Progress 07/15/19 to 06/30/23
Outputs
Target Audience:(1) The project PI (Jia) and key personnel (Chater) and PI's graduate students (Traband and Wang)presented project progress and disseminated the acquired knowledge in joint lab meetings, in which the PI (Jia), co-PI (Roose), and citrus scientists and researchers on campus meet every month for synergy activities. This target audience includes UCR professors, researchers, scientists, students and others. (2) The project PI (Jia) organize weekly lab meeting where key personnel (Chater) and participating graduate student (Traband) reported project progress and disseminated the acquired knowledge. (3) The project PI (Jia) and graduate student (Traband) presented progress and disseminated the acquired knowledge in a monthly joint zoom meeting for leaf-shape research in blueberry, cranberry and citrus, which involves researchers and scientists on both the East and West coasts of the US and some researchers in China. (4) The project PI (Jia) presented and discussed some of the work in the international Plant and Animal Genome conference. The graduate student (Traband) presented some of the results in the American Society of Plant Biologists conference. (5) One methodology paper has been published inApplications in Plant Sciences. One manuscript was submitted toHorticulturae for pear review. The leaf shape data has been made publicly available. Two and more papers will be published based on this project. (6) When all papers are published, the metabolimic data will be made publically available so other researchers and breeders may use it. Changes/Problems:There have been no significant changes in the project. However, the COVID-19 pandemic has had a major impact, resulting in delays in project progress. We have successfully published two papers (please refer to this year's product), and we are currently working on the major publication(s) related to GWAS analysis (Objective 1) of leaf metabolite profiles and multi-omics analysis (Objective 3). Once these planned manuscripts undergo peer review, we will promptly deposit the metabolite profile data into a publicly available database, ensuring accessibility for other researchers. All future publications resulting from this project will acknowledge the support provided by NIFA. We deeply appreciate your continued support. What opportunities for training and professional development has the project provided?1. A postdoc (John Chater) has been involved in all the research activities for training purposes, paving his career path to a faculty and an expert in agricultural sciences. Dr. Chater is currently a tenure-track Assistant Professor in the Department of Horticultural Sciences, Citrus Research and Education Center, at University of Florida. 2. A Ph.D. graduate student in plant biology major (Ryan Traband) has been involved in all of the research activities, which allows for hand-on experiences in field work, web-lab experimental assay, and dry-lab bioinformatics analysis. Such a training program will prepare Ryan for a future expertise in the food and agricultural sciences, with an emphasis on breeding improved crops by leveraging cutting-edge multi-omics based technologies. Ryan has successfully passed the qualifying exam this year. Ryan has submitted a first-author manuscript to Horticulturae, and publsihed a coauthor paper in Applications in Plant Sciences. 3. A second Ph.D. graduate student in GGB program (Xuesong Wang) has been involved in the bioinformatics analysis of leaf shape data. Xuesong published a coauthur paper inApplications in Plant Sciences. 4. Six undergraduate students have been involved in leaf sample collection. 5. Three high-school interns were involved inthe project. How have the results been disseminated to communities of interest?1. Results fromthis FACT project have been mainly disseminated to the UCR research communities through joint lab meetings, in which the PI (Jia), co-PI (Roose), and citrus scientists and researchers on campus meet every month for synergy activities. This community includes UCR professors, researchers, scientists, students and others. In these monthly meetings, the project PI (Jia), key personnel (Chater), andgraduate students (Traband & Wang) presented project progress, proposed methodologies, maps, and acquired and preliminary data and knowledge to the audience. 2. The project PI (Jia) organize weekly lab meeting where key personnel (Chater) andgraduate students (Traband & Wang) reported project progress and disseminated the acquired knowledge to the lab members. 3. The project PI (Jia) and graduate students (Traband &Wang) presented progress and disseminated the acquired knowledge in a monthly joint zoom meeting for leaf-shape research in blueberry, cranberry and citrus, which involves researchers and scientists on both the East and West coasts of the US and some researchers in China. A paper has been published inApplications in Plant Sciences and another manuscript has been submitted toHorticulturae. 4. The project PI (Jia) presented and discussed some of the work in the international Plant and Animal Genome conference. The graduate students (Traband & Wang) presented some of the results in the international Plant and Animal Genomeconference (poster presentation). What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
