Source: NORTH CAROLINA STATE UNIV submitted to
VACCINIUMCAP: LEVERAGING GENETIC AND GENOMIC RESOURCES TO ENABLE DEVELOPMENT OF BLUEBERRY AND CRANBERRY CULTIVARS WITH IMPROVED FRUIT QUALITY ATTRIBUTES
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
NEW
Funding Source
Reporting Frequency
Annual
Accession No.
1020223
Grant No.
2019-51181-30015
Project No.
NC09879
Proposal No.
2019-03177
Multistate No.
(N/A)
Program Code
SCRI
Project Start Date
Sep 1, 2019
Project End Date
Aug 31, 2023
Grant Year
2019
Project Director
Iorizzo, M.
Recipient Organization
NORTH CAROLINA STATE UNIV
(N/A)
RALEIGH,NC 27695
Performing Department
Horticultural Science
Non Technical Summary
This project will establish a nationwide coordinated transdisciplinary research approach to develop and implement marker assisted selection (MAS) capacity in Vaccinium breeding programs, to enable breeders to select and pyramid fruit characteristics (FCs) that positively contribute to fruit quality and market value. Vaccinium crops (blueberry and cranberry) provides vital contributions to human health and well-being, and collectively constitutes the economic backbone of many U.S. rural communities. Vaccinium genetic and genomic resources are developing rapidly but have not been translated to routine practical application. Specific objectives are to: (1) establish a cost effective genotyping platform to expand marker-trait association analysis (MTA) in Vaccinium, exploiting the shared ancestry of Vaccinium crops; (2) identify DNA markers linked to fruit characteristics and elucidate how and which fruit characteristics affect fruit quality, relative to consumer preferences, decay during mechanical harvest, processing and distribution; (3) develop DNA assays to implement MAS in core Vaccinium core breeding programs with a common focus on fruit quality traits; (4) enlarge market potential, and increase consumption of Vaccinium fruits by using socio-economic knowledge of consumer preferences to inform breeding; and (5) enhance sustainability of cultivar development by transferring MAS technologies to public and private U.S. Vaccinium breeding programs through training current and future breeders as well as engaging the production, distribution, processing and marketing sectors, allied scientists, and consumers. This Coordinated Agricultural Project proposal addresses SCRI Focus Area 1 (70%) and Focus Area 2 (30%).
Animal Health Component
0%
Research Effort Categories
Basic
40%
Applied
5%
Developmental
55%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011120108130%
2011121108130%
6071120309010%
2041120100010%
2041121100010%
5031120102010%
Goals / Objectives
Status: Vaccinium (blueberry and cranberry) breeders have little empirical data to assign level of importance to fruit characteristics (FCs) relative to consumer preferences, decay during production, processing and distribution, and few tools to select for high fruit quality. As a result, blueberry and cranberry cultivars often produce fruit with inconsistent appearance, texture and sensory profiles that do not consistently meet consumer expectations, processing and production quality needs. The Vaccinium industry recognized the need to improve fruit quality as the key breeding target for continued success.Mission statement: Address major bottlenecks for growth of U.S. Vaccinium industry, by creating a nationwide coordinated transdisciplinary research approach to develop and implement marker assisted selection (MAS) capacity in Vaccinium breeding programs, to enable breeders to select and pyramid fruit characteristics (FCs) that positively contribute to fruit quality and market value. In the long term, this mission will increase production of fruit with improved characteristics that meet the ever-changing industry, market, and consumer preferences.Specific project objective are: 1) Establish genomic resources to enable effective association mapping studies in blueberry and cranberry; 2) Discover DNA markers and fruit characteristics that maximize industry profitability and match consumer preferences in blueberry and cranberry; 3) Deliver molecular and genetic resources to improve blueberry and cranberry fruit quality traits that maximize industry profitability and match consumer preferences; 4) Assess the potential socio-economic impact of blueberry and cranberry fruit quality improvements on market demand; 5) Engage U.S. Vaccinium breeders and stakeholder groups to transfer advanced phenomics and genomics tools to build a more coordinated and efficient cultivar development system.
Project Methods
Obj. 1.The comparative genomic team will use a selected set northern highbush (NHB), southern highbush (SHB) and cranberry (CB), to assemble the pangenome that is aimed at identifying the core and dispensable portions of the genome. The core genome represents genes shared by all genotypes, whereas the dispensable portion includes the genes present only in a subset of the genotypes. Core genomes will be compared to identify the core genes shared by NHB, SHB, and CB. The genotyping team will use the pangenome as a reference to identify SNPs, test and validate a cost-effective high-throughput genotyping platform.Obj. 2.The statistical genetics and phenomic teams (blueberry and cranberry) will use high-throughput genotyping platform and phenomic approaches to identify alleles for fruit characteristics (chemical composition, texture, and appearance) by QTL and GWAS analysis. The fruit quality team will use a pre-selected set of blueberry cultivars to identify blueberry FC sub-components (eg. firmness, sugars) that contribute to extended shelf life, meeting consumer preferences and to reduce bruising damages during mechanical harvest. This outcomes, will allow us to establish a link between DNA markers associated with FCs, and fruit quality attributes.Obj. 3. The statistical genetic team will validate FC-QTLs across multiple genetic backgrounds. Validated FC-QTLs will be used as a target site to develop and validate a high-throughput affordable assay for Vaccinium FCs, that can be used to implement marker assisted selection (MAS). The breeding teams will use validated SNPs to identify breeding parents and 'pyramid' multiple positively associated markers into superior genotypes. Multiple superior FCs allele donors, and F1 progenies with pyramided FC alleles will be made available to breeders U.S.-wide.Obj. 4.The socio economic team will combine blueberry sensory tests and choice experiments, biometrics parameters and willingness to pay elicitations to identify FCs and sensory characteristics that affect (positively and/or negatively) purchasing behavior. For cranberry, an online survey and a choice experiment will be conducted with a representative sample of U.S. consumers to (a) quantify consumerss discount for cranberry products with an "added-sugar" line on the nutrition facts panel label, (b) measure heterogeneity in responses across consumer segments, and (c) evaluate the effect of information framing. The results will be used to assess consumers' accuracy in evaluating sugar content and evaluate how this affects purchase intent and willingness to pay.Obj. 5.The Extension team and the Data Management teams, in collaboration with all project participants will develop multiple outreach activities/tools (on-line platforms, webinars, workshops, forums, coomodity group meetings) to engage Vaccinium stakeholders by: 1) transferring and training them on project deliverables, 2) educating them about project outcomes, 3) fostering new collaborations, and 4) soliciting feedback on the project to fine-tune research and extension activities. Target stakeholders are national and international blueberry and cranberry partners that represent breeders, researchers (breeder's allied scientists), mentees/trainees (staff, mentored students and post docs), extension specialists, industry stakeholders (producers, processors, distributors, and nurseries), as well as the members of the Advisory Panel (AP) that represent these audiences. An external evaluator will work with the Project Management and Extension Teams to regularly gather, analyze, and interpret feedback from breeders and extension audiences, including systematic collection of input on project goals, activities, progress, mid-course corrections, and communication and extension strategies.

