Source: UNIVERSITY OF FLORIDA submitted to
FACT: FRESHID - MACHINE LEARNING FOR THE MOLECULAR EVALUATION OF FRESH PRODUCE QUALITY
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
NEW
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1026048
Grant No.
2021-67021-34484
Project No.
FLA-HOS-006073
Proposal No.
2020-08839
Multistate No.
(N/A)
Program Code
A1541
Project Start Date
Mar 15, 2021
Project End Date
Mar 14, 2025
Grant Year
2021
Project Director
Liu, T.
Recipient Organization
UNIVERSITY OF FLORIDA
G022 MCCARTY HALL
GAINESVILLE,FL 32611
Performing Department
Horticulture Sciences
Non Technical Summary
Fresh fruits and vegetables are an important component of the human diet, but their quality often deteriorates before reaching consumers due to ongoing biochemical processes and compositional changes.Freshness is an important and fleeting state, and its progressive loss after harvest cannot be easily evaluated. Until now this race against time has been almost entirely subjective, mostly based on external visual criteria. To the consumer, freshness is synonymous with proximity to the harvest time and retention of nutritional value.The current lack of objective indices for definingfreshnessof fruits or vegetables limits our capacity to control product quality and leads to food waste. In the proposed work,we will combine machine learning technologies and multi-omics tools to understand post-harvest senescence and microbial spoilage of fresh produce and then develop a simple imaging approach (FreshID) to evaluate fruit and vegetable quality, particularly nutritional and texture-related attributes such as maturity, storage ability, and firmness.This proposed comprehensive research program will identify the genes, proteins and compounds that can serve asfreshness-indicators and will then use these indicators todevelop of an algorithm to accurately estimate the freshness and/or produce spoilage.The outcomes of this proposed research will provide mechanisms for early detection of poor-quality produce and, by leveraging these mechanisms throughout the food production pipeline, understand how food waste can be reduced. Additionally, the FreshID toolbox of molecular markers associated with plant senescence can be used duringbreedingfor pre-harvest traits that could delay postharvest senescence. The goals of the proposed research are advances in both basic research and applied plant science that will impactfood security and human health. The developed tool would allow a new level of post-harvest logistics, supporting availability of high-quality, nutritious, and fresh produce.
Animal Health Component
0%
Research Effort Categories
Basic
40%
Applied
50%
Developmental
10%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2012499104050%
4021430202050%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms; 402 - Engineering Systems and Equipment;

Subject Of Investigation
1430 - Greens and leafy vegetables; 2499 - Plant research, general;

