Progress 10/01/23 to 09/30/24
Outputs
PROGRESS REPORT Objectives (from AD-416): Objective 1: Conduct research to develop genetic resource maintenance, evaluation, or characterization methods and, in alignment with the overall National Plant Germplasm System (NPGS) Plan, apply them to priority temperate-adapted fruit, nut, and other specialty crop genetic resources to avoid backlogs in plant genetic resources and information management. Sub-objective 1.A: Building on the data and information included in the NPGS Plan to develop and implement a detailed plan for conducting research to develop methods for effectively addressing backlogs in accession regeneration, backup, germination/viability testing of seeds, pathogen-testing and �clean-up�, record digitizing, trait evaluation and characterization, and upload all data to GRIN-Global. Sub-objective 1.B: Develop improved methods for conserving temperate crop germplasm in field plantings and container production in protected environments. Sub-objective 1.C: Expand the DNA genetic marker databases of Fragaria, Pyrus, Corylus, Vaccinium, Rubus, and Humulus, with existing DNA fingerprinting sets and develop or optimize fingerprinting sets for genotyping other genera, and enter information to GRIN-Global. Sub-objective 1.D: Implement targeted and/or high-throughput genotyping systems for genome-wide association and linkage and trait mapping in Vaccinium and Fragaria, core collection establishment in Rubus and Pyrus, development of Fire blight resistance markers in Pyrus, and enter information to GRIN-Global. Sub-objective 2.E: Provide support for data collection, management, and analysis from phenotyping evaluations that add value to NCGR small fruit genetic resources, and that enhance the development and commercialization of new blueberry, caneberry, and strawberry cultivars. Objective 2: Acquire, distribute, and maintain the safety, genetic integrity, health, and viability of priority temperate-adapted fruit, nut, and other specialty crop genetic resources and associated descriptive information. Sub-objective 2.A: Acquire international and domestic germplasm samples of Corylus, Fragaria, Humulus, Pyrus, Mentha, Ribes, Rubus, Vaccinium, and their crop wild relatives via plant exploration and exchange. Sub-objective 2.B: Establish and maintain crop genetic resources emphasizing temperate fruit, nut, and specialty crop germplasm (both cultivated and crop wild relatives). Apply established genetic marker tools to identify duplication and eliminate unnecessary redundancy to maximize efficient germplasm management. Sub-objective 2.C: Collaborate with other genebank sites to implement backup conservation methods for our eight primary genera, including growing plants in field plantings and long-term cryopreservation. Sub-objective 2.D: Apply bioassay, ELISA, and PCR tests for detecting known virus, viroid, and phytoplasma pathogens in primary plant collections. Eliminate pathogens from selected accessions with improved methods for heat therapy and meristem culture. Sub-objective 2.E: Distribute germplasm during the appropriate season for each crop to national and international researchers at public, private, and educational bodies. Approach (from AD-416): Objective 1: 1.A: Develop research plans for preventing backlog and for fast tracking conservation activities described in the NPGS plan using a collaborative and multi-step approach. Preventing losses to accessions and records is the number one NCGR priority. 1.B: Establish improved conservation methods upon and after transition to new screenhouse design, which include a fully automated control of environmental conditions to maximize winter chilling/dormancy and mitigate excessive summer heat while providing effective exclusion of aphids and other virus vectors. 1.C: Expand existing molecular databases for hazelnut, blackberry, blueberry, pear, and hop and develop new databases/tests for raspberry, currant, gooseberry and mint. 1.D: Apply/develop high throughput genotyping techniques to: conduct genome wide association studies (GWAS) for fruit quality in blueberry and strawberry; establish core collections in red raspberry, pear, wild strawberry, and cranberry; and to develop a DNA test for fireblight in pear. Objective 2: 2.A: Acquire samples of Corylus, Fragaria, Humulus, Pyrus, Mentha, Ribes, Rubus, Vaccinium, and their related pome fruits from North America, North Africa, Central Asia, Asia, and Northern Europe to fill current gaps in NPGS collections as described in the Crop Vulnerability Statements. 2.B: Efficiently maintain genetic integrity and diversity of germplasm prioritizing five genera: Corylus, Fragaria, Pyrus, Rubus, and Vaccinium. 2.C: Establish security backup for the accessions in our collections using whole-plant local clonal backup, whole-plant remote clonal backup, tissue culture and/or cryopreservation where possible, and as seed. 2.D: Develop and implement a pathogen testing scheme for field and for screenhouse/greenhouse-grown germplasm. 2.E: Distribute genetic resources through the GRIN-Global online order processing under the NPGS conditions of distribution. This report documents progress for project 2072-21000-059-000D, titled, �Understanding Ecological, Hydrological, and Erosion Processes in the Semiarid Southwest to Improve Watershed Management�, which started in December 2020. In support of Sub-objective 1.A and Sub-objective 2.C, ARS researchers in Corvallis, Oregon, developed plant propagation, maintenance, and backup plans to decrease size of field plantings, including (1) plans to move backup collections of Actinidia and Rheum, and a non-primary collection of Sambucus from field plantings into containers; (2) plans to move a portion of a primary collection of Ribes to containers and assess duplicates and mis-identifications using genotypic data; and (3) collaborations with NLGRP to increase cryopreservation of Sambucus seed, Ribes, Pyrus and Cydonia dormant buds and support evaluation of methods to cryopreserve Sambucus and Cydonia dormant buds. In support of Sub-objective 1.A, ARS researchers collaborated with researchers on improving evaluation of genetic resources including, (1) determining novel anthocyanin profiles of two subtropical Vaccinium species, and (2) identifying three mechanical parameters that breeders can select for when breeding for fruit texture in blueberry. For Sub-objective 1.B and Sub-objective 2.D, ARS researchers developed