1) Objective 2 was completed.All the intended data, including leaf metabolite data, leaf shape data, and genomic data for 200+ citrus,have been collected for this project. 2) Due to the impact of COVID-19, the progress of the project has been postponed. We have published two papers (see this year's product) but are still working on the major publication(s) regarding GWAS analysis (Objective 1) of leaf metabolite profiles and multi-omics analysis (Objective 3). Once the planned manuscripts are submitted for peer review, we will promptly deposit the metabolite profile data in a publicly available database, making it accessible to other researchers for further use.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Bowman, C., Traband, R., Wang, X., Knowles, S., Lo, S., Jia, Z., Vorsa, N., Herniter, I. (2023) Multiple Leaf Sample Extraction System (MuLES): Another method for automated morphometric leaf studies. Applications in Plant Sciences. e11513. doi: 10.1002/aps3.11513
- Type:
Journal Articles
Status:
Under Review
Year Published:
2023
Citation:
Ryan C. Traband, Xuesong Wang, Jill Lui, Lei Yu, Yoko Hiraoka, Ira A. Herniter, Christian Bowman, Mariano Resendiz, Zixian Wang, Sara P. Knowles, Sassoum Lo, Daniel H. Chitwood, Louis Santiago, Tracy Kahn, Danelle Seymour, Mikeal L. Roose, John M. Chater, Zhenyu Jia (2023) Exploring the Phylogenetic Relationship among Citrus through Leaf Shape Traits: A Morphological Study on Citrus Leaves. Horticulturae
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Progress 07/15/21 to 07/14/22
Outputs
Target Audience:Due to the COVID-19 pandemic situation which has resulted in shelter in place orders and strict social distancing guidelines, there have been limitations on which types of activities would be allowable by the university. Despite the challenges caused by the COVID-19 pandemic, we have achieved the following outreach and extension activities, reaching a wide target audience: (1) The project PI (Jia) and key personnel (Chater) presented project progress and disseminated the acquired knowledge in joint lab meetings, in which the PI (Jia), co-PI (Roose), and citrus scientists and researchers on campus meet every month for synergy activities. This target audience includes UCR professors, researchers, scientists, students and others. (2) The project PI (Jia) organize weekly lab meeting where key personnel (Chater) and participating graduate student (Traband) reported project progress and disseminated the acquired knowledge. (3) The project PI (Jia) and graduate student (Traband) presented progress and disseminated the acquired knowledge in a monthly joint zoom meeting for leaf-shape research in blueberry, cranberry and citrus, which involves researchers and scientists on both the East and West coasts of the US and some researchers in China. (4) The project PI (Jia) presented and discussed some of the work in the international Plant and Animal Genome conference (online). The graduate student (Traband) presented some of the results in the American Society of Plant Biologists conference (in person). Changes/Problems:Due to the potential impact by pests and diseases, three trees of the planned 250 accessions have been removed from the CVC. However, this change will not substantially reduce the sample size for the GWAS and the multi-omic analysis, so it will not be a concern for the FACT project. What opportunities for training and professional development has the project provided? A postdoc (John Chater) has been involved in all the research activities for training purposes, paving his career path to a faculty and an expert in agricultural sciences. Dr. Chater is currently a tenure-track Assistant Professor in the Department of Horticultural Sciences, Citrus Research and Education Center, at University of Florida. A Ph.D. graduate student in plant biology major (Ryan Traband) has been involved in all of the research activities, which allows for hand-on experiences in field work, web-lab experimental assay, and dry-lab bioinformatics analysis. Such a training program will prepare Ryan for a future expertise in the food and agricultural sciences, with an emphasis on breeding improved crops by leveraging cutting-edge multi-omics based technologies. Ryan has successfully passed the qualifying exam this year. A second