Field Of Science
1040 - Molecular biology; 2020 - Engineering;
Goals / Objectives
Our specific objectives are:1) Discover invisible post-harvest changes that impending senescence and microbial spoilage in vegetables and fruits using imaging analysis;2) Identify genes, protein markers and chemical compounds that indicate freshness;3) Correlatehyperspectral imaging data with freshness indicators to develop an approach, FreshID.The FreshID approach has the potential to define afreshness signaturethat occurs prior to visible deterioration.A long-term goal of the proposed research is to aid development of an innovative FreshID device that can accurately estimate the freshness of produce. The value of such a device, an imager or lens offreshness signatureslies in the ability to accurately gauge produce freshness, independent of its original harvest condition or its microbial contamination status. In addition, the FreshID toolbox including these indicators and molecular markers associated with freshness can be used in the process of breeding for delaying post-harvest degradation and extending the shelf life of vegetables and fruits.
Project Methods
Hyperspectral imaging of broccoli senescence to indicate the freshness of vegetablesThe value of hyperspectral imaging stems from its promise of being able to identify and distinguish between different materials (or chemical compositions) at a sub-pixel level. This is often accomplished through spectral unmixing analysis (that is, estimating the materials found in a scene and each pixel's percentage associated with each material). However, standard spectral unmixing analysis fails to use all available information about a scene and is generally limited to simple mixing models that do not take into account known physical realities associated with hyperspectral imagery (such as variability and locally constrained materials). Furthermore, unmixing of hyperspectral data is an ill-posed inverse problem and multiple solutions exist. Many methods have been developed to estimate solutions by constraining the solution space using sparse assumptions, geometrical constraints, and other approaches. These methods do not constrain the problem using scene-specific information to guide analysis to the right answer but, instead, constrain it based on broad assumptions.In this work, we have extensive knowledge about the objects being images and this knowledge can be leveraged to improve hyperspectral analysis and unmixing. Information such as time since harvest, nutritional content, maturity and firmness can be used to constrain the model used for unmixing and analysis. Specifically, we will develop a hierarchical Bayesian model and associated parameter estimation algorithms forSemi-Supervised Partial Membership Latent Dirichlet Allocation(sPM-LDA) for hyperspectral unmixing. The proposed sPM-LDA approach will leverage ancillary information to guide analysis, account for spectral variability, allow for localized materials/chemical compositions, and incorporate spatial information.RNA-Seq:Total RNA in samples ground in liquid N2will be extracted using TRIzol and RNeasy Plant Mini Kits (QIAGEN) and used for construction of a sub-library for multiplexing. The RNA-Seq for broccoli will be performed at the Interdisciplinary Center for Biotechnology Research (ICBR) at the University of Florida. A Biomek FXP Laboratory Automation Workstation with TRobot, which performs every aspect of liquid handling, will be used for library creation and sequencing. The platform is capable of walk-away automation of the preparation and sequencing of 200 RNA-Seq libraries a week using TruSeq RNA sample prep and NextSeq 500 system (Illumina). This equipment supports 2x 150-bp sequencing. One high output run result in ~400 million reads of sequencing.Data analysis of RNA-Seq:Sequence reads will be mapped to available genomes forBrassicaoleraceaandBrassica rapa(http://plants.ensembl.org/Brassica_oleracea&http://plants.ensembl.org/Brassica_rapa).For RNA-Seq data analysis, the Galaxy platform at UF Research Computing will be used. Workflow for read alignment will begin with fastq groomer, fastq QC, and fastq trimmer, then HISAT2 (daehwankimlab.github.io/hisat2/).Parameters will be adjusted for read lengths (typically about 150 bp for NexSeq500), but default settings will otherwise be used. Resulting bam files from HISAT2 will be analyzed for expression levels using Cufflinks, Cuffcompare, and Cuffdiff (http://bowtie-bio.sourceforge.net/index.shtml; Trapnell et al. 2012,http://cufflinks.cbcb.umd.edu/). Data will be extracted using the CummeRbund module (http://compbio.mit.edu/cummeRbund) in R (http://www.r-project.org)or blast2go (http://www.blast2go.com).Protein extraction and sample preparation:Proteinswill be extracted and purified from ground broccoli floret samples using a modified phenol extraction, followed by ammonium acetate-methanol precipitation. Eluted peptides will be ionized by a nano-electrospray source that integrates the LC-MS system. We will use the standard protocols provided by the UF-ICBR. Protein concentration in all extracts will be determined using the RC/DC™ protein assay kit and interfering compounds will be compensated for using the manufacturer's protocol. Bovine serum albumin will be employed as a standard. Proteins will be labeled using the stable dimethyl isotopes.Metabolomicsanalysis:We will prepare samples provided by UF-ICBR facilities to make compound volatiles. GC-MS-based metabolomics profiling and data analysis will be conducted by the ICBR. Integrated omics data enable the discovery of novel factors regulating the senescence and signaling pathways in broccoli.

Progress 03/15/22 to 03/14/23

Outputs
Target Audience:The targeted audiences included students,reesearchers, farmers, local growers, stake-holders.This study constitutes a proof-of-concept for a new, innovative approach to identify the true physiological age of fresh produce as a measure of freshness, quality, and remaining postharvest life that has thus far been out of reach. The project has contributed to the following project: a. USDAMulti-State project: NE1836: Improving Quality and Reducing Losses in Specialty Fruit and Vegetable Crops through Storage Technologies. Duration 10/01/2023 to 09/30/2028Duration 10/01/2023 to 09/30/2028 b.USDA Multi-State project: N-294: Improving Quality and Reducing Losses in Specialty Fruit and Vegetable Crops through Storage Technologies. Duration 10/01/2023 to 09/30/2028. c. It has drawn attention from local news, TV station, Padcast channel. The full list can be found at the Product section. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? We have provided machine learning and genomics analysis training for graduate students and undergraduate students. Threegraduate students and more than seveundergraduate students have been recruited and conduct internships to this project. The PD has contributed and taughtFreshID projectrelated online course. How have the results been disseminated to communities of interest? The project has drawn considerable attention to communities including newspapers (Fresh Grower etc), TV station 20 (CBS4 news), news report (The Growing Produce, The Morning AgClips etc), Podcast. The entire list can be found in the 'Target Audience' sections. What do you plan to do during the next reporting period to accomplish the goals? We are going to submit tworesearch article and one review article related to this project in2023. The results of this project will be presented in local, national and international conference as well as extension related workshops for local growers, farmers and consumers. We will collaborate with industry personel to devlelop FreshID App and easy-accessibel device to measure freshness of vegetables and fruit.