a strategy to maintain and coordinate locations of virus infected plants until new testing or virus cleanup protocols are established, including (1) increasing space in greenhouses and screenhouses for virus infected Mentha, Humulus, Ribes, Pyrus, and Fragaria; (2) implementing protocols for sample collections in field and in greenhouses and screenhouses that decrease risk of disease transfer; and (3) updating information in GRIN- Global to note that distribution of virus infected plants is restricted. Also, in support of Sub-objective 1.B, ARS researchers continued collaborative research evaluating factors altering horticultural crop health, including (1) completing trials; (2) establishing how pathogens associated with Phytophthora root rot in plants differ in sensitivity to fungicides root rot; (3) optimizing detection methods and determining how temperature, irrigation practices, and plant spacing influence disease caused by Calonectria pseudonaviculata, a foliar pathogen; (4) determining the potential phytotoxicity of erythritol, a novel control method for Drosophila suzukii, in blueberry, cherry, and wild Himalayan blackberry; and (5) how fertilizing rhododendron with silicon enhances resistance to azalea lace bug, Stephanitis pyrioides. ARS researchers have written manuscripts from two studies and published two peer-reviewed and one trade journal manuscript. Two more manuscripts have been submitted to peer-reviewed journals. In further support of Sub-objective 1.B, ARS researchers in Corvallis, Oregon, continued collaborative research evaluating factors altering horticultural crop health, including collaboration assessing the distribution of dagger nematodes and associated nematode transmitted viruses in Pacific Northwest small fruit crops. Also related to Sub-objective 1.B, ARS researchers continued collaborative research assessing how cultural practices and plant anatomy and phenology give insight into drought tolerance mechanisms and can be used to develop informed irrigation practices and selection of genotypes for different environments, including (1) completing trials evaluating differences in stem hydraulics, plant water use, and phenology of multiple cultivars and native plants; and (2) starting trials to evaluate whether induced polyploidy improves the ability of different genera to withstand water stress. A manuscript is in the process of being written for one study. Three peer-reviewed manuscripts and one trade journal manuscript were published. One manuscript was submitted to a peer- reviewed journal and one to a trade journal. In support of Sub-objective 1.C, and Sub-objective 2.B, ARS researchers reviewed the use of hazelnut and pear genotypic resources and developed two DNA fingerprinting sets that (1) distinguishes red currant, black currant, and gooseberries, and (2) identified potentially aphid-resistant seedlings in two black raspberry families. ARS researchers also developed two new DNA assays, including (1) in 272 red raspberry cultivars and identified 66 cultivars that need further investigation for identity confirmation, and (2) in hop that can distinguish female and male hop plants at the seedling level, and trained a USDA breeder in its application in the breeding program. Six peer-reviewed articles describing these studies were published. For Sub-objective 1.D, ARS researchers assisted the USDA initiative Breeding Insight in developing and testing a blueberry genotyping tool that can facilitate and speed up the development of cultivars with desired characteristics. ARS researchers participated in the development of genomic resources in blueberry and cranberry, that identified genes expressed across each of these crops as well as genes only expressed in some of the cultivars. They used this information to develop a genotyping tool for blueberry of greater than 22,000 markers that can identify chromosomal regions controlling traits that are measured in those same blueberry individuals and using the genotypic data for genome wide association for fruit texture and quality. Two peer-reviewed articles were published. In support of Sub-objective 2.E, ARS researchers distributed a total of over 3,500 accessions corresponding to 14,542 items, which included accessions of Mentha (78), Ribes (81), Actinidia (205), Sambucus (27), Fragaria (863), Humulus (379), Pyrus (653), Rubus (349), Vaccinium (715), and their wild relatives. Artificial Intelligence (AI)/Machine Learning (ML) Neither artificial intelligence (AI) or machine learning (ML) methods were used for this project during FY 2024. ACCOMPLISHMENTS 01 Affordable and convenient diagnostic assay to distinguish male and female hops. Hop cones, which are the end-product used in brewing beer, are produced exclusively by female hop plants. Plant breeders seeking to identify new and improved varieties of hop are primarily selecting among female plants. Prior to flowering male and female plants are visually indistinguishable and breeders typically wait one to two years for plants to mature to determine plant sex by observing floral structures. ARS researchers in Corvallis, Oregon, used a large collection of 855 hop lines with known sex, sequencing data, and association mapping to develop a DNA test that was shown to be 96% accurate in identifying hop sex. The marker is diagnostic, accurate, affordable, and highly scalable, and has the potential to improve efficiency in hop breeding. 02 A high density genotyping platform for blueberry. Blueberry is one of the most economically important berry crops in North America. The development of a standardized genotyping platform that targets a specific set of chromosomal regions can be a practical solution to unify the scientific and breeding community toward blueberry improvement. ARS researchers in Corvallis, Oregon, developed a genotyping platform that targeted 22,000 regions and yielded 194,365 DNA variants when assessed in a diversity set of 192 samples, including cultivated and other related wild species. This genotyping tool worked well across highbush and rabbiteye blueberry types. Phylogenetic analysis using a subset of the variants mostly conformed to known relationships. The platform also offers flexibility about the number of regions targeted as well as the depth of sequencing for accurate genotyping in a polyploid species like blueberry. This genotyping platform will accelerate the development and improvement of blueberry cultivars through genomic-assisted breeding tools. 