Location: Vegetable Crops Research
2021 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 marker-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 U.S. cranberry mating disruption program has incorporated a new pheromone carrier type (micro-encapsulated carriers) and has tested higher loading levels. 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. Given the importance of native bees for cranberry pollination, these findings refine bee conservation strategies. We are developing methodologies for evaluating different cranberry cultivars for their photosynthesis, water use efficiency, and nutrient uptake. We are also implementing low-cost, effective phenotyping tools to track cranberry varieties' growth and development in the field. This imaging platform should allow us to integrate high throughput phenomics into cranberry research programs ranging from quantifying diversity to nutrient management as a feasible low-cost solution. In addition, the digital phenotyping tool and information derived will help breeders in genotype selection based on desired traits and breed new cultivars that interest cranberry growers. 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. Analysis of the historical breeding stages of the recently domesticated American cranberry. The American cranberry is a recently domesticated species with less than 200 years of breeding history. Trait data suggests that cultivated cranberries have changed significantly in terms of fruiting habits (e.g., fruit size, color, and yield) compared to wild materials. However, due to the few generations of selection and short domestication history of the crop, it is unclear how much they differed genetically. Moreover, the extent that domestication and breeding efforts have shaped cranberry remains mostly obscure. Thus, a historical collection composed of 362 accessions, spanning wild germplasm, first-, second-, and third-generation selection cycles was studied by ARS researchers at Madison, Wisconsin, to unravel the breeding and domestication history of cranberry. Genetic analyses showed differences among the stages of cranberry domestication and subsequent breeding. For example, genetic analyses revealed a progressive loss of diversity when transitioning from early domestication stages to current cranberry forms. Loss of diversity can be detrimental to the resilience of the cranberry crop and future breeding efforts. Breeding cycles differed and showed a marked increase for total yield and average fruit weight, but not for fruit chemistry traits (acid, sugar, and pigment content). Genetic analysis allowed us to identify genetic markers associated with average fruit weight and fruit rot, which are two traits of great agronomic relevance and could be further used to accelerate cranberry genetic improvement and benefit growers and consumers. Cranberry marker-assisted selection could be extremely helpful for cranberry for breeding using the information revealed by the present study.
2. The chromosome-level genome assembly of cranberry and its wild relative to fuel future cranberry breeding. The American cranberry is an iconic North American fruit crop of great cultural and economic importance. Cranberry can be considered a fruit crop model due to its unique fruit nutrient composition, overlapping generations, recent domestication, both sexual and asexual reproduction modes, and the existence of cross-compatible wild species. Development of cranberry molecular resources started very recently; however, further genetic studies are now being limited by the lack of a high-quality genetic code database. These new high quality cranberry genetic resources will facilitate the dissection of the genetic mechanisms governing agronomic traits and further breeding efforts at the molecular level. Here, we report the first chromosome-scale genetic code assembly of cranberry, cultivar Stevens, and a draft genetic code of its closest wild relative species. We assembled more than 92% of the estimated cranberry genetic code into 12 chromosomes, which enabled gene model prediction and chromosome-level comparative analysis, divergence, and evolution with other plant species, including close relatives such as blueberry and kiwifruit. Finally, we identified a cluster of genetic sequences related to color variation in fruit. Our analysis of these genes indicates that they act as pigment biosynthesis regulators in cranberry. The chromosome-level cranberry genetic code, and the draft genetic code of its closest wild relative species, provide a much-needed resource for further investigation of the genetic architecture underlying trait variation. These genetic codes will support cranberry improvement efforts by facilitating the discovery of novel trait-gene associations useful in molecular based breeding strategies.
3. The genetic analysis of crop wild relatives of cranberries across their ranges in the U.S. to expand access to breeding materials. Wild cranberries are important for conservation and future use in breeding and genetic studies. Multiple wild cranberry species exist, which are often fertile if crossed, and are widely distributed in the U.S., but little is known about which populations are more important to conserve for future use in breeding. Crop wild relatives are important sources of novel genetic variation for plant breeding and have provided important traits related to productivity and sustainability for many crops. ARS researchers in Madison, Wisconsin, studied 21 wild populations of American cranberry (the domesticated species) and 24 populations of the closest cranberry wild relative (the small cranberry, not domesticated species) across much of their native ranges in the U.S. using genetic markers. High levels of genetic diversity were observed for both species across populations and unique genetic diversity for several populations. The genetic analyses also confirmed the field identification of a native population of cranberries on the Okanogan-Wenatchee National Forest in the state of Washington, far outside the previously reported range for the species. Knowledge of the genetic diversity in populations of these plants can inform effective strategies for their conservation and facilitate utilization to solve agricultural challenges such as the need of increasing yield, nutritional value, and resilience. These results will help to inform efforts of the Agricultural Research Service and the U.S. Forest Service to conserve the most diverse and unique wild cranberry populations through conservation in designated sites on National Forests. Ultimately, these populations will provide plant materials for the creation of hybrids to increase of genetic diversity of commercial cranberry to increase resilience and profitability of growers by the introduction of new traits through future breeding efforts.
