Progress 09/15/23 to 09/14/24
Outputs
Target Audience:During this reporting period we have interacted with citrus industry stakeholders through regional, state in-person events and seminars and through the preparation of extension materials. We are particularly focused on raising awareness of the ongoing research supported through this proposal to growers interested in the adoption of new HLB-tolerant rootstocks in CA, TX and FL. We delivered at least 9 presentations at events attended by citrus industry stakeholders. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?One postdoctoral research associates and two graduate students were trained on research of citrus production and rootstocks and/or genetic analysis of citrus germplasm. Graduate students and postdoctoral researchers receive mentorship in research and also career advancement. This occurs through training focused one-on-one and group meetings, encouragement to establish an individualized development plan to identify and accomplish long-term career goals, and access to career and networking events at the relevant universities. ? How have the results been disseminated to communities of interest?We have presented information on the data collected from these trials to grower and other stakeholder communities and will continue to do so in the upcoming reporting period, including at least 9 presentations on this project to audiences composed mostly of citrus industry stakeholders. The goal is to ensure there is interest and awareness of these new HLB-tolerant rootstock hybrids to facilitate rapid adoption in relevant regions upon release. ? What do you plan to do during the next reporting period to accomplish the goals?This project is in no cost extension. We expect the remainder of the funds to be spent in the next year and project objectives will transitions to those outlined in 2023-70029-41305.
Impacts
What was accomplished under these goals?
Objective 1:Continued evaluation of next generation rootstock hybrids (grafted with a common sweet orange scion) in a series of field trials will support the selection and release of rootstock hybrids with superior performance. Two rootstocks were selected from these trials released by the USDA in 2024 (SuperSour 4 and SuperSour 5). In the last year phenotypic data related to tree health, tree size, fruit crop size, and fruit quality was collected from 21 sweet orange rootstock field trials in Florida. A mansucript summarizing the results of HLB-tolerant rootstock response to citrus nematode is in the final stages of revision at Plant Health Progress. Injections of oxytetracycline are now favored in Florida as a tool for controlling the symptoms of HLB.We have started injecting trees in one trial with the SuperSour rootstocks and measured productivity to assess the rootstock "potential". In addition, we have performed a salinity study with selected SuperSour rootstocks in the greenhouse. This greenhouse experiment is complete and analysis is ongoing. Objective 2: Genotype calls have been produced for all parents (48) and hybrids (>350). This genetic data has been integrated with phenotypic data collected from 5 field trials with at least 6 years of fruit production. Initial genome-wide assocation mapping and genomic prediction results in this data set are promising. Candidate regions were identified and genomic prediction accuracies were quite good (r>0.6) for this initial subset of data. As more trial data is collected this data set is expected to improve.
Publications
- Type:
Journal Articles
Status:
Accepted
Year Published:
2023
Citation:
Bowman KD. 2023. Four new SuperSour rootstocks for improved production of sweet orange in a huanglongbing environment. HortScience 58(12):1622-1625.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2024
Citation:
M..I. Hamid, K.D. Bowman, D.K. Seymour, and P.E. Rolshausen. Evaluation of Huanglongbing-tolerant citrus hybrid rootstocks for resistance to Tylenchulus semipenetrans. Plant Health Progress. Under Revision.
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Progress 09/15/22 to 09/14/23
Outputs
Target Audience:During this reporting period we have interacted with citrus industry stakeholders through regional and state in-person events and seminars and through the preparation of extension articles and other associated material. We are particularly focused on raising awareness of the ongoing research supported through this proposal to growers interested in the adoption of new HLB-tolerant rootstocks, both in CA and FL. We delivered at least 7 presentations at citrus industry events. To reach a broader audience an extension article summarizing the ongoing research supported by this proposal was posted on 'Science for Citrus Health' (https://ucanr.edu/sites/scienceforcitrushealth/). These efforts highlighted the future project goals as well as information on specific rootstocks and their future availability. Changes/Problems:There are no major changes in the workplan. Research funds from this proposal were not available to support the collection of field data until January 2022 and spending reflects this challenge. What opportunities for training and professional development has the project provided?Two postdoctoral research associates and two graduate students were trained on research on citrus production and rootstocks and/or genetic analysis of citrus germplasm. Graduate students and postdoctoral researchers receive mentorship in research and also career advancement. This occurs through training focused one-on-one and group meetings, encouragement to establish an individualized development plan to identify and accomplish long-term career goals, and access to career and networking events at the relevant universities. How have the results been disseminated to communities of interest?We have presented information on the data collected from these trials to grower and other stakeholder communities and will continue to do so in the upcoming reporting period, including at least 7 presentations on this project to audiences comprised mostly of citrus industry stakeholders. The goal is to ensure there is interest and awareness of these new HLB-tolerant rootstock hybrids to facilitate rapid adoption in relevant regions upon release. ? What do you plan to do during the next reporting period to accomplish the goals?Collection of field trial data for 2023/2024 season is ongoing as anticipated and will continue for the duration of the project. Hybrids will be continually evaluated as data becomes available to identify top performing rootstock hybrids with enhanced tolerance to HLB. Testing of released rootstocks from Bowman's USDA-ARS program will continue in CA to evaluate their response to other soileborne pathogens. Whole-genome genetic variation data will be integrated with phenotypic data to facilitate genome-wide dissection of genetic control of tree performance and disease progression. New selections will continue to be submitted to clean budwood programs in Florida and California in anticipation of future release. All PIs will continue to disseminate research results through extension activities at the local, regional, and national level.
