Location: Vegetable Crops Research
2023 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
This is the final report for this project which terminated in March 2023. See the report for the replacement project, 5090-21220-007-000D, “Cranberry Genetics, Physiology, and Insect Management” for additional information.
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. To complement genetic mapping, we developed many new techniques to measure fruit quality, including digital external appearance, digital internal structure, firmness techniques, and chemistry traits, including flavonoids. We studied yield using traditional data collection methods and developed pilot digital and sensing yield detection techniques. We also developed high-throughput fruit quality data collection pipelines and created visualization software to understand these data. A new cranberry fruit quality laboratory was set up to increase the USDA capabilities for testing fruit quality and composition, producing mock products of sweetened dried cranberry (SDC), and testing the quality and composition of laboratory prepared SDC. The data collected in this laboratory will be used to elucidate relationships between the quality/composition of cranberry fruits and products, which will then contribute to the development of innovative farm practices, new varieties, and technologies to produce value-added cranberry-based food products with optimized quality and health-promoting benefits. Additionally, a research project was initiated to establish a library of phytochemical profiles across different varieties to provide basic knowledge necessary for the investigation of the potential health benefits of cranberry and also the development of value-added cranberry-based food and health-care products. Based on the above-mentioned phenotypic data collection advances, we developed and applied molecular tools to study and identify cranberry genes by mapping those genes found to control important traits, particularly for fruit quality and yield. We developed several high-density molecular maps and a composite map which we used to map traits of economic importance. Additionally, we developed association mapping and genomic selection techniques in cranberry. We also studied the expression stability of reference genes in different tissues and experimental conditions for accurate normalization of cranberry gene expression studies. Finally, we sequenced and published the first chromosome scale cranberry genome and identified genes controlling fruit color in cranberry. These efforts will help breed cranberry cultivars more efficiently by allowing markers-assisted breeding.
Objective 2: Develop new enhanced cranberry germplasm and cultivars by integrating genetic and genomic breeding approaches with conventional cranberry breeding. We developed the Wisconsin Cranberry Research Station in Black River Falls, Wisconsin. The station is completely operational with a wet lab, cranberry storage facilities, and over 3750 diversity and breeding plots were planted along with 100 acres of a variety of cultivars for research and production. This work was a collaboration between the USDA and cranberry growers to establish the first cranberry research station in Wisconsin. The various research plots include cultivars, natural diversity, breeding crosses, and experiments established to test the horticultural needs, performance, and selection of important cranberry cultivars.
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. We collaborated with the U.S. cranberry growers on the deployment and refinements of the application timing for the ARS bio-insecticide. This bio-insecticide is comprised of two native Wisconsin nematodes (Oscheius onirici and Heterorhabditis georgiana) and has been shown repeatedly to be highly effective when applied at small- or large-scales. It can be sprayed via standard grower spray equipment (boom-arm applications).
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. The U.S. cranberry mating disruption program generated data on efficacy against the Sparganothis fruitworm. This provided the final year of efficacy data for the company that manufactures the pheromones (and the carrier) to pursue a product registration.
Sub-objective 4.B. Investigate the biology and ecology of native pollinators to ensure the sustainable production of cranberries.
On-farm bee nursery posts for native bee fauna were manufactured and established on commercial cranberry sites. Occupancy rates were encouraged, and after bee emergence species were identified. Grower involvement has allowed for the expansion of these nesting structures.
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.
We developed algorithms to analyze field images collected using different cameras and determine the cranberry phenological stages. The data was used to gain insight into the growth and development of cranberries and to identify phenological differences between cultivars. We developed methodologies for evaluating different cranberry cultivars for their photosynthesis, water use efficiency, and nutrient uptake. We initiated a project to aid in characterizing the cultivar's responses to multiple environments (Wisconsin, Massachusetts, and New Jersey) and in evaluating different traits in response to heat and water stress.