Impacts
What was accomplished under these goals? Under these goals, what we have accomplished are listed below: 1. We have one manuscript using Fresh ID tools that has been revised and wait for the final decision. 2. We are working on three manscripts and two of them should be submitted within 1-2 months. 3. We also prepare one methodolgy and one review article on this project.

Publications

  • Type: Journal Articles Status: Submitted Year Published: 2023 Citation: Xiaolei Guo, Alina Zare, and Liu T. (2023) Hyperspectral imaging analysis for the evaluation of chilling injury in postharvest avocado fruit. Postharvest Biology and Technology.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Yogesh Ahlawatf, Song Li, Eleni D. Pliakoni, Jeffrey Brecht, Liu T. (2022). Identification of senescence-associated genes in broccoli (Brassica oleracea) following harvest. Postharvest Biology and Technology. 183, 11729.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Chase K., Belisle C, Sargent S, Sandoya G, Huang C, Begcy K. Liu T. (2022) Characterization of senescence associated genes in Lactuca sativa with respect to shelf life. Florida Society for Horticultural Science.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Garcia E, Liu T. (2022) Establishing gene editing technology to generate seedless passion fruit. The American Society for Horticultural Science Meeting.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Xiaolei Guo, Alina Zare, and Liu T. (2023) Deep Interactive Annotation to Support Hyperspectral Image Analysis.NAPPN (North American Plant Phenotyping Network).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Liu, T., Guo X., Zare A. (2023). Imaging-based Machine Learning for Evaluating Freshness of Fruit and Vegetables. The PAG30 Plant & Animal Genome Meeting. San Diego, CA