Progress 09/01/20 to 08/31/21

Outputs
Target Audience:Blueberry and cranberry breeders; post-harvest physiologists, food scientists, germplasm collection curators, molecular geneticists, and other allied scientists of these crops; nurseries, producers, processors, marketers, and marketing organizations of Vaccinium crops; and consumers of these crops. Changes/Problems:Obj. 1 Due to COVID-19 and delay of funding release from the USDA-NIFA during Year 1 the following activities were not performed as planned: Sequencing of the transcriptome from 12 cranberry samples was delayed resulting in a delay in downstream analysis (finalize the pan-genome construction) and developing the cranberry SNP catalog was delayed (Obj. 1b-c). Activities that were delayed have already restarted and will be completed in Year 3. To compensate for some of the impacted activities, team members completed complementary activities including finalizing linkage maps and new genomes and performing comparative analysis to improve the quality of the available genomes by the Comparative Genomics Team. Obj. 2 Given that the NIR method for organic acids was not predictive and that evaluating organic acids (OA) by HPLC in very large number of samples is not feasible, the Fruit Quality and Statistical Genetic Teams are considering evaluating OA in a mapping population and a subset of the GenStudy set. For Obj. 2c, the original plan was to use the 20 NHB and 20 SHB cultivars from Florida and Oregon (named OR and FL FqStudy Set) to perform shelf life and bruising analysis in addition to the sensory tests. Difficulties due to COVID-19 to get undamaged fruit led to using NC material for shelf life and bruising analysis instead (NC-FqStudy set). Due to COVID-19, transplanting of the cranberry diversity panel at Dr. Vorsa location had to be postponed, delaying phenotyping FCs in this material. New activities were developed to address year 1-2 challenges and AP recommendations. To ensure success of the genetic studies and expand our capacity to detect and validate QTLs across studies, additional materials including four mapping populations and a new cranberry diversity panel were added to the project for genetic studies. Additional work to evaluate fruit cluster and how it affects mechanical harvest was performed by Dr. Li, complementary with VacCAP objectives. Obj. 3 Due to COVID-19 some activities related to Obj. 3a were delayed. However the team anticipated to year 1-2 beginning of activities associated with the development and validation of DNA assay. Obj. 5 Due to COVID-19, some activities were not performed as planned: Workshops that were to be held at the International Vaccinium Symposium (ISHS) were delayed, since the symposium has been postponed to 2024. Due to a logistical delay of the development of the pangenome, the webinar on pangenome was also postponed. Engagement with the public and commodity groups was limited due to shutdown of physical meetings due to COVID-19. To address these challenges, workshops will be held at our next annual meeting in 2022, and we will continue to develop training videos for new methodologies developed by the team. Grower engagement at meetings and conferences will be done in a hybrid model with both virtual and in-person presentations. Outreach to the general public may simply be limited due to the unique situation from Covid-19, but we will continue to advertise, educate, and promote our project where and when feasible. What opportunities for training and professional development has the project provided?Project participants include 6 post-doctoral associates and 12 technicians, 13 graduate students and undergraduate students fully or partially funded by the project across all the VacCAP team programs. These trainees and technicians are participating in VacCAP activities of phenotyping, genomic analysis, DNA profiling, development of DNA-informed breeding strategies, data management and communication. These personnel are gaining knowledge, experience, and skills in accurate measurement of fruit characteristics, fruit physiology, phenotyping engineering, quantitative genetics, bioinformatics, design and implementation of genetic tests, and breeding program planning and management. In addition, these participants are members of project Teams and undertake targeted training through webinars, workshops and one to one in person training on texture analysis. How have the results been disseminated to communities of interest?Updates about the VacCAP project, and preliminary results were disseminated to the scientific community, including the U.S.-wide community of Vaccinium crop breeders, through 14 peer reviewed publications, 27 posters and oral presentations at regional, national and international conferences (including American Society of Horticultural Science and International Vaccinium Symposium). The information was also disseminated to the broader Vaccinium community (producers, processors and distributors) through 15 oral presentations at commodity group meetings and 8 VacCAP/GDV newsletter articles, and participation to a blueberry podcast series. Two workshops, two webinars and two instructional video were delivered to transfer project outcomes/deliverables. Stakeholders and the more general public were also engaged by feeding project updates and new information related to the project mission through two web sites (VacCAP and GDV) and tweeter account (@VacciniumCAP). To engage the public and students, VacCAP PIs, participated in and/or organized four outreach events targeting K12, middle, high schools, and college students including students representing minorities. Events include blueberry and cranberry field days, science fairs, and short lab training classes. Outreach activities aimed at introducing students to plant science and horticulture, food science, scientific lab experience based on protocol/research. All these activities placed specific attention on the importance on the central role of breeding for blueberry and cranberry productions but also more general crop productions. Lab activities include DNA extraction, PCR, basic chemistry analysis (eg. pH, Brix) and sensory analysis. These events contribute to enhance public understating and interest in learning and careers in plant science, and more specifically plant breeding. What do you plan to do during the next reporting period to accomplish the goals?Objective 1. Establish genomic resources to enable effective association mapping studies in blueberry and cranberry. Finalize sequencing of CB transcriptome and genome annotation for all cranberry genotypes Finalize construction of the pangenome (blueberry-specific, cranberry-specific, and pan-Vaccinium) and identify cultivar-specific genes associated with fruit quality Initiate and finalize compilation of cranberry SNPs catalog Finalize selection of 50,000 probes to use in the testing phase for blueberry and cranberry Complete testing phase for blueberry and initiate genotyping Initiate and complete testing phase for cranberry Objective 2. Discover DNA markers and fruit characteristics that maximize industry profitability and match consumer preferences in blueberry and cranberry; Complete phenotyping GenStudy, FqStudy sets and analyze year 1 and 2 phenotypic data; Complete cell wall analysis in blueberry post-harvest; Continue testing new protocols and evaluate new traits in GenStudy and FqStudy sets Perform QTL mapping in biparetnal populations Objective 3. Deliver molecular and genetic resources to improve blueberry and cranberry fruit quality traits that maximize industry profitability and match consumer preferences; Complete phenotyping ValStudy sets and analyze year 1 and 2 phenotypic data; Continue testing protocols for simple DNA assay on a set of existing FC-QTLs; Analyze blueberry DNA assay data (KASP) Test DNA assays for MA and CA developed for cranberry in more diverse populations to evaluate sensitivity and specificity Validate performance of genotypes selected during year 1-2 for advancing them into trial or to use as a parent in new crosses Plant seedlings in nurseries so they are evaluated for their potential contribution to FC Objective 4. Assess the potential socio-economic impact of blueberry and cranberry fruit quality improvements on market demand. Select plant material, and finalize experimental design for second year blueberry sensory panels that includes WTP elicitation. Finalize the analyses of the data collected in year 2 and prepare manuscripts for dissemination of results. Select plant material, and finalize experimental design for evaluating consumer behavior response to fruit tasting pricing using biometric parameters study Finalize the data analyses collected during year 2 to estimate consumers' reactions to "added-sugar" labelling and labelling information in cranberry products Objective 5. Engage U.S. Vaccinium breeders and stakeholder groups to transfer advanced phenomics and genomics tools to build a more coordinated and efficient cultivar development system On-line platforms: Update VacCAP and GDV, and train core and non-core labs on GDV through new training video. Develop a second issue of the GDV newsletter to update national and international partners on new tools and resources available on GDV. Newsletter and other media: release two newsletters; publish articles in trade magazines; maintain VacCAP accounts on social media; Webinars: deliver three webinars; Blueberry volatiles; Pangenome; Firmness and texture in blueberry and cranberry; Workshops: deliver two in-person workshops/trainings focusing on Fruit texture and quality analysis Develop instructional videos that will be posted on the project website and YouTube channel, and distributed to our audience through our newsletter and social media posts. These videos will feature the use of new methodologies for fruit quality phenotyping developed by our team members, as well as evaluation and comparisons of equipment available to stakeholders. In conjunction with the training videos, and when applicable, PDF files with step-by-step protocols will be available on our website. Commodity group meetings: disseminate progress and results to commodity group meetings. Annual meeting: organize the VacCAP annual meeting (possibly in person) Continue to engage and educate the general public about the project outcomes and impacts through outreach activates our website, newsletter, and social media. Project evaluation: continue project evaluation activity to improve communication and effectiveness of extension activities.