4. Flowers as hubs for the microbial symbionts of bees. ARS investigators in Madison, Wisconsin, are examining the roles of floral substrates as the ‘hubs’ of microbial transmission among native bee fauna. Native bees are especially important for cranberries, and the survival of such bees depends on microbial symbionts within the pollen-provision. Microbes have been shown to be critical to the development of bee larvae, but the various mechanisms and key players are less well understood. ARS scientists have shown that flowers serve as the pick-up and drop-off sites for beneficial bacteria and yeasts. Microbial communities pre-digest the pollen grains within the larva’s pollen-provision. These microbes function much like those within the rumen of a cow, providing access to amino acids and lipids that would otherwise be unavailable to the young developing bees. Importantly, ARS scientists have shown that these communities of microbes are not specific to certain bee species, but rather are shared widely among bee species. The mechanisms of transmission are mediated by flowers in the landscape and ensure that critical microbial groups are harbored long enough to be broadly distributed among pollinator populations. This work is critically important for agriculture, because pollinators are critical to fruit set.
5. Microbial processing of bee pollen. Bee larvae develop almost exclusively on the resources within pollen-nectar provisions. However, before bee larvae can adequately digest and assimilate nutrients from pollen, microbes (external microbes, not gut symbionts) are necessary for accessing the cytoplasm within pollen grains. In the absence of such microbial processing, ARS researchers have shown that bee larvae starve to death, despite having ample supplies of pollen. Agricultural practices have been shown to alter the beneficial microbial communities within bee pollen-provisions, reducing microbial populations and causing bee declines. The roles of specific microbial species in the successional stages of pollen breakdown are poorly known, but what has been recently discovered by ARS researchers is that the particular blend of pollen—and the presence of microbes—within the pollen-provision is critical to the successful development of young bees. What this means is that the microbes supplied by the mother bee are key to making the pollen-provision nutritious enough to complete development. Without the microbes, ARS scientists have shown that the larvae struggle to develop, resulting in smaller, less fit adult bees emerging in the spring. These findings establish a platform for future work that will illuminate the biochemical mechanisms by which bacteria and yeasts access pollen grains, and transform the pollen mass into a blend of microbial biomass and pollen cytoplasm. Ultimately, understanding the basic biology and ecology of bees and their microbial symbionts will help to conserve the native pollinator populations that U.S. cranberry production relies upon. Given the consistency of bee declines, there is a significant need to understand how agricultural practices may be affecting the pollinator services provided by diverse bee populations.
Review Publications
Zalapa, J.E., Rodriguez-Bonilla, L., Williams, K.A., Rodríguez-Bonilla, F., Matusinec, D., Maule, A., Coe, K., Wiesman, E.C. 2020. The genetic diversity of crop wild relatives, Vaccinium macrocarpon Aiton and V. oxycoccos L., across their ranges in the US, with special emphasis on National Forests. Plants. 9(11). Article 1446. https://doi.org/10.3390/plants9111446.
Diaz-Garcia, L., Garcia-Ortega, L., González-Rodríguez, M., Delaye, L., Iorizzo, M., Zalapa, J.E. 2021. Chromosome-level genome assembly of the American cranberry (Vaccinium macrocarpon Ait.) and its wild relative Vaccinium microcarpum. Frontiers in Plant Science. 12. Article 633310. https://doi.org/10.3389/fpls.2021.633310.
Diaz-Garcia, L., Covarrubias-Pazaran, G., Johnson-Cicalese, J., Vorsa, N., Zalapa, J.E. 2020. Genotyping-by-sequencing identifies historical breeding stages of the recently domesticated American cranberry. Frontiers in Plant Science. 12. Article 633310. https://doi.org/10.3389/fpls.2020.607770.
Dharampal, P.S., Hetherington, M., Steffan, S.A. 2020. Microbes make the meal: Oligolectic bees require microbes within their host pollen to thrive. Ecological Entomology. 45(6):1418-1427. https://doi.org/10.1111/een.12926.
Takizawa, Y., Takano, Y., Choi, B., Dharampal, P., Steffan, S.A., Ogawa, N., Ohkouchi, N., Chikaraishi, Y. 2020. A new insight into isotopic fractionation associated with de-carboxylation in organisms: implications for amino acid isotope approaches in biogeoscience. Progress in Earth and Planetary Science. 7. Article 50. https://doi.org/10.1186/s40645-020-00364-w.
Keller, A., Mcfrederick, Q., Dharampal, P., Steffan, S.A., Danforth, B., Leonhardt, S. 2020. (More than) Hitchhikers through the network: The shared microbiome of bees and flowers. Current Opinion in Insect Science. 44(April 2021):8-15. https://doi.org/10.1016/j.cois.2020.09.007.