Ph.D. graduate student in GGB program (Xuesong Wang) has been involved in the bioinformatics analysis of leaf shape data. Six undergraduate students have been involved in leaf sample collection. A high-school intern was recruited for the project. How have the results been disseminated to communities of interest? At this stage, the preliminary results for this FACT project have been mainly disseminated to the UCR research communities through joint lab meetings, in which the PI (Jia), co-PI (Roose), and citrus scientists and researchers on campus meet every month for synergy activities. This community includes UCR professors, researchers, scientists, students and others. In these monthly meetings, the project PI (Jia), key personnel (Chater), and the new graduate student (Traband) presented project progress, proposed methodologies, maps, and acquired and preliminary data and knowledge to the audience. The project PI (Jia) organize weekly lab meeting where key personnel (Chater) and participating graduate student (Traband) reported project progress and disseminated the acquired knowledge to the lab members. The project PI (Jia) and graduate student (Traband) presented progress and disseminated the acquired knowledge in a monthly joint zoom meeting for leaf-shape research in blueberry, cranberry and citrus, which involves researchers and scientists on both the East and West coasts of the US and some researchers in China. The project PI (Jia) presented and discussed some of the work in the international Plant and Animal Genome conference (online). The graduate student (Traband) presented some of the results in the American Society of Plant Biologists conference (in person). What do you plan to do during the next reporting period to accomplish the goals? We plan to complete the task of taking photos of representative leaves for the 250 accessions. The derivation of leaf shape phenotypes is expected to be completed at the start of the third reporting period. We plan to complete GWAS analysis for certain traits which will become available during the next reporting period. We also plan to start the development and execution of advanced bioinformatics methods to analyze phenomic (traditional traits, leaf shape phenotypes, and traits derived from drones), genomic, and metabolomic variables to identify genetic determinants for agronomically important traits. We plan to complete the development of the new multiscale association study based on available data. We will continue outreach and extension activities for disseminating the knowledge acquired from this project. We plan to start applying for grants to continue the research based on the findings and knowledge basis developed from this project.
Impacts
What was accomplished under these goals?
We used genomic data of the entire CVC to select 250 of the most genetically diverse accessions for the project, which is a first and most important step for the planned GWAS analysis. We collected composite leaf samples for each of 250 target CVC accessions, and metabolomic profiling of these leaf samples were completed UCR Metabolomics Core for metabolic profiles. We took photos for representative leaf samples for each of over 100 citrus accessions. The photos of the remaining 100+ accessions will be collected in Spring 2023. Bioinformatics algorithms are being used to derive leaf shape phenotypic data from these samples, which will be employed by the planned GWAS analysis and the new multiscale association study. We used drones to collect image data for the entire CVC. These image data are being analyzed to derive high throughput phenotypic data, including tree height, canopy volume, canopy surface area, tree health (chlorophyll content as quantified by SPAD meter), and pest and disease resistance. These traits will be analyzed using the planned GWAS analysis and the new multiscale association study. New maps of the CVC have been developed for identification and sampling of the target accessions, leveraging the combined use of traditional CVC map and drone images of CVC. All trees involved in the study are identified and plotted on the site maps so that trees can be identified or excluded for trees to be characterized for health and disease status, if applicable. These site maps allow for sampling protocols and planning in a randomized and efficient manner. We have developed an efficient protocol of sampling leaves from the target accessions of the CVC. This protocol had been used to successfully collect leaf samples from over 60 accessions within two consecutive days under the restrictive working conditions caused by COVID-19 in 2020. The same protocol has been applied this year to collect the remaining 75% of the planned leaf samples in an efficient manner. The available multi-dimensional data are being analyzed for publications.