03 A medium density genotyping platform for blueberry. Small public breeding programs have many barriers to adopting technology, particularly, creating and using genetic marker panels for genomic- based decisions in selection. ARS researchers in Corvallis, Oregon, collaborated with Breeding Insight on creating a panel of 3,000 loci distributed across the tetraploid blueberry genome for use in molecular breeding and genomic prediction. The creation of this marker panel brings cost-effective and rapid genotyping capabilities to public and private breeding programs. The open access provided by this platform will allow genetic data sets generated on the marker panel to be compared and joined across projects, institutions, and countries. This genotyping resource has the power to make routine genotyping a reality for any blueberry breeder. 04 A cost-efficient fingerprinting panel for red raspberry. A reliable and economic genotyping platform is needed to facilitate variety identification in red raspberry. DNA markers based on single nucleotide polymorphisms (SNPs), despite having lower diversity, are numerous across the genome and more easily converted to high-throughput assays restoring differential power. ARS researchers in Corvallis, Oregon, used the kompetitive allele-specific polymerase chain reaction (PCR) chemistry, an affordable and high-throughput platform, to develop a panel of these DNA markers to distinguish 272 red raspberry accessions for clonal identification. The panel consists of 48 markers that show high concordance with whole genome sequencing and recovery rate, as well as a minimal set of 24 markers that distinguished the same accessions differentiated by the larger panel. 05 Three parameters that predict post-storage texture in blueberry fruit. The shelf life of blueberry fruit depends on changes in fruit characteristics during storage such as texture. Since these changes affect consumer acceptance, breeders seek to understand factors that can predict extended shelf life in their new cultivars. ARS researchers in Corvallis, Oregon, collaborated on evaluating 20 mechanical texture parameters and four fruit appearance traits at harvest and six weeks post-storage in greater than 2,000 highbush blueberry plants. Post- storage changes were positively correlated with initial texture. Three of the 20 mechanical texture components contribute to blueberry texture. Selecting for high values for these three texture parameters and large size can contribute to select berries with better texture and appearance in post-storage. 06 A DNA test that identifies black raspberry plants. Black raspberry is a horticultural specialty crop of interest in North America. While the majority of black raspberry acreage is in Oregon and intended for the processing market, fresh market production occurs along the Ohio River Valley and the Great Lakes. Fourteen seedlings from two breeding families carrying aphid resistance growing in the field had lost their labels. Since these plants were highly productive for over nine years, they may be important sources of resistance to Black raspberry necrosis virus that can cause a shortened life span and small fruit size. ARS researchers in Corvallis, Oregon, developed a DNA-based fingerprinting set that could identify the two families to which these 14 field plants belong. A fingerprinting set of six DNA markers was optimized in a single test and identified nine plants that belong to one family and five to the other family. This black raspberry fingerprinting set of six DNA markers is economical, easy to use, and is a new tool for identity confirmation in black raspberry. 07 A fingerprinting test in currant and gooseberry. The USDA preserves a diverse collection of currants and gooseberries of more than 1,100 accessions from 41 countries. A cost effective DNA fingerprinting tool is needed to assist in managing the collection and identifying cultivars. ARS researchers in Corvallis, Oregon, developed a seven- marker fingerprinting set and used it to genotype 69 plants representing 53 accessions from the National Clonal Germplasm Repository (NCGR) collection. Genotyping identified: five cultivars with the same name but with different alleles; two genotypes with different names but the same fingerprint; two unknown accessions; and differences among suspected synonyms. This fingerprinting set accurately separated species and will provide another tool to better manage the botanical and horticultural identity of currant and gooseberry collections. 08 Developed a method for improving irrigation management based on plant anatomy and physiological and responses to drought. Trees in Oregon face increasing challenges from climate change, particularly commercially important trees in field cultivation. Stress resulting from the low soil moisture, high heat and low relative humidity resulting from the increasing frequency of heatwaves can scorch canopies and reduce growth, leading to decreased plant quality and economic losses for tree growers. To improve irrigation efficiency and achieve water conservation benefits without sacrificing plant quality, growers need to know how their trees respond to water deficits. ARS researchers in Corvallis, Oregon, collaborated on research to assess the physiological responses of field-grown trees to fluctuations in several environmental factors, such as soil moisture, atmospheric moisture, and temperature. Results revealed each species had distinctly different plant water management strategies. Optimizing irrigation management to address intrinsic differences in plant anatomy and hydraulic physiology among various types of trees can improve crop quality and reduce water use. Bridging knowledge gaps in plant hydraulic physiology can empower growers to adapt to evolving environmental conditions and ensure the resilience of tree production systems. 09 Quantified fungicide sensitivity of Phytopthora root rot in Red Raspberry to improve disease control measures. Phytophthora rubi is a harmful pathogen that causes root rot of red raspberries, resulting in plant death and significant yield losses. Fungicides have not been effective and there is concern about fungicide resistance. ARS researchers in Corvallis, Oregon, examined whether Phytophthora isolates collected from Red Raspberry fields were resistant to four fungicides. Most isolates were sensitive to all four fungicides, indicating that they should be effective for root rot management. However, ARS researchers in Corvallis, Oregon, determined that growers were likely applying the fungicides at the wrong rate, at the wrong time of year, or to the wrong part of the plant. Information will be used to optimize the best rates and methods for applying fungicides to achieve root rot control. 