Accomplishments
1. Genome anchoring of cranberry and blueberry flavonoid QTL. Consumption of blueberry, cranberry, bilberry and lingonberry is strongly associated with various of potential health benefits including reduced risk of cardiovascular disease, type-2 diabetes and improvements in cognitive function. Many of these benefits are derived from the relatively high concentrations of flavonoids, including the anthocyanin pigments that provide the attractive red and blue berry colors. To distil recent Vaccinium progress in the understanding of flavonoid regulation, ARS scientists in Madison, Wisconsin, used recent gains in both genomic tools and functional analysis to anchor flavonoid quantitative trait loci (QTL) in cranberry and blueberry. We used all available QTL flavonoid data in cranberry and blueberry, emphasizing those that were stable across years and/or detected across multiple genetic backgrounds, and we anchored such QTL to the physical maps. This work will help researchers prioritize QTL targets for breeding and genetic studies on flavonoid genetics to improve Vaccinium crops. This work will also help increase the understanding of flavonoid regulation and biosynthesis across a broader range of fruit crops.
2. Identification of genomic regions that are associated with environmental adaptation in wild cranberry. Wild plant populations become adapted to their local environment through natural selection. This adaptation may confer tolerance to environmental stresses, such as extreme temperatures, precipitation, or variable soil conditions. ARS scientists in Madison, Wisconsin, used several populations of wild cranberry, along with long-term climate data from the regions where these populations were collected, and DNA markers, to identify potential genomic regions that were associated with local environmental conditions. Among 126 DNA marker-environment associations detected, we identified several that genes in those regions with known influence on plant response to environment in other species. Confirming the influence of the genes in adaption to specific environmental conditions will help accelerate the breeding of more stress-tolerant cultivars.
3. Development of methods to measure cranberry texture and firmness to facilitate genetic selection for these priority traits. In the cranberry industry, texture and firmness of the fruit are priority traits. Despite this, no reliable methodology has been established to evaluate these traits in breeding programs. ARS scientists in Madison, Wisconsin, examined key methodologies, texture traits, parameters, and conditions that are crucial to achieve a correct and efficient measurement of texture in cranberry fruits. Methods were successfully implemented in cranberry resulting in a total of 47 texture features. These traits allowed the evaluation of the texture of the cranberry fruit. Scientists used the methods to elucidate factors that affect texture such as storage time, texture-fruit size relationship, and fruit temperature. These methods will be useful to test varieties and help breeding programs improve the texture of cranberries.
4. Successful development of a cranberry x blueberry fertile hybrid that expands the genetic base for cranberries, and potentially other berry crops. American cranberry has both limited diversity and a limited secondary genepool. ARS researchers in New Jersey and Wisconsin have succeeded in making a new hybrid using a tetraploid American cranberry line (V. macrocarpon) and a South American species, the Andean blueberry (V. meridionale). Andean blueberry was hybridized successfully as a male parent with 4x V. macrocarpon (American cranberry) and hundreds of offspring were produced. The hybrids displayed modest male and female fertility. The newly created hybrids are more upright, stockier, and more woody than diploid cranberry. The American cranberry stands to benefit significantly from the creation of these new hybrids and many possibilities exist for the selection of commercial types. In addition, Andean blueberry hybrids can also hybridize with commercial blueberry and lingonberry suggesting it may be possible to transfer traits between different berry crops and derive unique hybrid genotypes with the potential to become new marketable commodities.
5. Cranberry fall nitrogen fertilization promotes stem growth and increased fruit weight. Plant energy reserves play a key role in woody perennial plants' winter survival and growth resumption during the spring. Fall nitrogen (N) fertilization can be used to increase the availability of plant energy reserves to support and enhance vegetative growth and fruit production the following growing season, but the utility of this in cranberries had not been tested. ARS scientists in Madison, Wisconsin, tested the effect of fall N fertilization on subsequent fruit production by evaluating yield and vegetative growth. Fall N treatments consisted of plots receiving 0, 10, 20, and 40% of the standard N application (67 kg/ha) used during the growing season. Yield was not affected by either the fall fertilization treatments, but there was an increase in berry weight and a concomitant reduction in the number of fruits per unit area in the 40% fall N fertilization treatment. The lower number of fruits resulted from an increase in the proportion of vegetative stems. Increased berry weight is a highly desirable trait for sweetened dried cranberry production (SDC); therefore, fall nitrogen fertilization could be advantageous growers seeking to increase their fruit quality. In addition, fall nitrogen fertilization could be useful in the establishment of new beds, variety trials, or the recovery of vines that have experienced stress.