Publications
- Type:
Conference Papers and Presentations
Status:
Submitted
Year Published:
2022
Citation:
Ryan Traband, Xuesong Wang, Christian Bowman, Jill Lui, John M. Chater, Zhenyu Jia (2022) Genome Wide Association Study of Citrus Leaf Shape Diversity. The American Society of Plant Biologists conference. Poster Presentation
- Type:
Journal Articles
Status:
Submitted
Year Published:
2022
Citation:
Christian S. Bowman, Ryan Traband, Xuesong Wang, Sara P. Knowles, Sassoum Lo, Zhenyu Jia, Nicholi Vorsa, Ira A. Herniter (2022) Multiple Leaf Sample Extraction System (MuLES): A novel method for automated morphometric leaf studies. Frontiers in Plant Sciences
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Progress 07/15/20 to 07/14/21
Outputs
Target Audience:Due to the COVID-19 pandemic situation which has resulted in shelter in place orders and strict social distancing guidelines, there have been limitations on which types of activities would be allowable by the university. Despite the challenges caused by the COVID-19 pandemic, we have achieved the following outreach and extension activities, reaching a wide target audience: (1) The project PI (Jia) and key personnel (Chater) presented project progress and disseminated the acquired knowledge in joint lab meetings, in which the PI (Jia), co-PI (Roose), and citrus scientists and researchers on campus meet every month for synergy activities. This target audience includes UCR professors, researchers, scientists, students and others. (2) The project PI (Jia) organize weekly lab meeting where key personnel (Chater) and participating graduate student (Traband) reported project progress and disseminated the acquired knowledge. (3) The project PI (Jia) and graduate student (Traband) presented progress and disseminated the acquired knowledge ina monthly joint zoom meeting for leaf-shape research in blueberry, cranberry and citrus, which involves researchers and scientists on both the East and West coasts of the US and some researchers in China. Changes/Problems:Our drone technician, who is partially supported by the FACT project, has recently retired from campus due to the lack of funding, which will limit our ability to derived high-throughput phenotype data from the drone images of the CVC. We plan to apply for new grants so we can support a drone technician who can help with the FACT project in the third reporting period. Due to the potential impact by pests and diseases, three trees of the planned 250 accessions have been removed from the CVC. However, this change will not substantially reduce the sample size for the GWAS and the multi-omic analysis, so it will not be a concern for the FACT project. What opportunities for training and professional development has the project provided? A postdoc (John Chater) has been involved in all the research activities for training purposes, paving his career path to a faculty and an expert in agricultural sciences. Dr. Chater has been invited to an onsite interview for a faculty position in a famous university. A Ph.D. graduate student in plant biology major (Ryan Traband) has been involved in all of the research activities, which allows for hand-on experiences in field work, web-lab experimental assay, and dry-lab bioinformatics analysis. Such a training program will prepare Ryan for a future expertise in the food and agricultural sciences, with an emphasis on breeding improved crops by leveraging cutting-edge multi-omics based technologies. Ryan has successfully passed the qualifying exam this year. A second Ph.D. graduate student in GGB program (Xuesong Wang) has been involved in the bioinformatics analysis of leaf shape data. Three undergraduate students have been involved in leaf sample collection. How have the results been disseminated to communities of interest? At this stage, the preliminary results for this FACT project have been mainly disseminated to the UCR research communities through joint lab meetings, in which the PI (Jia), co-PI (Roose), and citrus scientists and researchers on campus meet every month for synergy activities. This community includes UCR professors, researchers, scientists, students and others. In these monthly meetings, the project PI (Jia), key personnel (Chater), and the new graduate student (Traband) presented project progress, proposed methodologies, maps, and acquired and preliminary data and knowledge to the audience. The project PI (Jia) organize weekly lab meeting where key personnel (Chater) and participating graduate student (Traband) reported project progress and disseminated the acquired knowledge to the lab members. The project PI (Jia) and graduate student (Traband) presented progress and disseminated the acquired knowledge in a monthly joint zoom meeting for leaf-shape research in blueberry, cranberry and citrus, which involves researchers and scientists on both the East and West coasts of the US and some researchers in China. What do you plan to do during the next reporting period to accomplish the goals? The metabolomic profiling for the entire 250 target accessions is expected to be completed at the start of the third reporting period. We plan to complete the task of taking photos of representative leaves for the 250 accessions. The derivation of leaf shape phenotypes is expected to be completed at the start of the third reporting period. We plan to complete GWAS analysis for certain traits which will become available during the next reporting period. We also plan to start the development and execution of advanced bioinformatics methods to analyze phenomic (traditional traits, leaf shape phenotypes, and traits derived from drones), genomic, and metabolomic variables to identify genetic determinants for agronomically important traits. We plan to start the development of the new multiscale association study based on available data. We will continue outreach and extension activities for disseminating the knowledge acquired from this project. We plan to start applying for grants to continue the research based on the findings and knowledge basis developed from this project.
Impacts
What was accomplished under these goals?