10 Leaf volatiles affect pathogenicity of foliar pathogens of a globally important ornamental crop, boxwood. Boxwood blight is an introduced fungal disease that affects the $141 million U.S. boxwood nursery industry. Research on the disease is hampered because spore germination is poor when the fungus is grown in the laboratory. ARS researchers in Corvallis, Oregon, collaborated on research to identify ways for improving spore germination. Results indicate that the presence of volatiles from leaves enhances spore germination. Results are important for improving research methods that require high germination rates and for developing boxwood blight disease control methods. 11 Evaluated the vulnerability of pear genetic resources in the United States. Pears represent an important part of consumer diets, and have the fourth highest production of non-citrus fruits, measured by fresh weight, in the United States. They are maintained clonally and grown as composite plants, consisting of a scion (fruit-bearing) cultivar grafted onto a rootstock cultivar. Up to 98% of existing production relies on only a few scion and rootstock cultivars, leaving the standing crop vulnerable to threats. Pears are faced with a wide range of biotic and abiotic threats and production vulnerabilities, some of which can be limited by integrating resistance and horticultural traits from wild and cultivated materials from around the world. ARS researchers in Corvallis, Oregon, collaborated with U.S. pear researchers in determining that the crop vulnerability status of pears in the United States is currently moderate to high, with increasing threats and challenges. 12 Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts. Molecular tools are needed to help guide breeding efforts for blueberry and cranberry. ARS researchers in Corvallis, Oregon, collaborated on developing and analyzing the first almost complete set of genes or 'pangenome' for both blueberry and cranberry. Their analysis of these pangenomes revealed that both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Genes that are not shared by all cultivars, are significantly enriched with functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. 13 An intersectional hybrid between Darrow�s blueberry and lingonberry. There is a need to introduce new species germplasm into commercial highbush blueberry for improvement of blueberry fruit quality and resistance to abiotic stress. In order to develop breeding schemes to accomplish this, the breeding community needs to understand the breeding behavior and potential crossing barriers between genetically distant blueberry species. In evaluating species crossability, ARS researchers in Corvallis, Oregon, collaborated in making hybrids between Darrow�s blueberry and lingonberry. The fertility of the best of these hybrids was extensively evaluated. Both male and female fertility were found to be low; however, a small number of backcross hybrids were generated. These hybrids may allow the introgression of this germplasm into commercial highbush blueberry and/or allow the production of improved lingonberries. This information will be of interest to researchers and breeders of blueberry and lingonberry. 14 Unique anthocyanin profile identified for wild blueberry from Ecuador and the Philippines. The global demand for blueberry fruit exceeds the current supply and is projected to keep increasing for the foreseeable future. While U.S. blueberry cultivars dominate the international market, indigenous and local peoples in tropical and subtropical regions where blueberry species are native have gathered wild blueberry fruit from native stands. The Filipino �ayusep� and the Ecuadorian �morti�o� are important sources of income and nutrition in specific highland communities. Understanding the physical and chemical traits of subtropical and tropical blueberries can help plant breeders and researchers diversify the crops grown for local incomes and expand the cultivated range for domestic blueberries and related crops. ARS researchers in Corvallis, Oregon, evaluated fruit from these wild blueberry species. While fruit size and sugar content were comparable to that of the cultivar O�Neal, anthocyanin content was significantly higher in these species which also had unique profiles. 15 Altering fertilizer management in the face of a changing environment. Control release fertilizers (CRF) are used in the production of both container grown and field crops. Fertilizer release determined by manufacturers do not correlate well with release in production situations because of daily and seasonal environmental fluctuations. CRF materials may become less predictable given the temperature variability associated with climate change. ARS researchers in Corvallis, Oregon, collaborated on research that documented CRF release during a recent unprecidented early season heat wave in Oregon. Results highlight the impact that heatwaves can have on nutrient delivery by CRF and indicate that adaptation strategies for managing fertilizer may be necessary given the likelihood that extreme temperatures will continue to impact horticultural production systems for years to come. 16 Use of manufacturing byproducts to improve soil health. The use of waste byproducts in agriculture can contribute to broader environmental sustainability goals, such as reducing waste and greenhouse gas emissions. ARS researchers in Corvallis, Oregon, collaborated on research to investigate the potential of using tectonite dust, a mineral byproduct of composite manufacturing, as a soil amendment to enhance soil fertility and water-holding capacity. Results indicated amendment with tectonite improved early plant growth and establishment as well as yield by enhancing soil health (improved structure, nutrient availability, and water retention). This study highlights how agricultural use of byproducts from manufacturing processes can improve environmental and economic sustainability. Tectonite has the potential to play a significant role in addressing water scarcity and enhancing crop productivity in arid regions like central Oregon.