Impacts
What was accomplished under these goals? Obj. 1. Expanded Genomic resources. A bilberry and 2 cranberry genomes were released, and enabled identification of genes controlling anthocyanin accumulation in these two species. Completed construction of the blueberry pangenome graph, conserved genes were identified and are targeted to design the genotyping platform. Advanced development of the Vaccinium Genotyping platform. Compiled the blueberry SNP catalog that includes >5.8M SNPs, of which 4,675 SNPs represent known QTL loci (e.g. QTL for fruit size, firmness). A target capture technique was chosen for developing the VacCAP genotyping platform and will target 20,000 and 15,000 loci for blueberry and cranberry, respectively. A consortium that include 10 members from core and non-core labs was formed and committed to genotype >7,000 samples in 2022. SNPs located in blueberry core genes and QTLs are being targeted to select 50,000 probes to initiate testing them in 192 diverse blueberry samples. These outcomes are laying foundations to significantly expand application of molecular tools in blueberry and cranberry breeding and genetic programs. Obj. 2. Advanced phenotyping methods. Blueberry: developed the following new phenotyping protocols/methods: 1) a QR barcode system to manage samples across core labs; 2) a Near Infrared Spectrometry methods to predict sugar content; 3) texture with a needle probe to measure skin subcomponents; 4) an image-based method to evaluate blueberry fruit cluster traits; 5) a web application software that determine blueberry bruise; 6) initiated evaluating field/portable tools for firmness analysis. Cranberry: completed testing and comparison of four texture analysis methods/probes (penetration probe, blade, compression and shear). Phenotyped genetic study sets. Blueberry: continued evaluating fruit characteristics (FCs) representing texture, appearance traits (size, scar diameter/tear, wet scar), shelf life indicators (wrinkle/shrivel, mold and leakage) and chemistry (pH, TA, SSC, sugars, volatiles). In Y2 evaluated Northern Highbush (NHB, N=960), and Southern Highbush (SHB, N=980) GenStudy sets, and 2 mapping populations (N=196/364). Except for chemical composition all traits were evaluated at the harvest time and 6-7 week post storage under controlled conditions. Cranberry: evaluated texture, external-internal appearance, fruit weight, yield, % fruit rot, total anthocyanin, Brix and titratable acidity and fruit wax across 5 mapping populations (N= 172/71/211/141/68). Blueberry and cranberry Y1-2 data are being integrated and analyzed. FC genetic studies. Blueberry: identified 18 QTLs for pH, TA, TSS, Weight. 8 QTLs were stable across years. Cranberry: Completed two QTL studies that identified 6 QTLs for fruit weight, 5 QTLs for fruit rot resistance, 1 QTLs for Yield and 2 QTLs for organic acids. FQ Studies. 60 cultivars were harvested in NC and used to conduct the following fruit quality experiments: 1) FQ-shelf life and bruising studies. Evaluated FCs and shelf life indicators at harvest and followed biweekly in post-harvest (3°C) for 6 weeks to evaluate changes in FCs, and fruit chemistry. Bruising was also evaluated at harvest. Fruit chemistry (pH, TA, SSC, soluble sugars, and organic acids) are being evaluated. 2) Cell wall composition. Developed a protocol for cell wall composition and determined cell wall components in pulp and peel of crisp, firm, and soft cultivars at harvest. Compositional analysis is being completed. Data from all these fruit quality experiments are being integrated and used to identify FCs that contribute to fruit quality traits. Completed a study to compare texture probes and correlation with sensory. The study highlighted: a) all the methods discriminated the cultivars; b) the needle probe was able to detect difference in skin thickness observed for the epithelial and hypodermal tissues; c) the compression test was useful associate texture to sensory parameters (springiness, chewiness and resilience) that affect consumer overall liking. Obj. 3. Phenotyped germplasm for FC-QTL validation. Blueberry: phenotyped FCs and shelf life indicators on NHB (N=134), and SHB (N=109) ValStudy sets. Cranberry: phenotyped yield, fruit rot, fruit weight, organic acids content, fruit wax, Brix, total anthocyanins and titratable acidity in five mapping populations. Y1-2 data are being integrated and analyzed. Advanced validation of FC-QTLs. Anchored 52 and 3 existing QTLs for FCs, to the blueberry and cranberry reference genomes, respectively. For each trait, QTLs that overlap across genetic studies are being considered as validated. QTL for citric and malic acids in cranberry were validated and used to design DNA assays for Marker Assisted Selection. Advanced simple DNA assay design. Blueberry: initiated testing of High Resolution Melting and Kompetitive allele specific PCR targeting loci associated with volatiles. Cranberry: 2 SSR and 4 SNP markers were tested in mapping populations and were found to be highly specific (0.81-0.94) and sensitive (0.91-1) for predicting low, moderate and high citric and malic acid content. QTL for other traits are being validated and DNA assays being tested. Leveraged FC phenotypic data for breeding selection. Phenotypic data collected during Y1 enabled blueberry and cranberry breeders (core labs) to advance selections into replicated trials and to make new crosses aiming at combining multiple FQ traits. Obj 4. Performed blueberry willingness to pay (WTP) and sensory surveys., A WTP and consumer preference survey were performed for 20 SHB and 20 NHB varieties. The WTP survey was done in conjunction with sensory test conducted in Florida and Oregon. Responses from a total of 240 panelists were collected. Evaluation of texture and chemistry analysis for these set of material was initiated. Data are being integrate and analyzed to identify salient sensory attributes and fruit characteristics. Performed cranberry consumer survey. Completed a survey to estimate consumers' reactions to "added-sugar" labelling and labelling information in cranberry products (dried cranberries and cranberry juice). Responses from 4,000 cranberry consumers cross U.S. were collected and data are being analyzed. Obj. 5. All activities initiated in Y1 were continued and new activities were developed. Updated On-line platforms: added new data and newly developed information in the Genome Database for Vaccinium (GDV) and VacCAP website (see other products). Products developed and and made available through the online platforms includes: 1) two VacCAP newsletters; 2) the first GDV newsletter with updates on the new resources available on GDV; 3) two instructional videos featuring the use of new methodology to evaluate fruit quality of blueberries. Over 8,000 users/viewers and 148 newsletter subscribers had access to these updated products. Maintained the VacCAP Twitter account that has 260 followers and had 4,750 visits in Y2. Webinars/Forum: delivered a webinar to train users from core and non-core labs on tools available on GDV. Organized two online meetings to finalize the design of the Vaccnium genotyping platform and form the consortium. Workshops: in conjunction with the American Society for Horticultural Science meeting organized a two workshops, focusing on high-throughput phenotyping for fruit chemistry and on texture analysis in berries and led presentations on computational analysis and tools for genetic studies and genomic selection in polyploid crops.Presented at commodity group meetings: provided project updates at 15 grower association meetings in U.S. Annual meeting and Project evaluation: the VacCAP annual meeting was organized on-line on Nov.5, 2021. Survey for gathering input from participants in project webinars, workshops and advisory meeting were deployed. Feedback and recommendations gained from Y1 were integrated into Y2 activities and recommendations gained in Y2 are being considered in planning Y3 activities.

Publications

  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Diaz-Garcia1 L, Garcia-Ortega LF, Rodríguez MG, Delaye L, Iorizzo M and Zalapa J. 2021. Chromosome-level genome assembly of the American cranberry (Vaccinium macrocarpon Ait.) and its wild relative Vaccinium microcarpum. Frontiers in Plant Science, 12:633310.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Diaz-Garcia L, Covarrubias-Pazaran G, Johnson-Cicalese J, Vorsa N, Zalapa J. 2020. Genotyping-by-sequencing identifies historical breeding stages of the recently domesticated American cranberry. Frontiers in Plant Science, 11:607770. doi:10.3389/fpls.2020.607770.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Diaz JT, Foegeding EA, Stapleton L, Kay C, Ferruzzi MG, Iorrizo M, and Lila MA. 2021. Foaming and sensory characteristics of protein-polyphenol particles in a food matrix. Food Hydrocolloids, 123, 107148.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Fong SK, Kawash J, Wang Y. et al. 2021. A low malic acid trait in cranberry fruit: genetics, molecular mapping, and interaction with a citric acid locus. Tree Genetics & Genomes 17, 4.
