds and hybrids, horticultural, genetic, and genomic information will be carefully considered to ensure that strategic crosses are accomplished. Objective 3: A novel, effective bio-insecticide will be developed for arthropod pest suppression in commercial cranberry marshes. Two highly virulent nematode species, both native to Wisconsin, will comprise the bio-insecticide, and the nematode blend will ultimately be developed such that it can be applied at large-scales using standard spray equipment. Arthropod population suppression will be assessed among pest species and non-target species alike. Objective 4: A multi-species mating disruption system will be developed to control the top three insect pests of Wisconsin cranberries. The sex pheromones of these insect species will be loaded into carriers that can be applied efficiently via standard fertilizer-application equipment. We will also examine the capacity of the cranberry plant to prime its chemical defenses after 'eavesdropping' on the pheromones of its major pests. Bee-microbe symbioses will be investigated as a means to better understand and protect the native pollinators of cranberries.

Progress Report
The progress reported relates to Objectives 1-4. We are studying yield and quality traits in cranberry using traditional data collection methods. We are also developing high-throughput fruit quality data collection and visualization software to massively collect and understand these data. Molecular tools are being applied to study and identify cranberry genes by mapping those genes found to control important traits. We have developed several high- density molecular maps and a composite map which we are using to map traits of economic importance. In the future, these efforts will help breed cranberry cultivars more efficiently by allowing markers-assisted breeding. The Wisconsin cranberry research station is near completion. This work has been a collaboration with cranberry growers to establish a cranberry research station in Wisconsin. Various plots and experiments have been planned and established to test the horticultural needs, performance, and selection of important cranberry cultivars. The US cranberry mating disruption program has incorporated a new pheromone carrier type (micro-encapsulated carriers) and has tested higher loading levels. The pheromones have also been loaded into organic fertilizer pellets. A bio-insecticide comprised of native Wisconsin nematodes has recently been shown to be highly effective when applied at large scales and can be sprayed via standard grower spray equipment. Bee-microbe interactions continue to be investigated and appear to be vital for larval bee development. We have established a laboratory to study cranberry physiological and molecular responses to nutrient and water management. We are developing methodologies for screening different cranberry cultivars for their photosynthesis, water use efficiency, and nutrient uptake. Progress has been made in using phenocams (digital camera set up at a fixed location to capture time-lapse images) to evaluate the growth dynamics of different cranberry cultivars in the high temporal resolution. We initiated the process of setting up image-based low-cost phenocams cameras in cranberry fields. This imaging platform should allow us to integrate high-throughput phenomics (study of observable characteristics) into cranberry research programs ranging from quantifying diversity to nutrient management as a feasible low-cost solution. We are also studying the expression stability of reference genes in different tissues and experimental conditions for accurate normalization of cranberry gene expression studies.

Accomplishments
1. Development of methods to measure fruit quality in cranberry. Due to the lack of methodologies to measure fruit quality in cranberry, USDA-ARS researchers in Madison, Wisconsin, developed a high-throughput computer-vision method to measure the internal structure of cranberry fruit, which may in turn influence cranberry fruit firmness. We measured the internal fruit structure and analyzed the fruit firmness of cranberries over the ripening period. We provided data which allows growers to better select cranberry varieties to grow. We also provided researchers data to explore the relationship between firmness and internal fruit characteristics. Our study highlights the potential use of internal structure and firmness data for breeding varieties with superior fruit quality. This method can be used as a decision-making tool for cranberry processing, especially to determine optimal harvesting timing and to ensure high quality fruit for different cranberry products. In particular, this study introduces a novel method to define key parameters useful for dried fruit production, which is currently the most profitable and in high demand cranberry product in the market.

2. Cranberry history review and future work. USDA-ARS researchers in Madison, Wisconsin, reviewed and summarized 200 years domestication, breeding, and genetics work in cranberry. The summary defined cranberry traits of economic importance, such as yield or productivity, disease resistance, fruit anthocyanins (red pigment), sugar content, and increasingly fruit quality traits for sweetened-dried-cranberry products such as fruit firmness and size. The review also summarized molecular advances made in the crop and available marker-trait associations identified recently for productivity, berry size, pigment content, fruit rot resistance and other traits. This review provides authoritative information about cranberry breeding and genetics knowledge and research.