Impacts
(N/A)
Publications
- Yocca, A., Platts, A., Alger, E., Teresi, S., Mengist, M., Benevenuto, J., Ferrao, L., Jacobs, M., Babinski, M., Magallanes-Lundback, M., Bayer, P., Golicz, A., Humann, J., Main, D., Espley, R., Chagne, D., Albert, N., Montanari, S., Vorsa, N., Polashock, J.J., Diaz-Garcia, L., Zalapa, J.E., Bassil, N.V., Munoz, P., Iorizzo, M., Edger, P. 2023. Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts. Horticulture Research. 10(11). Article uhad202. https://doi.org/ 10.1093/hr/uhad202.
- Nackley, L., Van Lehman, L., Van Lehman, O., Owen Jr., J.S., Scagel, C.F. 2024. Investigating the benefits of tectonite dust as an amendment for bark substrates and dryland crops. Plants. 13(1). Article 126. https://doi. org/10.3390/plants13010126.
- Park, H.E., Nebert, L., King, R., Busby, P., Myers, J.R. 2023. Influence of organic plant breeding on the rhizosphere microbiome of common bean (Phaseolus vulgaris L.). Frontiers in Plant Science. 14. Article 1251919. https://doi.org/10.3389/fpls.2023.1251919.
- Clare, S.J., Driskill, M., Millar, T.R., Chagne, D., Montanari, S., Thomson, S., Espley, R.V., Munoz, P., Benevenuto, J., Zhao, D., Sheehan, M. , Mengist, M.F., Rowland, L.J., Ashrafi, H., Melmaiee, K., Kulkarni, K.P., Babiker, E.M., Main, D., Olmstead, J.W., Gilbert, J.L., Havlak, P., Hung, H., Kniskern, J., Percival, D., Edger, P., Iorizzo, M., Bassil, N.V. 2024. Development of a targeted genotyping platform for reproducible results within tetraploid and hexaploid blueberry. Frontiers in Horticulture. 2. Article 1339310. https://doi.org/10.3389/fhort.2023.1339310.
- Mengist, M.F., Pottorff, M., Mackey, T.A., Ferrao, F., Casorzo, G., Lila, M., Luby, C., Giongo, L., Perkins-Veazie, P., Bassil, N.V., Munoz, P., Iorizzo, M. 2024. Assessing predictability of post-storage texture and appearance characteristics in blueberry at breeding population level. Postharvest Biology and Technology. 214. Article 112964. https://doi.org/ 10.1016/j.postharvbio.2024.112964.
- Anderson, T., Durst, R., Leonard, S., Hummer, K., Luby, C., Bassil, N.V. 2023. Anthocyanin profiles of two subtropical Vaccinium species and �O�Neal� southern highbush blueberry. Journal of the American Pomological Society. 77(3): 176-185.
- Bassil, N.V., King, R., Nyberg, A.M., Zurn, J., Clare, S.J., Reinhold Aboosaie, L.A., Postman, J., Gilmore, B., Flores, G.N., Volk, G.M., Jenderek, M.M., Montanari, S., Chagne, D., Bus, V., Brewer, L., Dardick, C. D., Gottschalk, C.C., Durel, C., Denance, C. 2023. Progress on the molecular characterization of the USDA National Pear Collection. Acta Horticulturae. 1384:273-280. https://doi.org/10.17660/ActaHortic.2023.1384. 36.
- Bassil, N.V., King, R., Peterson, M.E., Dossett, M., Hardigan, M.A. 2024. A black raspberry fingerprinting set identifies seedlings in two families. Acta Horticulturae. 1388:115-120. https://doi.org/10.17660/ActaHortic.2024. 1388.16.
- Bassil, N.V., Mehlenbacher, S. 2023. DNA markers in hazelnut: A progress report. Acta Horticulturae. 1379:61-72. https://doi.org/10.17660/ ActaHortic.2023.1379.10.
- Bushakra, J., Alvarez, A., King, R., Green, J., Nyberg, A.M., Bassil, N.V. 2024. Developing a single sequence repeat (SSR) fingerprinting set to characterize the NCGR Ribes Collection. Acta Horticulturae. 1388:107-114. https://doi.org/10.17660/ActaHortic.2024.1388.15.