  • Type: Journal Articles Status: Submitted Year Published: 2021 Citation: Kawash J, Colt K, Hartwick NT, Abramson BW, Vorsa N, Polashock JJ, Michael TP. 2021. Contrasting a reference cranberry genome to a crop wild relative provides insights into adaptation, domestication, and breeding. bioRxiv 2021.06.27.450096.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Giongo L, Matteo A, Pottorff M, Mainland M, Perkins-Veazie P and Iorizzo M. 2021. Comparative multi-parameters approach to dissect texture subcomponents of blueberry at harvest and postharvest. Postharvest Biology and Technology, Volume 183, 111696.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Jung S, Lee T, Gasic K, Campbell BT, Yu J, Humann J, Ru S, Edge-Garza D, Hough H and Main D. 2021. The Breeding Information Management System (BIM): an online resource for crop breeding. Database, Volume 2021, 2021, baab054.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Jung S, Cheng CH, Buble K, Lee T, Humann J, Yu J, Crabb J, Hough H and Main D. 2021. Tripal MegaSearch: a tool for interactive and customizable query and download of big data. Database,Volume 2021, 2021, baab023.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Karppinen K, Lafferty DJ, Albert NW, Mikkola N, McGhie T, Allan AC, Afzal BM, Häggman H, Espley RV and Jaakola L. 2021. MYBA and MYBPA transcription factors co-regulate anthocyanin biosynthesis in blue-coloured berries. New Phytologist.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Mengist MF, Bostan H, Young E, Kay K, Ashrafi H, Gillitt N, Ballington J, Ferruzzi MG, M.A. Lila MA and Iorizzo M. 2021. High density linkage map construction and identification of loci regulating fruit quality traits in blueberry. Horticulture Research, 8, 169.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Samkumar A, Jones D, Karppinen K, Dare AP, Sipari N, Espley RV, Martinussen I and Jaakola L. 2021. Red and blue light treatments of ripening bilberry fruits reveal differences in signalling through abscisic acid-regulated anthocyanin biosynthesis. Plant, Cell & Environment, 1⿿19.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Wu C, Deng C, Hilario E, Albert NW, Lafferty D, Grierson ERP, Plunkett BJ, Elborough C, Saei A, Günther CS, Ireland H, Yocca A, Edger PP, Jaakola L, Karppinen K, Grande A, Kylli R, Lehtol VP, Allan AC, Espley RV, Chagné D. 2021. A chromosome?scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition. Molecular Ecology Resources,
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Wu C, Deng C, Hilario E, Albert N, Lafferty W, Grierson D, E. R. P., Plunkett BJ, Elborough C, Saei A, Günther CS, Ireland H, Yocca A, Edger PP, Jaakola L, Karppinen K, Grande A, Kylli R, Lehtola VP, Allan AC, et al. Chagné D. 2021. A chromosome-scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition. Molecular Ecology Resources, 00, 1⿿6.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Xueping N, Changying L, Huanyun J and Takeda F. 2021. Three-dimensional photogrammetric reconstruction and deep learning instance segmentation to extract berry fruit harvestability traits. ISPRS Journal of Photogrammetry and Remote Sensing.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Yocca, AE, Edger, PP. 2021. Machine learning approaches to identify core and dispensable genes in pangenomes. Plant Genome, e20135.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Ferraro F. 2021.Genome-wide association of fruit-quality traits reveals the genetic basis for blueberry flavor. In: Application and perspectives of genome wide association studies (GWAS) and genomic selection (GS) in Diploid and Polyploid Horticultural Crops Workshop. ASHS Annual Conference, August 5-9, 2021, Denver, Colorado.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Giongo L, Ajelli M, Pottorff M, Coe K, Perkins-Veazie P, Bassil N, Hummer K, Farneti B, Iorizzo M. Comparative study on texture: a key for blueberry quality breeding. August 31, 2021, Proceedings of the XII International Vaccinium Symposium. Virtual format.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Giongo L, Ajelli M, Pottorff M, Perkins-Veazie P and Iorizzo M. 2021. Assessing blueberry and texture traits associated with consumer acceptance and shelf life. ASHS Annual Conference, August 5-9, 2021, Denver, Colorado.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Humann J, Cheng CH, Lee TL, Buble K, Jung S, Yu J, Hough H, Crabb J, Frank M, Scott K, Iorizzo M and Main D. 2021. Using the Genome Database for Vaccinium for genetics, genomics, and breeding research. XII International Vaccinium Symposium, August 30-September 1, 2021, Halifax, Nova Scotia, Canada. Virtual.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Iorizzo M, Mengist MF, Bostan H, Curaba J, Pottorff M. 2021. From genome to genes and DNA markers to improve agronomic performance and quality of fruit and vegetables crops. Genetyka Aplikacyjna Ro?lin XXI, September 22-24, 2021, Warsaw, Poland. Virtual.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Catrin S, Günther, Dare AP, McGhie TK, Deng C, Jaakola L, Lafferty DJ, Plunkett BJ, Grierson ERP, Turner JL, Albert NW and Espley RV. 2021. Spatiotemporal modulation of flavonoid metabolism in Vaccinium berries. International Conference on Polyphenols (ICP), Turku, Finland.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Espley RV, Catrin S, Günther, Dare AP, Albert NW, Lafferty DJ, McGhie T, Deng C, Plunkett BJ, Turner JL, Jones L, Grierson ERP, Schwinn KE, Davies KM, Allan AC, Jaakola L. 2021. The spatio-temporal accumulation and regulation of anthocyanin in Vaccinium. August 31, 2021, XII International Vaccinium Symposium, Dalhousie, Canada.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Iorizzo M., M.A. Lila, P. Perkins-Veazie, M. Pottorff, C. Finn, N. Vorsa, P. Edger, N. Bassil, P. Munoz, J. Zalapa, K.R. Gallardo, A. Atucha, D. Main, L. Giongo, C. Li, J. Polashock, C. Sims, E. Canales, L. M. Coe, D. Chagne, R. Espley and L. De Vetter. 2021. VacciniumCAP, a community-based project to develop advanced genetic tools to improve fruit quality in blueberry and cranberry. Proceedings of the XII International Vaccinium Symposium. August 30-September 1, 2021, Halifax, Nova Scotia, Canada. Virtual.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Jung S, Lee T, Cheng CH, Gasic K, Humann J, Yu J, Hough H and Main D. 2021. An update on the Breeding Information Management System (BIMS). Proceedings of the ASHS Annual Conference; Aug 5-9, 2021; Denver, Colorado.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Main D, Jung S, Lee T, Cheng CH, Gasic K, Humann J, Yu J, Hough H, Iorizzo M. 2021. Using the GDV Breeding Information Management System. Proceedings of the International Vaccinium Symposium, August 30-September 1, 2021, Halifax, Nova Scotia, Canada.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Mengist MF, Burtch H, Debelo H, Pottorff M, Bostan H, Nunn C, Corbin S, Kay CD, Bassil N, Hummer K, Lila MA, Ferruzzi MG, Iorizzo M. 2021. Diversity of phenolic bioaccessibility in blueberry germplasm: towards the development of a genetic framework to improve the efficiency of bioactive delivery. ASHS Annual Conference, August 5-9, 2021, Denver, Colorado.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Mengist MF, Bostan H, Kay K, Gillitt N, Ashrafi H, Ferruzzi MG, Lila MA and Iorizzo M. High density linkage map construction and identification of loci regulating fruit quality traits in blueberry. 2021. ASHS Annual Conference, August 5-9, 2021, Denver, Colorado.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Munoz P. 2021. Operational application of genomic selection in tetraploid blueberry. In: Application and perspectives of genome wide association studies (GWAS) and genomic selection (GS) in Diploid and Polyploid Horticultural Crops Workshop. ASHS Annual Conference, August 5-9, 2021, Denver, Colorado.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Perkins-Veazie P, Ma G, Pottorff M, Lila MA and Iorizzo M. 2021. New tools for rapid fruit quality analysis in blueberry. August 31, 2021, Proceedings of the XII International Vaccinium Symposium. Virtual format.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Perkins-Veazie P, Ma G, Pottorff M, Lila MA and Iorizzo M. 2021. New tools for rapid fruit quality analysis in blueberry. Acta Horticulturae.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Perkins-Veazie P. 2021. Faster Methods for Postharvest Compositional Analysis. HortScience 56.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Trandel MA, Perkins-Veazie P, Iorizzo M and Johanningsmeier S. 2021. Method optimization and cell wall analysis for peel and pulp of blueberry cultivars. ASHS Annual Conference, August 5-9, 2021, Denver, Colorado.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Perkins-Veazie P. 2021. Introduction and overview of texture and instruments. HortScience 56.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Phillips M, Diaz-Garcia L, Grygleski E, Giongo L, Atucha A, Iorizzo M and Zalapa J. 2021. Cranberry challenges in distinguishing soft and firm berries. ASHS Annual Conference, August 5-9, 2021, Denver, Colorado.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Samkumar A, Karppinen K, Martinussen I, Espley R, Jaakola L. 2021. Light quality from supplemental light-emitting diodes modulates biosynthesis of secondary metabolites in ripening bilberry (Vaccinium myrtillus L.) fruit. August 30, 2021, XII International Vaccinium Symposium, Dalhousie, Canada. Virtual format.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Trandel MA, Perkins-Veazie P, Iorizzo M and Johanningsmeier S. 2021. Exploring the plant cell wall in blueberry varieties of different texture. Acta Horticulturae.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Trandel MA, Perkins-Veazie P, Iorizzo M and Johanningsmeier S. 2021. Optimization of blueberry cell wall extraction from grinding through hydrolysis. HortScience, 56.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Yalcin O, Finn C, Mackey T, Pottorff M, Iorizzo M, Hardigan M, Luby C, Bassil NV. 2021. Towards QTL analysis of phenological and fruit quality traits in a tetraploid highbush blueberry population. ASHS Annual Conference, August 5-9, 2021, Denver, Colorado.