3. Study of genetic diversity of wild cranberry populations. Most cranberry cultivars share the same genetic background based on only a few Eastern wild selections. This limits the breeding pool for selection to support the cranberry industry. Therefore, USDA-ARS researchers in Madison, Wisconsin, studied 36 wild populations of wild cranberries in the Upper Midwest. We demonstrated the presence of high diversity that represents untapped and previously undiscovered cranberry variation in natural areas of the states of Wisconsin and Minnesota. Due to the lack of exploration, Wisconsin growers have been forced to use cranberry cultivars developed for other growing areas in the Eastern US. The challenges faced by growers in Wisconsin are unique, and these populations may possess unique adaptations and traits useful in breeding cultivars for central Wisconsin, which is the largest cranberry production area in the world.

4. Conservation of North America’s crop wild relatives. Crop wild relatives, the distant cousins of agricultural plants, are valuable for agriculture because they can be used for breeding to introduce new or improved traits. While, North America harbors a rich native flora, many of these species are threatened in their natural habitats and are underrepresented in genebanks (biorepositories for plants). USDA-ARS researchers in Madison, Wisconsin, worked along other university researchers to provide examples of productive collaborations focused on conserving wild cranberries and chile peppers. Five shared priorities were discussed for further action to: 1) understand and document North America’s crop wild relatives and wild utilized plants, 2) protect threatened species in their natural habitats, 3) collect and conserve the diversity of prioritized species, 4) make this diversity accessible and attractive for plant breeding, research, and education, and 5) raise public awareness of their value and the threats to their persistence. This work highlights the need of ambitious coordinated efforts among plant conservation, land management, agricultural science, and botanical education and outreach organizations to take the major strides necessary to secure, enhance the use of, and raise awareness with regard wild crop diversity.

5. Development of genetic markers for cranberry and other Vaccinium species of agricultural importance. Cranberries are one of the few species in the genus Vaccinium that is utilized as a crop. However, the genus is composed of many understudied and underused species, as is the case of wild blueberries and cranberries, lingonberries, and deerberries. Many of these species are cross-compatible and possess an array of traits of high agronomical value that may be commercially exploited through hybridization breeding. USDA-ARS researchers in Madison, Wisconsin, transferred 61 molecular markers across 16 Vaccinium species tested. The ability of the markers to discriminate the different species was tested, which can also be used to detect hybrids among different species. As consumer demand is increasing and continually evolving for specialty products such as dried cranberries, new varieties are needed that could be developed by hybridizing cranberries with different species. Such hybrids will be easily detectable based on the makers developed in this study. Breeders and consumers will benefit from the markers through the creation of high yield, better adapted cranberries with increased fruit quality for processing and for human nutrition. The developed markers constitute a toolset for breeders for the development of Vaccinium hybrids and to allow the development of population genetic studies of poorly understood species.

6. Novel nematode-based bio-insecticide. Wisconsin cranberries endure perennial, significant damage from a diversity of arthropod pests, which collectively represent the single greatest threat to berry production. Because certain soil-dwelling species (i.e., cranberry flea beetle) are poorly controlled by any registered insecticide, there is a need for effective control measures. Given issues with excessive pesticide residues in cranberries, the demand for effective biological control agents has increased markedly in recent years. To meet this demand, a highly virulent nematode-based bio-insecticide has been developed by USDA-ARS researchers in Madison, Wisconsin. This two-species nematode blend has proven itself to be as effective for cranberry flea beetle control as two insecticide sprays. This new bio-insecticide is comprised of native Wisconsin nematodes, and has been field-tested using grower equipment. The nematodes also have been shown to effectively attack pests within fruit. The capacity of the nematodes to kill pests while they’re ensconced within fruit represents a major new tool for dealing with fruit pests.