- Clare, S.J., King, R., Hardigan, M.A., Dossett, M., Montanari, S., Chagne, D., Ochsenfeld, C., Britton, C., Rapp, R., Bassil, N.V. 2023. Development of KASP fingerprinting panel for clonal identification in red raspberry (Rubus idaeus L.). Plant Breeding. 142(6):798-808. https://doi.org/10.1111/ pbr.13141.
- Clare, S.J., King, R., Tawril, A., Havill, J.S., Muehlbauer, G.J., Carey, S., Harkess, A., Bassil, N.V., Altendorf, K.R. 2023. An affordable and convenient diagnostic marker to identify male and female hop plants. G3, Genes/Genomes/Genetics. 14(1). Article jkad216. https://doi.org/10.1093/ g3journal/jkad216.
- Ehlenfeldt, M.K., Bassil, N.V., Zalapa, J.E., De La Torre, F., Luteyn, J.L. 2024. An intersectional hybrid between Darrow�s blueberry (V. darrowii Camp) and lingonberry (V. vitis-idaea L.). Plants. 13(11):1572. https:// doi.org/10.3390/plants13111572.
- Giongo, L., Ajelli, M., Pottorff, M., Coe, K., Perkins-Veazie, P., Bassil, N.V., Hummer, K.E., Farneti, B., Iorizzo, M. 2023. Comparative study on texture: A key for blueberry quality breeding. Acta Horticulturae. 1357:107-114. https://doi.org/10.17660/ActaHortic.2023.1357.16.
- Hummer, K.E., Bramel, P., Bassil, N.V. 2023. Berry genetic resources: Decades of global conservation. Acta Horticulturae. 1381:27-36. https:// doi.org/10.17660/ActaHortic.2023.1381.4.
- Iorizzo, M., Lila, M., Perkins-Veazie, P., Luby, C.H., Vorsa, N., Edger, P. , Bassil, N.V., Munoz, P., Zalapa, J.E., Gallardo, R.K., 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.
- Ohkura, M., Beck, B.R., Scagel, C.F., Weiland, G.E. 2024. The effect of boxwood leaf volatiles on conidial germination of Calonectria pseudonaviculata, the causal agent of boxwood blight. Phytopathology. https://doi.org/10.1094/PHYTO-12-23-0507-R.
- Montanari, S., Deng, C., Koot, E., Bassil, N.V., Zurn, J.D., Morrison- Whittle, P., Worthington, M.L., Aryal, R., Ashrafi, H., Pradelles, J., Wellenreuther, M., Chagne, D. 2023. A multiplexed plant-animal SNP array for selective breeding and species conservation applications. G3, Genes/ Genomes/Genetics. 13(10). Article jkad170. https://doi.org/10.1093/ g3journal/jkad170.
- Nackley, L., Mccauley, D., Scagel, C.F. 2023. Hot mess: Heatwave effects on controlled-release fertilizer. HortScience. 58(11):1459-1460. https:// doi.org/10.21273/HORTSCI17325-23.
- Weiland, G.E., Scagel, C.F., Benedict, C., Wasko DeVetter, L., Beck, B.R. 2024. Fungicide sensitivity of Phytophthora isolates from the Washington red raspberry industry. Plant Disease. 108(7):2104-2110. https://doi.org/ 10.1094/PDIS-12-23-2641-RE.
- Zhao, D., Sapkota, M., Glaubitz, J., Bassil, N.V., Mengist, M., Iorizzo, M. , Heller-Uszynska, K., Mollinari, M., Beil, C., Sheehan, M. 2024. A public mid-density genotyping platform for cultivated blueberry. Genetic Resources and Crop Evolution. 5(9):36-44. https://doi.org/10.46265/genresj. WQZS1824.