We used genomic data of the entire CVC to select 250 of the most genetically diverse accessions for the project, which is a first and most important step for the planned GWAS analysis. We collected composite leaf samples for each of 250 target CVC accessions, and these leaf samples are being analyzed at the UCR Metabolomics Core for metabolic profiles. We took photos for representative leaf samples for each of over 60 citrus accessions. The photos of the remaining 200 accessions will be collected in this summer (2021). Bioinformatics algorithms are being used to derive leaf shape phenotypic data from these samples, which will be employed by the planned GWAS analysis and the new multiscale association study. We used drones to collect image data for the entire CVC. These image data are being analyzed to derive high throughput phenotypic data, including tree height, canopy volume, canopy surface area, tree health (chlorophyll content as quantified by SPAD meter), and pest and disease resistance. These traits will be analyzed using the planned GWAS analysis and the new multiscale association study. New maps of the CVC have been developed for identification and sampling of the target accessions, leveraging the combined use of traditional CVC map and drone images of CVC. All trees involved in the study are identified and plotted on the site maps so that trees can be identified or excluded for trees to be characterized for health and disease status, if applicable. These site maps allow for sampling protocols and planning in a randomized and efficient manner. We have developed an efficient protocol of sampling leaves from the target accessions of the CVC. This protocol had been used to successfully collect leaf samples from over 60 accessions within two consecutive days under the restrictive working conditions caused by COVID-19 in 2020. The same protocol has been applied this year to collect the remaining 75% of the planned leaf samples in an efficient manner.
Publications
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Progress 07/15/19 to 07/14/20
Outputs
Target Audience:Due to the COVID-19 pandemic situation which has resulted in shelter in place orders and strict social distancing guidelines, there have been limitations on which types of activities would be allowable by the university. Despite the challenges caused by the COVID-19 pandemic, we have achieved the followingoutreach and extension activities, reaching a wide target audience: 1) The project's PI (Jia), co-PI (Roose), key personnel (Chater), and collaborator (Kahn) participated in the 2020 Plant and Animal Genome (PAG) conference, specifically the Citrus Genome workshop to meet scientists, researchers, and breeders to discuss our FACT project. These scientists, researchers and breeders are of an international target audience and some genomic and admixture data that were presented in this conference are to be used for the GWAS and other bioinformatics methods for this FACT project. Getting feedback from this international target audience allowed for these preliminary data to be reviewed, vetted and discussed by others in the discipline. 2) The co-PI (Roose) and collaborator (Kahn) participated in theUCR Citrus Day for industry in January 2020 to meet with stakeholders to inquire about their most pressingneeds andto discuss how ourtechnology can be tailored to their needs. This target audience includes industry stakeholders such as growers, extension specialists that work with citrus growers and professors, researchers, and scientists from UCR and other academic and government institutions, including USDA-ARS. 3) The project PI (Jia) and key personnel (Chater) presented project progress and disseminated the acquired knowledgein jointlab meetings, in which the PI (Jia), co-PI (Roose), and citrus scientists and researchers on campus meet every month for synergy activities.This target audience includes UCR professors, researchers, scientists, students and others. Changes/Problems:One major change in approach was that we collected approximately 25% of the leaf samples for metabolomic analysis instead of 75% to 100% this year, per the timeline. The reason that this change was made is because of the COVID-19 pandemic which caused, and continues to cause, shelter in place orders and social distancing guidelines at University of California, Riverside and in our Department of Botany and Plant Sciences. Another reason why we collected 25% of the samples during this first season is because the UCR Metabolomics Core is functioning at reduced capacity due to COVID-19 and related social distancing and shelter in place policies. This caused there to be logistical challenges that were overcome by adding additional personnel to the project, which was another major change. Because we were only allowed one person per vehicle and shared vehicles became a hazard, the project personnel involved in the leaf sample data collection was instructed to drive their own vehicles. This also caused logistical challenges when considering transport of leaf samples submerged in liquid nitrogen from the CVC in the Department of Agricultural Operations to the Metabolomics Core Facility at Batchelor Hall. Because we were not allowed a second person in the vehicles, vehicle transport was not possible. In order to transport the samples, we purchased extra flask containers for liquid nitrogen transport and used a cart from my lab to transport sample manually on foot so that there is no hazard in the methods. We also purchased Falcon tubes because using ones from other labs was considered a hazard. What opportunities for training and professional development has the project provided? A postdoc (John Chater) has been involved in all the research activities for training purposes, paving his career path to a faculty and an expert in agricultural sciences. A Ph.D. graduate student in plant biology major (Ryan Traband) has been involved in all of the research activities, which allows for hand-on experiences in field work, web-lab experimental assay, and dry-lab bioinformatics analysis. Such a training program will prepare Ryan for a future expertise in the food and agricultural sciences, with an emphasis on breeding improved crops by leveraging cutting-edge multi-omics based technologies. How have the results been disseminated to communities of interest? At this stage, the preliminary results for this FACT project have been mainly disseminated to the UCR research communities through joint lab meetings, in which the PI (Jia), co-PI (Roose), and citrus scientists and researchers on campus meet every month for synergy activities. This community includes UCR professors, researchers, scientists, students and others. In these monthly meetings, the project PI (Jia), key personnel (Chater), and the new graduate student (Traband) presented project progress, proposed methodologies, maps, and acquired and preliminary data and knowledge to the audience. The project's PI (Jia), co-PI (Roose), key personnel (Chater), and collaborator (Kahn) participated in the 2020 Plant and Animal Genome (PAG) conference, specifically the Citrus Genome workshop to meet scientists, researchers, and breeders to discuss and disseminate the progress and prelimary results of our FACT project. These scientists, researchers and breeders are of an international target audience and some genomic and admixture data that were presented in this conference are to be used for the GWAS and other bioinformatics methods for this FACT project. Getting feedback from this international target audience allowed for these preliminary data to be reviewed, vetted and discussed by others in the discipline. The co-PI (Roose) and collaborator (Kahn) participated in the UCR Citrus Day for industry in January 2020 to meet with stakeholders to inquire about their most pressing needs and to discuss how our technology can be tailored to their needs. This target audience includes industry stakeholders such as growers, extension specialists that work with citrus growers and professors, researchers, and scientists from UCR and other academic and government institutions, including USDA-ARS. What do you plan to do during the next reporting period to accomplish the goals? Given the COVID-19 pandemic is no longer anticipated to a barrier for research activities in the next reporting period, we plan to complete sampling leaf samples for the target 250 CVC accessions. The metabolomic profiling for the entire 250 target accessions is expected to be completed at the start of the third reporting period. We plan to complete the task of taking photos of representative leaves for the 250 accessions. The derivation of leaf shape phenotypes is expected to be completed at the start of the third reporting period. We plan to complete GWAS analysis for certain traits which will become available during the next reporting period. We also plan to start the development and execution of advanced bioinformatics methods to analyze phenomic (traditional traits, leaf shape phenotypes, and traits derived from drones), genomic, and metabolomic variables to identify genetic determinants for agronomically important traits. We plan to start the development of the new multiscale association study based on available data. We will continue outreach and extension activities for disseminating the knowledge acquired from this project.
Impacts
What was accomplished under these goals?
We used genomic data of the entire CVC to select 250 of the most genetically diverse accessions for the project, which is a first and most important step for the planned GWAS analysis. We collected composite leaf samples for each of over 60 accessions (25% of the 250 target CVC accessions), and these leaf samples are being analyzed at the UCR Metabolomics Core for metabolic profiles. We took photos for representative leaf samples for each of over 60 citrus accessions. Bioinformatics algorithms are being used to derive leaf shape phenotypic data from these samples, which will be employed by the planned GWAS analysis and the new multiscale association study. We used drones to collect image data for the entire CVC. These image data are being analyzed to derive high throughput phenotypic data, including tree height, canopy volume, canopy surface area, tree health (chlorophyll content as quantified by SPAD meter), and pest and disease resistance. These traits will be analyzed using the planned GWAS analysis and the new multiscale association study. New maps of the CVC have been developed for identification and sampling of the target accessions, leveraging the combined use of traditional CVC map and drone images of CVC. All trees involved in the study are identified and plotted on the site maps so that trees can be identified or excluded for trees to be characterized for health and disease status, if applicable. These site maps allow for sampling protocols and planning in a randomized and efficient manner. We have developed an efficient protocol of sampling leaves from the target accessions of the CVC. This protocol has been used to successfully collect leaf samples from over 60 accessions within two consecutive days under the restrictive working conditions caused by COVID-19. The same protocol will be applied next year to collect the remaining 75% of the planned leaf samples.
Publications
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