7. On-farm pollinator management. Pollination is critical for cranberry production, and growers spend exorbitant sums each year on rented bees. USDA-ARS research in Madison, Wisconsin, has demonstrated that the spatial arrangement of honey bee hives on a cranberry marsh is exceedingly important for keeping bees foraging on-site. Certain locations on a marsh (at the edge of the marsh, with woodlands nearby) are associated with ‘cheating’ bees flying off-site to forage at non-cranberry flowers.

8. Bee-microbe symbiosis. Pollination is critical for cranberry production, and many native bee species provide significant pollination services for Wisconsin cranberries. Most of these bees are non-social, solitary bee species, which rely on pollen-borne microbes for larval development. The microbes within pollen-provisions have been shown to be extremely important for larval bee development. These microbes are not gut symbionts, but rather external symbionts that process and digest the pollen prior to consumption by the bee larva. Looking at one bumble bee species, ARS researchers have documented the biodiversity of the pollen-borne microbiome, which sets the stage for future work looking at specific microbial functions for pollen enrichment and preservation.

Review Publications
Vorsa, N., Zalapa, J.E. 2019. Domestication, genetics, and genomics of the American cranberry. Plant Breeding Reviews. 43:279-310. https://doi.org/10.1002/9781119616801.ch8.
Khoury, C.K., Greene, S.L., Krishnan, S., Miller, A., Moreau, T., Williams, K.A., Rodriguez-Bonilla, L., Spurrier, C.S., Zalapa, J.E., Nabhan, G.P. 2020. Toward integrated conservation of North America’s crop wild relatives. Natural Areas Journal. 40(1):96-100. https://doi.org//10.3375/043.040.0111.
Rodriguez-Bonilla, L., Rohde, J., Matusinec, D., Zalapa, J.E. 2019. Cross-transferability analysis of SSR markers developed from the American Cranberry (Vaccinium macrocarpon Ait.) to other Vaccinium species of agricultural importance . Genetic Resources and Crop Evolution. 66:1713-1725(2019). https://doi.org/10.1007/s10722-019-00826-1.
Guzman, A., Gaines-Day, H., Lois, A., Steffan, S.A., Brunet, J., Zalapa, J.E., Guedot, C. 2019. Surrounding landscape and spatial arrangement of honey bee hives affect pollen foraging and yield in cranberry. Agriculture, Ecosystems and Environment. 286:106624. https://doi.org/10.1016/j.agee.2019.106624.
Foye, S., Steffan, S.A. 2019. Two native Wisconsin nematodes represent virulent bio control agents in cranberries. Biological Control. 138:104042. https://doi.org/10.1016/j.biocontrol.2019.104042.
Diaz-Garcia, L., Rodriguez-Bonilla, L., Phillips, M., Lopez-Hernandez, A., Grygleski, E., Atucha, A., Zalapa, J.E. 2019. Comprehensive analysis of the internal structure and firmness in American cranberry (Vaccinium macrocarpon L.) fruit. PLoS One. 14(9):e0222451. https://doi.org/10.1371/journal.pone.0222451.
Rodriguez-Bonilla, L., Rodriguez-Bonilla, F., Matusinec, D., Wiesman, E.C., Schoville, S., Atucha, A., Zalapa, J.E. 2019. Exploring the genetic diversity of wild cranberry populations in the Upper Midwest. Crop Science. vol 59:2413-2428. https://doi.org/10.2135/cropsci2019.06.0367.
Foye, S., Steffan, S.A. 2020. A rare, recently discovered nematode, Oscheius onirici (Rhabditida:Rhabditidae), kills Drosophila suzukii (Diptera: Drosophilidae)within fruit. Journal of Economic Entomology. 113(2):1047-1051. https://doi.org/10.1093/jee/toz365.
Dharampal, P., Diaz-Garcia, L., Haase, M., Zalapa, J.E., Currie, C., Hittinger, C., Steffan, S.A. 2020. Microbial diversity associated with the pollen stores of captive-bred bumble bee colonies. Insects. 11(4):250. https://doi.org/10.3390/insects11040250.