Progress 03/15/21 to 03/14/22

Outputs
Target Audience:In this work, we identified candidate transcripts and related proteins that accurately reflect the physiological age or freshness during postharvest handling of broccoli (Brassica oleracea L.), other Brassica crops, and eventually additional unrelated species. The long-term goal of the proposed research is to aid development of an innovative tool to accurately estimate the freshness of produce. Such a tool would allow a new level of postharvest logistics, supporting availability of high-quality, nutritious, fresh produce. This pilot study constitutes a proof-of-concept for a new, innovative approach to identify the true physiological age of fresh produce as a measure of freshness, quality, and remaining postharvest life that has thus far been out of reach. This project has drawn considerable attentions. The major impacts includes: WCJB-TV20 news:The television channel was interested in covering this projectfor the station's What's Growing On segment. They have interviewed me. TV20 segment aired this project on May 13, 2021. The title of TV news is "What's Growing On: Scientists developing technology to read produce freshness signals." Here is the link:https://www.wcjb.com/2021/05/13/whats-growing-on-scientists-developing-technology-to-read-produce-freshness-signals/ Gainesville Sun newspaper:The title of this news report is 'Can't tell when fruits and veggies are going bad? UF researchers want to help'. The link to this report: https://www.gainesville.com/story/news/education/campus/2021/05/15/uf-ifas-and-engineering-scientists-study-food-decay-combat-waste/5071303001/ The Villages Daily Sun.The title of this news report is 'Florida trends: Preventing food waste and loss'. The link to this report: https://www.thevillagesdailysun.com/news/in_todays_daily_sun/florida-trends-preventing-food-waste-and-loss/article_7692238e-b142-11eb-a9c7-f382c7d5be2f.html Growing Produce: The title of the news report is 'How a Peek Inside Broccoli Genes Might Help Solve Food Waste Plight'. The link to this report: https://www.growingproduce.com/production/how-a-peek-inside-broccoli-genes-might-help-solve-food-waste-plight/ The Dailyadvant News: The title of the news report is 'How a Peek Inside Broccoli Genes Might Help Solve Food Waste Plight'. The link to this report: https://www.dailyadvent.com/news/9098ba2043f738da3da7dc3b84626cfe-How-a-Peek-Inside-Broccoli-Genes-Might-Help-Solve-Food-Waste-Plight The Growing America: The title of the news report is 'Fighting food waste: Researchers identify broccoli genes that affect freshness'. The link to this report: https://www.growingproduce.com/production/how-a-peek-inside-broccoli-genes-might-help-solve-food-waste-plight/ The Morning AgClips:The title of the news report is 'Fighting food waste: Researchers identify broccoli genes that affect freshness'. The link to this report: https://www.morningagclips.com/fighting-food-waste-researchers-identify-broccoli-genes-that-affect-freshness/ The Vegetables and Speciality Crops News (VSCnews): The title of the news report is 'Fresh Produce: How UF Scientists Are Using AI to Cut Food Waste, Loss'. The link to this report: https://specialtycropindustry.com/fresh-produce-florida-ai/ The News Break: The title of the news report is 'UF Scientists Use AI To Cut Food Waste'. The link to this report: https://www.newsbreak.com/news/2240387533315/uf-scientists-use-ai-to-cut-food-waste UF/IFAS News: The title of the news report is 'From Yellowed Broccoli to Mushy Avocados: How UF Scientists Are Using AI to Cut Food Waste, Loss'.The link to this report: http://blogs.ifas.ufl.edu/news/2021/05/04/how-uf-scientists-are-using-ai-to-cut-food-waste-loss/ UCDavis Postharvest Technology center "Research Highlights" newsletter. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?We have provided machine learning and genomics analysis training for graduate students and undergraduate students. Two graduate students and more than five undergraduate students have been recruited to this project. The PD has contributed to AI related online course, How have the results been disseminated to communities of interest?The project has drawn considerable attention to communities including newspapers (The Gainesville Sun, The Villages Daily Sun), TV station 20 (WCJB-TV20 news), news report (The Growing Produce, The Morning AgClips etc), Podcast (Streaming Science Podcast 2022). The entire list can be found in the 'Target Audience' sections. What do you plan to do during the next reporting period to accomplish the goals?We are going to submit two one research article and one review article related to this project in fall 2022. One of patent was under review right now. The results of this project will be presented in local, national and international conference as well as extension related workshops for local growers, farmers and consumers. We will collaborate with industry personel to devlelop FreshID App and easy-accessibel device to measure freshness of vegetables and fruit.

Impacts
What was accomplished under these goals? Under these goals, what we have accomplished are listed below: 1. We published one research article on the journal of Plant Phenomics to study freshness signature using AI and hyperspectral imaging; 2. We has published one review aricle on the journal of Frontier in Genetics; 3. Both transcriptional and proteomics analysis have been performed. A number of genes and proteins have been identified for freshness signature that will be tested in the second year; 4. One patent has been under reviewed.

Publications

  • Type: Journal Articles Status: Published Year Published: 2022 Citation: X Guo, Y Ahlawat, Liu T. A Zare, (2022) Evaluation of Postharvest Senescence in Broccoli Via Hyperspectral Imaging. Plant Phenomics. https://spj.sciencemag.org/journals/plantphenomics/2022/9761095/
  • Type: Journal Articles Status: Accepted Year Published: 2022 Citation: Liu T. Albornoz K., Deltsidis A., Beckles, D. (2022) Editoral: Postharvest Ripening, Senescence, and Technology. Frontier in Genetics. https://www.frontiersin.org/articles/10.3389/fgene.2022.920584/full
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2022 Citation: Liu, T., Guo X., Zare A. (2022). Imaging-based Machine Learning for Evaluating Freshness of Fruit and Vegetables. The XXIX Plant & Animal Genome Meeting. San Diego, CA
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2022 Citation: Liu, T., Guo X., Zare A. (2022). Machine Learning for the Molecular Evaluation of Fresh Produce Quality. XXXI International Horticultural Congress, August 14-20, 2022 - Angers, France.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2022 Citation: Liu, T., Guo X., Zare A. (2022). Machine Learning for Evaluating Freshness of Fruit and Vegetables. The XXIX Plant & Animal Genome Meeting. San Diego, CA
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2021 Citation: Liu T. (2021) Molecular Evaluation of Fresh Produce. Horticulture Research online webinar
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2021 Citation: Liu T. (2021) Machine Learning for the Molecular Evaluation of Fresh Produce. American Society of Horticultural Sciences (ASHS) Annual Conference.