Impacts
What was accomplished under these goals?
Objective 1: Data on field tree performance was collected during 2022-23 from 14 established replicated trials in Florida with sweet orange scion and containing about 350 different rootstocks. Data collected from trials included tree survival, tree size, canopy health, fruit yield, fruit quality, and CLas titer in leaf tissue. Tree care in the trials was continued using methods as is standard in commercial production in Florida. Comprehensive datasets through 2023 are being assembled for all trials to use for statistical and genetic analysis. Based on phenotypic and genetic analysis of the first set of 46 hybrids (doi: 10.3389/fpls.2023.1061663), as well as performance in additional trials, two selections were made in 2023 and are pending release by the USDA-ARS. Material for these hybrids as well as at least 30 other potentially promising hybrids is available as clean budwood from the FDACS program. Hybrid rootstocks from the USDA-ARS in Florida that are tolerant to HLB were also screened for their tolerance/resistance against four major California citrus root pathogens including Phytophthora nicotiana, Phytophthora citrophthora, Fusarium solani and the nematode Tylenchulus semipenetrans. These Florida citrus hybrid rootstocks included US-802, US-812, US-897, US-942, US-1283, US-1284, US-1516. Levels of resistance of these rootstocks were compared to the industry standard rootstocks Sour orange, Swingle citrumelo, Ridge and Cleopatra mandarin. The seeds of all citrus rootstocks were grown to seedlings under controlled conditions in growth chamber and challenged with the soilborne pathogens for 6 months (Aphis Permit# P526P-22-06877). Rootstock resistance was assessed as a measure of plant health phenotype (e.g., biomass, disease severity ratings) and abundance of pathogens. Fungi were quantified by qPCR following DNA extraction from roots. Nematodes were quantified by counting population from roots and soils. Sample processing and data analyses are currently being finalized. Resistance to these rootstocks to soilborne pathogens was also assessed by collecting root and soil samples from field trials in Florida. Nematode count from root and soil samples was done at University of Florida following sampling. Root and soil samples were also frozen and shipped to UC Riverside (Aphis Permit# 525-23-143-94712). Incidence and severity of Phytophthora and Fusarium pathogens will be evaluated by qPCR from root samples. A greenhouse study of salinity tolerance has also been initiated including the released rootstocks described. Objective 2: The genetic composition of the 350 rootstock hybrids combined with measurements of tree performance and fruit quality will enable genome-wide association mapping to dissect the genetic basis of traits associated with tolerance to HLB in the field. To initiate work on this objective and prepare for DNA extraction and sequencing, source plant material was identified for the 350 hybrids and parents and shipped from Ft. Pierce, Florida to Riverside, CA (APHIS permit #: P526P-22-03899). DNA extraction and sequencing for both parents and hybrids has been completed. Parents were sequenced to an average depth of 56X coverage and hybrids to a lower depth of ~15X coverage. SNP calling for parents has been completed with over 10 million genetic variants detected. SNP calling of hybrids is ongoing and upon completion will be integrated with phenotypic data to identify alleles associated with HLB tolerance across environments. Deng has tested the TELL-seq sequencing technology on two citrus rootstock cultivars and begun testing single marker assay technologies for eventual development of markers linked to HLB tolerance, including characterization of genetic variation in accessions of interest, including Poncirus trifoliata which is the most important source of HLB tolerance in citrus rootstocks. To identify sequence polymorphism and develop specific molecular markers, we re-sequenced the genomes of four additional accessions of P. trifoliata (Flying Dragon, Little Leaf, Pomeroy, and Rubideau) and its only related evergreen species (P. polyandra) and the genomes of seven citrus rootstock cultivars (US-802, US-812, US-897, US-942, Carrizo, Swingle, and X639) and three of their parents in the genus Citrus (Citrus grandis 'Siamese', C. paradisi 'Duncan' grapefruit, and C. reticulata 'Cleopatra'). Some of these varieties include parents of the 350 hybrids that form the basis of this proposal.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Bowman KD, McCollum G and Seymour DK (2023) Genetic modulation of Valencia sweet orange field performance by 50 rootstocks under huanglongbing-endemic conditions. Front. Plant Sci. 14:1061663. doi: 10.3389/fpls.2023.1061663
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Progress 09/15/21 to 09/14/22
Outputs