  • Type: Other Status: Published Year Published: 2021 Citation: Humann J and Main M. Genome Database for Vaccinium (https://vacciniumcap.org) XII International Vaccinium Symposium, August 30-September 1, 2021, Virtual. Poster
  • Type: Other Status: Published Year Published: 2021 Citation: Mengist M.F., H. Bostan, K. Kay, N. Gillitt, H. Ashrafi, M.G. Ferruzzi, M.A. Lila and M. Iorizzo. 2021. High density linkage map construction and identification of loci regulating fruit quality traits in blueberry. XII International Vaccinium Symposium, August 30-September 1, 2021, Virtual. Poster
  • Type: Other Status: Published Year Published: 2021 Citation: Pottorff M, Zielinski K, Mengist M, Honigs D, Grace M, Lila MA and Iorizzo M. 2021. A high-throughput phenotyping method using near infrared spectroscopy to measure anthocyanin content in blueberry. XII International Vaccinium Symposium, August 30-September 1, 2021, Virtual. Poster
  • Type: Other Status: Published Year Published: 2021 Citation: Yalcin O, Finn C, Mackey T, Pottorff M, Iorizzo M, Hardigan M, Luby C, Bassil NV. 2021. Towards QTL analysis of phenological and fruit quality traits in a tetraploid highbush blueberry population. ASHS Annual Conference, August 5-9, 2021, Denver, CO, USA. Poster
  • Type: Other Status: Other Year Published: 2021 Citation: Atucha A, and Zalapa J. 2021. Cranberry School. Wisconsin Dells, WI. January 28, 2021. Presentations for growers or other industry stakeholders
  • Type: Other Status: Other Year Published: 2021 Citation: DeVetter, L. 2021. Washington Small Fruit Conference. Lynden, WA. December 1, 2021. Virtual format. Presentations for growers or other industry stakeholders
  • Type: Other Status: Other Year Published: 2021 Citation: : DeVetter L, Bassil N, Luby C. 2021. VacCAP: Improving Fruit Quality. Blueberry Field Day. Oregon State University⿿s North Willamette Research & Extension Center in Canby, Oregon. July 15, 2021. Presentations for growers or other industry stakeholders
  • Type: Other Status: Other Year Published: 2021 Citation: Iorizzo, M. VacCAP project update. 2021. North Carolina Blueberry Council Annual Open House. January 13, 2021. Virtual format. Presentations for growers or other industry stakeholders
  • Type: Other Status: Other Year Published: 2021 Citation: Iorizzo M. 2021. Leveraging Genetic and Genomic Resources to Enable Development of Blueberry and Cranberry Cultivars with Improved Fruit Quality Attributes. NABC/USHBC Spring meeting. March 18, 2021. Presentations for growers or other industry stakeholders
  • Type: Other Status: Other Year Published: 2021 Citation: Muñoz, P. 2021. Spring Florida Blueberry Growers Association. March 8, 2021. Virtual format. Presentations for growers or other industry stakeholders
  • Type: Other Status: Other Year Published: 2021 Citation: Perkins-Veazie P. 2021. Postharvest of Berries. Berry Grower Meeting, Virginia State University. February 18, 2021. Virtual format. Presentations for growers or other industry stakeholders
  • Type: Other Status: Other Year Published: 2021 Citation: Polaschock, J. 2021. American Cranberry Grower Association Winter meeting, New Jersey. January 23, 2021. Virtual format. Presentations for growers or other industry stakeholders
  • Type: Other Status: Other Year Published: 2021 Citation: Polaschock, J. 2021. Blueberry Open House New Jersey. March 9, 2021. Virtual format. Presentations for growers or other industry stakeholders
  • Type: Other Status: Published Year Published: 2021 Citation: Polaschock, J. 2021. Cranberry Summer Field day. August 19, 2021. Presentations for growers or other industry stakeholders
  • Type: Other Status: Other Year Published: 2021 Citation: Sandler, H. 2021. University of Massachusetts Cranberry Station Annual Extension and Research Update Meeting. January 26, 2021. Virtual Format. Presentations for growers or other industry stakeholders
  • Type: Other Status: Other Year Published: 2020 Citation: Zalapa J. 2020. VacCAP project discussion. Wisconsin Cranberry Research Roundtable. Madison, WI. November 9, 2020. Presentations for growers or other industry stakeholders
  • Type: Other Status: Other Year Published: 2021 Citation: Iorizzo M. 2021. Blueberry research updates at the Piedmont Research Field Station. August 17, 2021. Presentations for growers or other industry stakeholders
  • Type: Other Status: Published Year Published: 2021 Citation: Atucha A, Russo J, DeVetter L, Gallardo K and Canales E. 2021. Buying Better Berries: What Does Fruit Quality Mean to Consumers? VacCAP Newsletter Issue 2, May 2021.
  • Type: Other Status: Published Year Published: 2021 Citation: Atucha A, Russo J, DeVetter L and Zalapa J. 2021. Piecing Together the Cranberry Genome Puzzle. VacCAP Newsletter Issue 2, May 2021.
  • Type: Other Status: Other Year Published: 2021 Citation: Atucha A, Russo J, DeVetter L, Bocock Band Serres R. 2021. Fruit Quality: An Industry Perspective. VacCAP Newsletter Issue 2, May 2021.
  • Type: Other Status: Published Year Published: 2021 Citation: Atucha A Russo J, DeVetter L, Sims C, Gallardo K and Canales E. 2021. Sensory Tasting Survey Helps Connect Fruit Quality Traits and Consumer Preferences in Blueberry. VacCAP Newsletter Issue 3, August 2021.
  • Type: Other Status: Published Year Published: 2021 Citation: Atucha A, Russo J, DeVetter L and Vorsa N. 2021. Fighting Fruit Rot: Dr. Nicholi Vorsa⿿s Breeding Program Focuses on Developing Resistant Cranberry Cultivars. VacCAP Newsletter Issue 3, August 2021.
  • Type: Other Status: Published Year Published: 2021 Citation: Humann J and Main D. 2021. Genome Database for Vaccinium Newsletter, Issue 1, September 2021.
  • Type: Other Status: Published Year Published: 2021 Citation: Atucha A, Russo J, DeVetter L and Li C. 2021. New Imaging Methods Help Researchers Find Blueberry Cultivars Resistant to Bruising. VacCAP Newsletter Issue 3, August 2021.