Review Publications
Neyhart, J.L., Kantar, M.B., Zalapa, J.E., Vorsa, N. 2022. Genomic-environmental associations in wild cranberry (vaccinium macrocarpon ait.). G3, Genes/Genomes/Genetics. https://doi.org/10.1093/g3journal/jkac203.
Lopez-Moreno, H., Phillips, M., Diaz-Garcia, L., Torres-Meraz, M.A., De La Torre, F., Berro, I., Loarca, J., Mura, J.D., Ikeda, S., Atucha, A., Giongo, L., Lorizzo, M., Zalapa, J.E. 2023. A survey of key methods, traits, parameters, and conditions for measuring texture in cranberry (Vaccinium macrocarpon Ait.). Horticulturae. 9(4). Article 479. https://doi.org/10.3390/horticulturae9040479.
Iorizzo, M., Lila, M., Perkins-Veazie, P., Luby, C.H., Vorsa, N., Edger, P., Bassil, N.V., Munoz, P., Zalapa, J.E., Gallardo, K.R., Atucha, A., Main, D., Giongo, L., Li, C., Polashock, J.J., Sims, C., Canales, E., Devetter, L., Coe, M., Chagne, D., Colonna, A., Espley, R. 2023. VacciniumCAP, a community-based project to develop advanced genetic tools to improve fruit quality in blueberry and cranberry. Acta Horticulturae. 1362:71-80. https://doi.org/10.17660/ActaHortic.2023.1362.11.
Edger, P.P., Iorizzo, M., Bassil, N.V., Benevenuto, J., Ferrao, L.F., Giongo, L., Hummer, K.E., Lawas, L.F., Leisner, C.P., Li, C., Munoz, P., Ashrafi, H., Atucha, A., Babiker, E.M., Canales, E., Chagne, D., DeVetter, L., Ehlenfeldt, M.K., Espley, R.V., Gallardo, K., Gunther, C.S., Hardigan, M.A., Hulse-Kemp, A.M., Jacobs, M.L., Lila, M., Luby, C.H., Main, D., Mengist, M.F., Owens, G.L., Perkins-Veazie, P., Polashock, J.J., Pottorff, M., Rowland, L.J., Sims, C.A., Song, G., Spencer, J., Vorsa, N., Yocca, A.E., Zalapa, J.E. 2022. There and back again; historical perspective and future directions for Vaccinium breeding and research studies. Horticulture Research. 9. Article uhac083. https://doi.org/10.1093/hr/uhac083.
Rojas-Barrow, P., Boivar-Medina, J., Workmaster1, B., Zalapa, J.E., Atucha, A. 2022. Cranberry fall nitrogen fertilization promotes subsequent season vegetative growth. HortScience. 58:1(6-10). https://doi.org/10.21273/HORTSCI16848-22.
Ehlenfeldt, M.K., Polashock, J.J., Rowland, L.J. 2022. Fertile intersectional hybrids of 4x andean blueberry (Vaccinium meridionale) and 2x lingonberry (V. vitis-idaea). HortScience. 57:525-531. https://doi.org/10.21273/HORTSCI16285-21.
Albert, N.W., Lorizzo, M., Mengist, M.F., Montanari, S., Zalapa, J.E., Maule, A., Edger, P.P., Yocca, A., Platts, A., Pucker, B., Espley, R.V. 2023. Vaccinium research expands our understanding of complex flavonoid accumulation profiles and regulation in fruit. Journal of Plant Physiology. 1-15 (2023). https://doi.org/10.1093/plphys/kiad250.