Target Audience:During this reporting period we have interacted with citrus industry stakeholders through regional, state in-person events and seminars. We are particularly focused on raising awareness of the ongoing research supported through this proposal to growers interested in the adoption of new HLB-tolerant rootstocks, both in CA and FL. Seymour presented information on new HLB tolerant rootstocks at the California Citrus Conference in October, 2021 and at UCR Citrus Day, an field-day at UCR for growers and other stakeholders. These presentations highlighted the future goal and timeline for future availability of HLB-tolerant rootstocks in both regions. Changes/Problems:There are no major changes in the workplan. Research funds from this proposal were not available to support the collection of field data until January 2022 and spending reflects this challenge. What opportunities for training and professional development has the project provided?Two postdoctoral research associates were trained to analyze citrus genome sequencing data. Graduate students and postdoctoral researchers receive mentorship in research and also career advancement. This occurs through training focused one-on-one and group meetings, encouragement to establish an individualized development plan to identify and accomplish long-term career goals, and access to career and networking events at the relevant universities. ? How have the results been disseminated to communities of interest?We have presented information on the data collected from these trials to grower and other stakeholder communities and will continue to do so in the upcoming reporting period, including a presentation by Bowman on this topic in October 2022. The goal is to ensure there is interest and awareness of these new HLB-tolerant rootstock hybrids to facilitate rapid adoption in relevant regions upon release. ? What do you plan to do during the next reporting period to accomplish the goals?Collection of field trial data for 2022/2023 season is ongoing as anticipated and will continue for the duration of the project. Hybrids will be continually evaluated as data becomes available to identify top performing rootstock hybrids with enhanced tolerance to HLB. Permits have been obtained to move seed and leaf material from Florida to California for greenhouse studies at UCR to start assessing under controlled conditions resistance levels of citrus hybrid rootstocks to Phytophthora and nematodes. Rolshausen lab will visit Florida to begin assessing under field conditions resistance levels of citrus hybrid rootstocks to Phytophthora and nematodes. Whole-genome sequence data will be produced and genetic variants identified in both parents and hybrids and will facilitate genome-wide dissection of genetic control of tree performance and disease progression. New selections will continue to be submitted to clean budwood programs in Florida and California in anticipation of future release. All PIs will continue to disseminate research results through extension activities at the local, regional, and national level.
Impacts
What was accomplished under these goals?
Objective 1: Field performance data was collected from October 2021 to April 2022 from the 16 sweet orange rootstock field trials to be used for the ECDRE project. Data collected from the trials included tree survival, tree size, canopy health, amount of fruit crop, and several fruit quality factors that are important for sweet orange. Some data has been collected monthly since October 2021, but research funds from this proposal were not available to support these activities until January 2022, despite the award date in September 2021. Nine rootstock hybrids with excellent field performance in early planted trials associated with this project have been submitted to the California Citrus Clonal Protection program for introduction into California, as planned. Material for these hybrids is available as clean budwood from the FDACS program. Three of the nine have been released by the USDA already and would be freely available in CA once they have completed quarantine and clean-up. To initiate testing of soilborne pathogens in the greenhouse in California Rolshausen has an APHIS permit (#P526-211124-004) to move citrus seeds from the USDA-ARS in Florida (Dr Bowman) to UC Riverside (Dr. Rolshausen). A manuscript summarizing the performance of 46 rootstocks in the first of the 16 field trials planted is near submission. The phenotypic data presented in this manuscript forms the basis of the first selections to be made from this material with tentative release in early 2023. Objective 2: The genetic composition of the 350 rootstock hybrids combined with measurements of tree performance and fruit quality will enable genome-wide association mapping to dissect the genetic basis of traits associated with tolerance to HLB in the field. To initiate work on this objective and prepare for DNA extraction and sequencing, source plant material was identified for the 350 hybrids and parents and shipped from Ft. Pierce, Florida to Riverside, CA (APHIS permit #: P526P-22-03899). DNA extraction and sequencing is in progress. Initial estimates of heritability were obtained for approximately 30 traits related to tree performance and disease progression using pedigree-based analysis of the first trial of 46 new hybrids. The heritability for traits related to overall yield and tree size (a proxy for health) was substantial (>0.4), indicating there is rootstock-mediated genetic control of HLB-tolerance in the common scion. We will work to dissect the specific variants underlying these differences with the whole-genome sequence data generated for this project. Deng has tested the TELL-seq sequencing technology on two citrus rootstock cultivars and begun testing single marker assay technologies for eventual development of markers linked to HLB tolerance.
Publications
- Type:
Journal Articles
Status:
Accepted
Year Published:
2021
Citation:
Bowman Kim D., McCollum Greg, Albrecht Ute. A New Strategy for Breeding Superior Citrus Rootstocks. Frontiers in Plant Science (2021). DOI=10.3389/fpls.2021.741009
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