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Progress 10/01/22 to 09/30/23
Outputs
PROGRESS REPORT Objectives (from AD-416): Objective 1: Conduct research to develop genetic resource maintenance, evaluation, or characterization methods and, in alignment with the overall National Plant Germplasm System (NPGS) Plan, apply them to priority temperate-adapted fruit, nut, and other specialty crop genetic resources to avoid backlogs in plant genetic resources and information management. Sub-objective 1.A: Building on the data and information included in the NPGS Plan to develop and implement a detailed plan for conducting research to develop methods for effectively addressing backlogs in accession regeneration, backup, germination/viability testing of seeds, pathogen-testing and �clean-up�, record digitizing, trait evaluation and characterization, and upload all data to GRIN-Global. Sub-objective 1.B: Develop improved methods for conserving temperate crop germplasm in field plantings and container production in protected environments. Sub-objective 1.C: Expand the DNA genetic marker databases of Fragaria, Pyrus, Corylus, Vaccinium, Rubus, and Humulus, with existing DNA fingerprinting sets and develop or optimize fingerprinting sets for genotyping other genera, and enter information to GRIN-Global. Sub-objective 1.D: Implement targeted and/or high-throughput genotyping systems for genome-wide association and linkage and trait mapping in Vaccinium and Fragaria, core collection establishment in Rubus and Pyrus, development of Fire blight resistance markers in Pyrus, and enter information to GRIN-Global. Sub-objective 2.E: Provide support for data collection, management, and analysis from phenotyping evaluations that add value to NCGR small fruit genetic resources, and that enhance the development and commercialization of new blueberry, caneberry, and strawberry cultivars. Objective 2: Acquire, distribute, and maintain the safety, genetic integrity, health, and viability of priority temperate-adapted fruit, nut, and other specialty crop genetic resources and associated descriptive information. Sub-objective 2.A: Acquire international and domestic germplasm samples of Corylus, Fragaria, Humulus, Pyrus, Mentha, Ribes, Rubus, Vaccinium, and their crop wild relatives via plant exploration and exchange. Sub-objective 2.B: Establish and maintain crop genetic resources emphasizing temperate fruit, nut, and specialty crop germplasm (both cultivated and crop wild relatives). Apply established genetic marker tools to identify duplication and eliminate unnecessary redundancy to maximize efficient germplasm management. Sub-objective 2.C: Collaborate with other genebank sites to implement backup conservation methods for our eight primary genera, including growing plants in field plantings and long-term cryopreservation. Sub-objective 2.D: Apply bioassay, ELISA, and PCR tests for detecting known virus, viroid, and phytoplasma pathogens in primary plant collections. Eliminate pathogens from selected accessions with improved methods for heat therapy and meristem culture. Sub-objective 2.E: Distribute germplasm during the appropriate season for each crop to national and international researchers at public, private, and educational bodies. Approach (from AD-416): Objective 1: 1.A: Develop research plans for preventing backlog and for fast tracking conservation activities described in the NPGS plan using a collaborative and multi-step approach. Preventing losses to accessions and records is the number one NCGR priority. 1.B: Establish improved conservation methods upon and after transition to new screenhouse design, which include a fully automated control of environmental conditions to maximize winter chilling/dormancy and mitigate excessive summer heat while providing effective exclusion of aphids and other virus vectors. 1.C: Expand existing molecular databases for hazelnut, blackberry, blueberry, pear, and hop and develop new databases/tests for raspberry, currant, gooseberry and mint. 1.D: Apply/develop high throughput genotyping techniques to: conduct genome wide association studies (GWAS) for fruit quality in blueberry and strawberry; establish core collections in red raspberry, pear, wild strawberry, and cranberry; and to develop a DNA test for fireblight in pear. Objective 2: 2.A: Acquire samples of Corylus, Fragaria, Humulus, Pyrus, Mentha, Ribes, Rubus, Vaccinium, and their related pome fruits from North America, North Africa, Central Asia, Asia, and Northern Europe to fill current gaps in NPGS collections as described in the Crop Vulnerability Statements. 2.B: Efficiently maintain genetic integrity and diversity of germplasm prioritizing five genera: Corylus, Fragaria, Pyrus, Rubus, and Vaccinium. 2.C: Establish security backup for the accessions in our collections using whole-plant local clonal backup, whole-plant remote clonal backup, tissue culture and/or cryopreservation where possible, and as seed. 2.D: Develop and implement a pathogen testing scheme for field and for screenhouse/greenhouse-grown germplasm. 2.E: Distribute genetic resources through the GRIN-Global online order processing under the NPGS conditions of distribution. This report documents progress for project 2072-21000-059-000D, Conservation and Utilization of Temperate-Adapted Fruit, Nut, and Other Specialty Crop Genetic Resources, which started February 2023 and continues research from project 2072-21000-049-000D, Management of Temperate-Adapted Fruit, Nut, and Specialty Crop Genetic Resources and Associated Information. The USDA ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, is a genebank that conserves temperate fruits, nuts, and specialty crops for research. The genebank continues to conserve more than 12,700 unique plant specimens of eight genera of horticultural and agronomic crops along with their wild relatives. This genebank is assigned to conserve hazelnuts, strawberries, hops, mint, pears, currants, gooseberries, blackberries, raspberries, blueberries, and cranberries. The primary collections are a library of living plants, maintained as orchards in the field, containerized plants in the screenhouse, or seeds representing species populations. Seeds are preserved in freezers on-site and off-site in Fort Collins, Colorado, and Spitsbergen, Norway. Valuable or vulnerable accessions are backed up as dormant buds or shoot apices under cryogenic conditions at a