Progress 09/01/19 to 08/31/20

Outputs
Target Audience:Blueberry and cranberry breeders; post-harvest physiologists, food scientists, germplasm collection curators, molecular geneticists, and other allied scientists of these crops; nurseries, producers, processors, marketers, and marketing organizations of Vaccinium crops; and consumers of these crops. Changes/Problems: Due to operational restrictions (total or partial lockdown) employed by funded institutions to prevent the spread of COVID-19 infections and delay of funding release from the USDA-NIFA the following activities were not performed as planned: sequencing of the 36 blueberry and cranberry samples was delayed resulting in a delay in downstream analysis (Obj. 1); Southern Highbush GenStudy set was not harvested and phenotyped (Obj. 2); the cranberry diversity panel could not be transplanted in the field (Obj.2); one newsletter could not be developed; workshops that were to be held at the Vaccinium International Symposium could not be organized (symposium was postponed to 2021); the first annual meeting was organized on-line. Furthermore, engagement with the public and commodity groups was limited due to shutdown of physical meetings due to COVID-19. To compensate for some of these delayed and cancelled activities, some data analysis work from complementary projects was completed (eg. completed additional chromosome scale genome assemblies and performed comparative analysis, completed linkage maps and QTL mapping for SNPs catalog, identified possible genes and SNPs from existing QTLs to target for DNA assay design) and are being used to complement VacCAP planned activities. What opportunities for training and professional development has the project provided?Project participants include 5 post-doctoral associates and 15 technicians, 13 graduate students and undergraduate students fully or partially funded by the project across all the VacCAP team programs. These trainees and technicians are participating in VacCAP activities of phenotyping, genomic analysis, DNA profiling, development of DNA-informed breeding strategies, data management and communication. These personnel are gaining knowledge, experience, and skills in accurate measurement of fruit characteristics, fruit physiology, phenotyping engineering, quantitative genetics, bioinformatics, design and implementation of genetic tests, and breeding program planning and management. In addition, these participants are members of project Teams and undertake targeted training such as a workshop and a one to one in person training on texture analysis. How have the results been disseminated to communities of interest?Introduction about the VacCAP project, and preliminary results were disseminated to the scientific community, including the U.S.-wide community of Vaccinium crop breeders, through 8 peer reviewed publications, 11poster and oral presentations at regional, national and international conferences (including Plant and Animal Genome Conferences). The information was also disseminated to the broader Vaccinium community (producers, processors and distributors) through 14 oral presentations at commodity group meetings, 2 article in trade magazines, 7 news articles, and the VacCAP newsletter. To engage the public and students, VacCAP PIs, participated in and/or organized eight outreach events targeting K12, middle, high schools, and college students including students representing minorities. Events include blueberry and cranberry field trips, science fairs, and short lab training classes. Outreach activities aimed at introducing students to plant science and horticulture, food science, scientific lab experience based on protocol/research. All these activities placed specific attention on the importance on the central role of breeding for blueberry and cranberry productions but also more general crop productions. Lab activities include DNA extraction, PCR, basic chemistry analysis (eg. pH, Brix) and sensory analysis. These events attract thousands of attendees and contribute to enhance public understating and interest in learning and careers in plant science, and more specifically plant breeding. What do you plan to do during the next reporting period to accomplish the goals?Objective 1. Establish genomic resources to enable effective association mapping studies in blueberry and cranberry. Finalize genome assembly and annotation for all 36 genotypes and construct the pangenome (blueberry specific, cranberry specific, and pan-Vaccinium); Identify cultivar-specific genes associated with fruit quality; Develop blueberry haplotype map; Complete SNP catalog and phase SNPs; Prepare DNA from 188 blueberry and 100 cranberry samples to genotype for the testing phase; Organize the genotyping forum and form the Vaccinium Genotyping Consortium; Finalize choice of genotyping platform and select SNPs for the testing phase; Objective 2. Discover DNA markers and fruit characteristics that maximize industry profitability and match consumer preferences in blueberry and cranberry; Phenotype FCs and shelf-life indicators from the blueberry and cranberry GenStudy sets; Complete analysis of blueberry year 1 and cranberry year 1-2 data; Finalize material collection, begin DNA extraction from GenStudy sets; Begin genotyping GenStudy set; Perform FQ analysis: sensory, shelf-life and bruising; Objective 3. Deliver molecular and genetic resources to improve blueberry and cranberry fruit quality traits that maximize industry profitability and match consumer preferences; Phenotype blueberry and cranberry ValStudy Sets; Prepare material, and plan genotyping needs for ValStudy sets; Finalize and test protocol for simple DNA assay on a set of existing FC-QTLs (VOC); Develop a list of genotypes harboring superior FCs based on year 1 phenotypic data; Make crosses and store seeds; Objective 4. Assess the potential socio-economic impact of blueberry and cranberry fruit quality improvements on market demand. Finalize blueberry willingness to pay (WTP) questionnaire and experimental design. Implement WTP survey in conjunction with sensory analysis panel. Begin analysis of WTP data; Draft questionnaire and experimental design to study consumer behavior response to fruit tasting pricing using biometric parameter. Finalize list of plant materials to be used in study; Distribute cranberry survey to panel of U.S. consumers via Qualtrics. Collect and analyze survey data; Objective 5. Engage U.S. Vaccinium breeders and stakeholder groups to transfer advanced phenomics and genomics tools to build a more coordinated and efficient cultivar development system On-line platforms: Train core and non-core labs on GDV. Update VacCAP and GDV Distribute updates to national and international partners; Newsletter and other media: release two newsletters; publish articles in trade magazines; maintain VacCAP accounts on social media; Webinars: deliver two webinars; phenotyping fruit texture and pangenome; Workshops: deliver two workshops; fruit quality at ASHS and training core labs on use of data management systems; Commodity group meetings: disseminate progress and results to commodity group meetings. Annual meeting: organize the VacCAP annual meeting in conjunction with the Vaccinium International Symposium (Halifax, Canada, August 28-Sept 3) Project evaluation: continue project evaluation activity to improve communication and effectiveness of extension activities.

Impacts
What was accomplished under these goals? Project Objectives and Annual Progress Obj.1. To develop the Vaccinium pangenome the genomes of 36 blueberry and cranberry cultivars were sequenced and the assembly for fifteen genotypes was completed. Three chromosome scale genome assemblies representing blueberry wild diploid species and one cranberry cultivar were completed, and three new linkage maps were constructed. These resources are used to improve the quality of the available blueberry and cranberry genome assemblies, and for genome-wide analyses to identify regions of the genome that contain introgression from related Vaccinium species used by various breeding programs. The pangenome will be used to develop a high-throughput genotyping platform (HTGP) and will limit ascertainment bias in the SNP selection. Multiple activities were initiated to develop the Vaccinium HTGP. SNP markers (47,025) from blueberry and cranberry linkage maps and QTL studies and 667 DNA and RNA sequence sets of Vaccinium genotypes were collected to establish a catalog of Vaccinium SNPs to detect and validate new SNPs. Plant material was collected from blueberry (188) and cranberry (100) genotypes to use for testing the Vaccinium genotyping platform. Engaged 18 core and non-core labs (stakeholders) to evaluate the technical needs for a Vaccinium HTGP. Feedbacks highlighted the following platform needs: cost effective; able to estimate allele dosage; limit ascertainment bias; serve multiple applications, in particular GWAS; and be easy to use via limiting work needed for scoring the SNPs. Overall the outcomes of these activities lay the foundation to build the resources and the network needed to expand application of molecular tools in blueberry and cranberry breeding and genetic programs. Obj.2. To perform marker traits association studies for fruit characteristics (FCs) and shelf-life indicators, new phenotyping methods/protocols were tested and implemented to phenotype the blueberry and cranberry Genetic Study sets. Blueberry: Developed a data collection system to simultaneously evaluate and collect phenotypic data for 20 FCs representing texture and appearance, shelf life indicators (wrinkle, mold, and leakage) and to calculate storage performance (eg. FCs storage indexes). Fruits from the Northern Highbush (NHB) GenStudy set (N=973) and one mapping population (DxJ, N=189) were phenotyped at harvest and six weeks post-harvest (stored at 4?). Preliminary results indicates a wide range of variation for most of the traits. Fruits for non-volatile chemistry analysis are being processed by the Phenotyping team. To identify FCs that contribute to fruit quality traits, a new subset of texture parameters and indexes were tested using three methods (penetration, compression and puncture). The new parameters are being correlated with sensory analysis, shelf-life indicators and with a handy fruit texture analysis device. Preliminary analysis indicates that the different methods can discriminate genotypes, and in some case the different tissue layers. Also method for chemical compositional analysis are being tested, and along with the texture analysis will be used to establish a link between DNA markers associated with FCs and fruit quality attributes. Cranberry: three methods (puncture, compression, and shearing) for texture analysis were evaluated. The compression method was the most powerful to discriminate cultivars and was chosen for downstream analysis. Texture, external appearance, internal appearance, non-volatile chemical composition was phenotyped on 3 mapping populations (MP1, N= 171, MP2, N=71, MP3, N=211) and resistance to fruit rot evaluated in MP3. Preliminary analysis indicates a wide range of variation for most of the traits. The use of accurate and objective phenotypic methods to evaluate FCs in blueberry and cranberry, represent a key step to empower the following up marker traits association studies. Obj. 3. To validate existing and/or new FCs QTLs, a subset of the Validation Study set (161 NHB blueberry genotypes) was phenotyped for FCs, shelf-life indicators and storage performance and are being processed for non-volatile chemistry analysis. Cranberry advanced selections bred for fruit rot resistance (FRR) were also evaluated. Phenotypic data obtained from the ValStudy and GenStudy sets are also being analyzed to identify parents carrying desirable FCs and to use them in new crosses. To develop simple DNA assay targeting FCs, data from previous blueberry and cranberry QTL studies were used to identify target candidate genes. NBS-LLR resistance genes and genes involved in the synthesis of volatile (VOC) metabolites, and anthocyanin (ANT) were identified in the cranberry and blueberry genomes. A genetic study for citric and malic acids (CITA) in cranberry was completed and a multi-allelic Mendelian locus CITA identified. The genomic location of existing FRR, ANT, CITA and VOC QTLs are used to identify their overlap with candidate genes. Also DNA extraction and genotyping high-throughput assays for blueberry were started. This activity establishes a foundation to validate existing and new FC QTLs, and develop cost-effective DNA assay. DNA assay for FCs and new crosses made based on molecular and phenotypic data will provide a foundational work to accelerate breeding for fruit quality in blueberry and cranberry breeding programs. Obj. 4. Finalized the development of a survey to elicit preferences and willingness to pay for different levels of sugar content in dried cranberry and cranberry juice. The survey will also collect information on consumers' perceptions of food science and technology, and the tradeoffs to accept novel breeding technologies when the benefit is to receive a healthier (less sugar) product. Cranberry industry stakeholders actively participated on designing the survey and distribution of the survey is being planned. The outcomes of this study will guide cranberry breeders and the processing/distribution industry in formulating targeted marketing strategies for the promotion of cranberry products. Obj. 5. All activities aiming at engaging the stakeholders were initiated during year 1. On-line platforms: the VacCAP web site was released. The Genome Database for Vaccinium was updated, by adding new genetic and genomic data (see other products) and upgraded to the Tripal 3 database platform. Created a standard Blueberry Trait Ontology in collaboration with USDA ARS scientists for use in both the Breeding Insight and BIMS platforms. Newsletters and other media: developed and released the first issue of the VacCAP newsletter. Published two articles in trade magazines (see products) to introduce the objectives of the VacCAP project. Created and maintained a VacCAP Twitter account (58 follower) and established a YouTube channel with one video currently uploaded (19 views). Webinars: delivered a webinar titled to introduce the Breeding Information System Management (BIMS) and the Field Book App. The webinar resulted in 11 new BIMS user accounts being created. Workshops: delivered three workshops with cranberry processors to introduce high throughput FCs analysis including texture. Industry representatives expressed interest in implementing the new technologies in their processing lines. Commodity group meetings: Delivered 14 presentations at grower association meetings across nine US states and Canada to introduce the VacCAP project. Annual meeting: the first VacCAP annual meeting with members of the Advisory Panel was organized on-line on Feb. 25, 2020. Panel recommendations were discussed at the annual project meeting, and appropriate adjustments made to project activities. Project evaluation: developed an online survey portal for gathering input from participants in project webinars, workshops and meetings. Feedback and recommendations gained from year one activities are being considered in planning future activities.

Publications

  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Ni, X., Li, C., Jiang, H., & Takeda, F. (2020). Deep learning image segmentation and extraction of blueberry fruit traits associated with harvestability and yield. Horticulture Research, 7(1), 1-14. https://doi.org/10.1038/s41438-020-0323-3
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Mengist MF, Grace MH, Xiong J, Kay CD, Bassil N, Hummer K, Ferruzzi MG, Lila MA and Iorizzo M. 2020. Diversity in metabolites and fruit quality traits in blueberry enables ploidy and species differentiation and establishes a strategy for future genetic studies. Frontier in Plant Science, 11:370. https://doi.org/10.3389/fpls.2020.00370.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Farneti B, Emanuelli F, Giongo L, Toivonen P, Iorizzo M, Folta KM and Finn CE. 2020. Editorial: Interdisciplinary approaches to improve quality of soft fruit berries. Frontiers in Plant Science, section Crop and Product Physiology, 11:592222. https://doi.org/10.3389/fpls.2020.592222
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Diaz-Garcia L, Rodriguez-Bonilla L, Phillips M, Lopez-Hernandez A, Grygleski E, Atucha A and Zalapa J. 2019. Comprehensive analysis of the internal structure and firmness in American cranberry (Vaccinium macrocarpon L.) fruit. PlosOne, 14(9): e0222451. https://doi.org/10.1371/journal.pone.0222451.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Kay Fong S, Kawash J, Wang Y, Johnson-Cicalese J, Polaschock J and Vorsa N. 2020. A low citric trait in cranberry: genetic and molecular mapping of a locus impacting fruit acidity. Tree Genetics & Genomes, 16:42. https://doi.org/10.1007/s11295-020-01432-4.
  • Type: Journal Articles Status: Submitted Year Published: 2020 Citation: Kay Fong S, Kawash J, Wang Y, Johnson-Cicalese J, Polaschock J and N. Vorsa (2020). A low malic acid trait in cranberry fruit: genetics, molecular mapping and interaction with a citric acid locus. Tree Genetics & Genomes.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: G�nther CS, Dare AP, McGhie TK, Deng C, Lafferty DJ, Plunkett BJ, Grierson ERP, Turner J L, Jaakola L, Albert NW and Espley RV. 2020. Spatiotemporal modulation of flavonoid metabolism in blueberries. Frontiers in Plant Science, 11.545. https://doi:10.3389/fpls.2020.00545
  • Type: Book Chapters Status: Published Year Published: 2019 Citation: Vorsa N. and J. Zalapa. 2019. Domestication, Genetics, and Genomics of the American Cranberry. Plant Breeding Reviews, Volume 43:279-310
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Eddy D. Research Team Seeks to Boost Berry Quality, Jan. 3, 2019. Growing Produce magazine https://www.growingproduce.com/fruits/berries/research-team-seeks-to-boost-berry-quality
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Giongo L. and Iorizzo M. Sinergie di ricerca per lindustria di mirtillo gigante e cranberry. Rivista di Frutticoltura e Ortofrutticoltura. Vol. 2 (2020), 2-4
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Ni, X., Li, C., Jiang, H. Blueberry harvestability trait extraction from 2D images and 3D point clouds based on deep learning and photogrammetric reconstruction. Paper Number: 2001338. ASABE Annual International Meeting. Omaha, Nebraska. July 12-15, 2020.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Iorizzo M., Lila M.A., Perkins-Veazie P., Pottorff M., Finn C, Vorsa N., Edger P., Bassil N., Munoz P., Zalapa J., Gallardo K.R., Atucha A., Main D., Giongo L., Li C., Polashock J., Sims C., Canales E., DeVetter L., Chagne D., Espley R., Coe M. VacciniumCAP, a community-based project to develop advanced genetic tools to improve fruit quality in blueberry and cranberry. XXVII Plant & Animal Genome, January 11-15, 2020, San Diego, California, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Mengist M.F., Grace H.M., Xiong J., Kay. D.C, Bassil N., Hummer K., Ferruzzi M., Lila M.A., M. Iorizzo. Diversity in metabolites and fruit quality traits in blueberry enables ploidy and species differentiation and establishes a strategy for bioactive genetic studies. XXVII Plant & Animal Genome, January 11-15, 2020, San Diego, California, USA.