collaborating site in Fort Collins, Colorado. A subset of the hazelnut collection is planted in collaboration at an ARS site in Parlier, California. In addition, duplicate collections of kiwifruit and butternuts are planted in Corvallis, Oregon, for the ARS Davis, California, genebank and of rhubarb for the ARS genebank Pullman, Washington. In support of Objective 1, NCGR staff constructed six temporary structures and moved the container collections of strawberry, caneberry, and blueberry from the five screenhouses that were recently demolished in preparation for replacement by new automated screenhouses. The mint and hop collections were moved to an existing greenhouse that is not being used by ARS researchers from the Horticultural Crops Production and Genetic Improvement Research Unit (HCPGIRU). Drip irrigation and shading were established for over 5,000 plants that are being housed in these temporary structures. A new DNA test was developed for red raspberry and was used to fingerprint 272 plants from the NCGR collection. This test identified 66 cultivars that need further investigation for identity confirmation. A new breeder-friendly DNA test was also developed for identifying male/female hop plants. In blueberry a genotyping platform that can assay over 22,000 chromosomal regions was developed and is being used by ARS researchers as well as other blueberry researchers in the United States, France, New Zealand and Italy. ARS scientists described plant specimen of mountain ash available through the National Plant Germplasm system and contributed four success stories to the U-GRIN (Germplasm Resources Information Network) online educational platform about plant specimen at the Corvallis, Oregon, genebank that have met critical agricultural needs. These plants include: �Monocacy� hop, a unique plant from �Maryland that initiated the brewing of three local beers; �Florida 4B�, a plant from Florida that is the founder of southern highbush blueberries; �Perpetua� and �Echo� blueberries, reflowering ornamental plants for northern climates which provide a new market class for this fruit crop; and �Gasaway� hazelnut, the source of resistance to Eastern Filbert Blight disease and a cultivar that saved the Oregon hazelnut industry. In support of Objective 2, ARS researchers in Corvallis, Oregon, collaborated with ARS scientists at Fort Collins, Colorado, to back-up important pear, currant, and gooseberry trees/plants through cryopreservation of dormant buds. More than 1,000 plant specimens were distributed to stakeholders from Australia, Belgium, Canada, France, Germany, the Netherlands, the United Kingdom and the United States for research purposes. ACCOMPLISHMENTS 01 New genebank educational resources for blueberry, hop, and hazelnut plants to meet critical agricultural needs. The National Clonal Germplasm Repository in Corvallis, Oregon, preserves plants that contribute needed traits to the industries they serve. Plant genebank personnel, educators, breeders, and conservationists need accessible training resources to better use genebank resources. ARS researchers in Corvallis, Oregon, developed new educational resources for an ebook educational platform that is publicly available and publishes topics related to plant genetic resources management and use. Information included success stories about the genebank use to meet critical agricultural needs, including �Monocacy� hop, a unique plant from Maryland that initiated the brewing of three local beers; �Florida 4B�, a plant from Florida that is the founder of southern highbush blueberries; �Perpetua� and �Echo� blueberries, reflowering ornamental plants for northern climates which provide a new market class for this fruit crop; and �Gasaway� hazelnut, the source of resistance to Eastern Filbert Blight disease and a cultivar that saved the Oregon hazelnut industry. 02 Unravelling the complexity of mountain ash (Sorbus), a plant with unfulfilled crop potential. Mountain ash (Sorbus) and its close relatives are valuable trees for ornamental landscape uses and provide fruits that can be utilized for food, medicinal, and beverage purposes. Potential improvement of Sorbus to expand its use is hampered by its genetic complexity and lack of quantitative evaluation of genetic resources conserved in plant repositories. ARS researchers in Corvallis, Oregon, led efforts to describe Sorbus species conserved at National Clonal Repository Germplasm in Corvallis, Oregon, and the Woody Landscape Germplasm Repository at the U.S. National Arboretum in Washington, D.C. This information provides a historical context to the complex nature of the Sorbus and its relatives and a framework for future directions of Sorbus conservation and use that will be useful for genetic conservation and future breeding efforts.
Impacts
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Publications
- King, R., Bassil, N.V., Rounsaville, T.J., Reinhold, L.A. 2023. Sorbus sensu lato: A complex genus with unfulfilled crop potential. Journal of the American Pomological Society. 77(2):110-127.
- Bassil, N.V., Lewers, K.S. 2023. Hop �Monocacy� � Northeastern adaptation. In: Volk, G.M., Chen, K., Byrne, P., editors. Plant Genetic Resources: Success stories. Fort Collins, CO: Colorado State University. Available: https://colostate.pressbooks.pub/pgrsuccessstories/chapter/hop-monocacy- northeastern-adaptation/.
- Bassil, N.V., Oliphant, J.M., Munoz, P. 2023. Blueberry Florida 4B � Southern production. In: Volk, G.M., Chen, K., Byrne, P., editors. Plant Genetic Resources: Success stories. Fort Collins, CO: Colorado State University. Available: https://colostate.pressbooks.pub/pgrsuccessstories/ chapter/blueberry-florida-4b-southern-production/.
- King, R., Bassil, N.V. 2023. Blueberry 'Perpetua' and 'Echo' - Repeat flowering. In: Volk, G.M., Chen, K., Byrne, P., editors. Plant Genetic Resources: Success stories. Fort Collins, CO: Colorado State University. Available: https://colostate.pressbooks.pub/pgrsuccessstories/chapter/ blueberry-perpetua-and-echo-repeat-flowering/.
- Bassil, N.V., Mehlenbacher, S. 2023. Hazelnut �Gasaway� � EFB resistance. In: Volk, G.M., Chen, K., Byrne, P., editors. Plant Genetic Resources: Success stories. Fort Collins, CO: Colorado State University. Available: https://colostate.pressbooks.pub/pgrsuccessstories/chapter/hazelnut- gasaway-efb-resistance/.
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