  • Type: Conference Papers and Presentations Status: Submitted Year Published: 2019 Citation: M. Iorizzo, M.A. Lila, P. Perkins-Veazie, M. Pottorff, C. Finn, N. Vorsa, P. Edger, N. Bassil, P. Munoz, J. Zalapa, K.R. Gallardo, A. Atucha, D. Main, L. Giongo, C. Li, J. Polashock, C. Sims, E. Canales, L. DeVetter, D. Chagne, R. Espley, M. Coe. VacciniumCAP, a community-based project to develop advanced genetic tools to improve fruit quality in blueberry. XII International Vaccinium Symposium.
  • Type: Conference Papers and Presentations Status: Submitted Year Published: 2019 Citation: M. Pottorff, R. Kock, L. Giongo, M. Fentie, P. Munoz, T. Mackey, N. Bassil, P. Perkins-Veazie, M. Iorizzo. An automated and integrated phenotyping method to capture fruit texture characteristics, stem scar diameter and fruit weight in blueberry. XII International Vaccinium Symposium.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Deng C, G�nther CS, Lafferty D, Dare AP, McGhie TK, Grierson E, Albert NW, Espley RV (2020) Deciphering the blue colour in blueberries XXVII Plant & Animal Genome, January 10th 11-15, 2020, San Diego, California, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Plunkett BJ, Lafferty D, Dare AP, Albert NW, G�nther CS, McGhie TK, Turner JL, Jones L, Grierson E, Schwinn KE, Davies KM, Allan AC, Jaakola L, Espley RV (2019) Filling the Void  boosting the nutritional value of blueberry. 10th International Workshop on Anthocyanins, September 9-11, 2020, Trento, Italy.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Plunkett BJ, Lafferty D, Dare AP, Albert NW, G�nther CS, McGhie TK, Turner JL, Jones L, Grierson E, Schwinn KE, Davies KM, Allan AC, Jaakola L, Espley RV (2019) Filling the Void  boosting the nutritional value of blueberry. TropAg, November 10-13, Brisbane, Australia.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Giongo Lara Blueberry and raspberry breeding in a view of higher fruit quality at harvest and post-harvest. 10/11/2019 Tanger (Morocco)
  • Type: Conference Papers and Presentations Status: Submitted Year Published: 2019 Citation: Giongo L, Ajelli M, Pottorff M, Perkins-veazie P, Bassil N, Hummer K, Farneti B, Iorizzo M. Comparative study on texture: a key trait for blueberry fruit quality breeding. XII International Vaccinium Symposium
  • Type: Other Status: Other Year Published: 2020 Citation: Zalapa J. Fruit Texture and quality measures. BC Cranberry Marketing Commission & BC Cranberry Growers Association Meeting. Invited research presentation. Richmond, Vancouver, Canada. February 17-19, 2020.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Iorizzo M. VacCAP: A community-based project to develop advanced genetic tools to improve fruit quality in blueberry and cranberry. Online talk, organized by Peruvian Ministry of Agriculture and National Institute of Agricultural Innovation. June 25, 2020.
  • Type: Other Status: Other Year Published: 2020 Citation: Cline W. and M. Iorizzo. VacCAP Project: A New Nationwide Project to Advance Breeding in Vaccinium Species. North Carolina Blueberry Council  54th Annual Open House and Trade Show, January 14-15, 2020, Fayetteville, NC, USA.
  • Type: Other Status: Other Year Published: 2020 Citation: Zalapa J. Genetic and trait research past, present, and future. BC Cranberry Marketing Commission & BC Cranberry Growers Association Meeting. Invited research presentation. Invited by Jeff Hamilton and Todd May. Richmond, Vancouver, Canada. February 17-19, 2020.
  • Type: Other Status: Other Year Published: 2020 Citation: Zalapa J. Genetics, genomics, and breeding in Cranberry. UMass and Cranberry Growers Association Meeting. Invited research presentation. Wareham, MA. January 30, 2020.
  • Type: Other Status: Other Year Published: 2020 Citation: DeVetter, LW. VacCAP: Leveraging Genetic and Genomic Resources to Enable Development of Blueberry and Cranberry Cultivars with Improved Fruit Quality Attributes. Oregon Cranberry School. Jan. 30, 2020, Bandon, OR, USA.
  • Type: Other Status: Other Year Published: 2020 Citation: Zalapa J. Wisconsin Cranberry School sponsored by the University of Wisconsin-Extension and the Wisconsin State Cranberry Growers Association. Developing techniques to measure cranberry firmness. Wisconsin Dells, WI. January 23, 2020.
  • Type: Other Status: Other Year Published: 2019 Citation: Zalapa J. Fruit quality measures. Wisconsin Cranberry Research Roundtable. Madison, WI. November 7, 2019.
  • Type: Other Status: Published Year Published: 2020 Citation: Phillips M., L. Diaz-Garcia, E. Grygleski, A. Atucha, M. Iorizzo, J. Zalapa. 2020. Cranberry fruit texture and quality measures. WI Cranberry School Proceedings Vol 28.
  • Type: Other Status: Other Year Published: 2019 Citation: Finn, C. Blueberry Breeding Program Update and VacCAP. Washington Small Fruit Conference. Dec. 5, 2019, Lynden, WA, USA.
  • Type: Other Status: Other Year Published: 2020 Citation: Zalapa J. and A. Atucha. Introducing VacCAP Project. Wisconsin State Growers Association Cranberry School, January 23, 2020, Wisconsin Dells, WI, USA.
  • Type: Other Status: Other Year Published: 2020 Citation: Polashock, J. VacCAP Project: A New Nationwide Project to Advance Breeding in Vaccinium Species. Annual Meeting of the American Cranberry Growers Association, January 23, 2020, Columbus, NJ, USA.
  • Type: Other Status: Other Year Published: 2020 Citation: R. Allen. VacCAP: Leveraging genetic and genomic resources to enable development of blueberry and cranberry cultivars with improved fruit quality attributes. Alma Blueberry Update January 8, 2020, Alma, GA.
  • Type: Other Status: Other Year Published: 2019 Citation: D. Main. Using crop databases and big-data to enable superior cultivar development. WA SMALL FRUIT CONFERENCE & LYNDEN AG SHOW, December 4-6, 2019, Lynden, WA.
  • Type: Other Status: Other Year Published: 2020 Citation: E. Canales. Market Planning. Mississippi Blueberry Education Workshop. January 23, 2020, Hattiesburg, MS.
  • Type: Other Status: Other Year Published: 2020 Citation: Building a Better Berry: A Cranberry Q&A With Dr. Juan Zalapa: VacCap Newsletter, August 25, 2020. https://www.vacciniumcap.org/buildingabetterberry
  • Type: Other Status: Published Year Published: 2020 Citation: UW scientists part of $12.8M effort to improve cranberries and blueberries: Wisconsin State Farmer, February 18, 2020. https://www.wisfarmer.com/story/news/2020/02/18/uw-scientists-part-effort-improve-cranberries-and-blueberries/4798444002/
  • Type: Other Status: Published Year Published: 2020 Citation: UW researchers receive grant pioneer research on cranberry genomes: Badger Herald, March 10, 2020. https://badgerherald.com/news/2020/03/10/uw-researchers-receive-grant-pioneer-research-on-cranberry-genomes/
  • Type: Other Status: Other Year Published: 2020 Citation: Wisconsin-based researchers work to breed better cranberries. SprectrumNews, February 24, 2020. https://spectrumnews1.com/wi/madison/news/2020/02/25/wisconsin-based-researchers-work-to-breed-better-cranberries
  • Type: Other Status: Other Year Published: 2020 Citation: WSU scientists team up to improve blueberries, cranberries. WSU Insider, Feb. 7, 2020. https://news.wsu.edu/2020/02/07/wsu-scientists-team-12-8-million-effort-improve-blueberries-cranberries/
  • Type: Other Status: Other Year Published: 2020 Citation: DeVetter, L.W. Dr. Chad Finn  Forever Inspiring the Berry Breeding Community. VacCAP Newsletter, Aug. 25, 2020. https://www.vacciniumcap.org/node/51
  • Type: Other Status: Other Year Published: 2020 Citation: D. Chagne. The importance of the humble blueberry. Genomics Aotearoa, Ferbruary 26, 2020. https://sciblogs.co.nz/genomics-aotearoa/2020/02/26/the-importance-of-the-humble-blueberry/