Progress 09/01/23 to 08/31/24
Outputs Target Audience:Hawaii's statewide coffee industry which includes producers and stakeholders. Changes/Problems:An additional (fifth) field trial has been planned as a backup. What opportunities for training and professional development has the project provided?In addition to a post-doc and 4 technicians HARC, this project allows Wang lab to train 7 interns from Career Skills Program (US Army, Schofield Barrack) and 8 high school interns from HARC Internship Programs on coffee plant maintenance, CLR controls, pollinations, sample collections, CLR bioassays, etc. An additional full-time technician at ARS was trained to provide full support to the bioassay pipeline in Keith lab. One technician and one post-doc were trained in Yu lab at ARS in Hilo. We anticipate greater interaction and training for Hawaii coffee producers in the next few years of the project as results are solidified and shared by project researchers. How have the results been disseminated to communities of interest?Research results and outreach is being disseminated via such methods as workshops, conferences, expos, field days, webinars, emails, newsletters, farm visits, phone calls, texts, in-person and small group meetings, publications, videos, and websites (Kawabata). Delivery methods such as newsletter announcements and conference and expo participation reach a broader audience. Whereas farm visits, phone calls, texts, emails, virtual and in-person events target the individual and small groups. Four PIs (Wang, Matsumoto, Keith, and Kawabata) participated in the webinar series organized by PI Kawabata on coffee leaf rust-related research. The videos can be found at Welcome Coffee Growers! - Home (hawaiicoffeeed.com). What do you plan to do during the next reporting period to accomplish the goals?Objectives 1 and 2. Install field trials in 4 growers fields and start collecting phenotypic data such as growth habits (Wang, Matsumoto). The first planting will be at Dole Foods on Oahu. Keith lab will increase capacity for disk testing to improve throughput of the testing pipeline. A laboratory with expanded capacity for testing leaf disks is currently being established and should increase throughput by 2-to-3 times the current capacity. We will complete the bioassays and genotyping of remaining ~900 Catimor F2 plants and install field trial in a 5th location at USDA PBARC as backup (Wang, Matsumoto) Objective 3. Complete NGS-based bulk segregant analysis (BSA) and comparative bulk transcriptome analysis (Yu). Genome sequencing extreme segregants of the mapping population and bulk segregation analysis. Sequencing transcriptomes of extreme segregants of the mapping population. Objective 1-3. Kawabata and staff will work with project researchers to continue disseminating results and project updates on such topics as coffee leaf rust and its management, coffee breeding, germplasm, SNP and other molecular markers, coffee cupping and quality, tree phenotypic data, metabolomic information, principal component analyses, and new selections as related to the project. As appropriate, new data from this project will be incorporated into CLR integrated pest management recommendations for Hawaii producers. Project information will be shared with farmers, processors, industry professionals, researchers, and interested agencies and stakeholders through a wide variety of methods such as those mentioned. Output, participation, and impact will be recorded and measured by post-event and longer-term industry surveys. Summaries will be made available to the project and industry.
Impacts What was accomplished under these goals?
Objective 1. Select CLR-resistant coffee cultivars with high beverage quality from the existing populations derived from the crosses between Catimor and Hawaiian commercial cultivars. With combined effort from Keith lab and Wang lab, we have identified a total of 210 resistant, 939 tolerant, and 894 susceptible Catimor F2 seedlings from 14 crosses. The ratios of resistant/tolerant to susceptible plants varies by crosses and F1 individuals with a stronger effect from the maternal parents. All the resistant/tolerant plants were genotyped (Wang and Zhang) results confirmed the parentages for 11 of the crosses. The progeny of the other three crosses were either results of self-pollinations of the female parents or mislabeling, therefore eliminated from the trials. The resistant/tolerant plants with confirmed parentage have been divided into 4 groups and will be field tested along with 10 parents in 4 growers' fields on 4 different islands once the growers complete field preparation. Objective 2. Produce and select new cultivars through crosses of new sources of CLR-resistant varieties (eg. Obata) with Hawaiian commercial cultivars to anticipate arrival of new CLR races. We (Keith and Wang) identified 183 resistant, 243 tolerant, and 162 susceptible Obata F1 seedlings from 25 crosses. Genotyping confirmed the parentage of 21 crosses. Almost all the susceptible plants came from the 4 failed crosses. The resistant/tolerant plants with confirmed parentage have also been divided into 4 groups awaiting field trials. Objective 3. Develop marker assisted breeding systems for CLR-resistance and high beverage quality. Four parental lines utilized in the mapping populations were subjected to genome sequencing using the PacBio long-read sequencing platform. These lines consisted of two CLR resistance Timor hybrids (T5175 and T8667) and twoCLR susceptible Hawaiian cultivars (Typica and Mokka). Hi-C sequencing facilitated the assembly of all four genomes into 22 pseudo-molecules, aligning with the haploid chromosome number. The contig N50 values ranged from 48.5Mb to 49.1Mb. A total of 222,771 SNP and 557,623 InDel markers have been identified from the genome sequences. Outreach for Objectives 1 to 3 (CoPI Kawabata): As research results become available, the dissemination of these science-based results and new project updates are being communicated to Hawaii's coffee industry by the UH-CTAHR Cooperative Extension Service. Outreach is being provided via such methods as workshops, conferences, expos, field days, webinars, emails, newsletters, farm visits, phone calls, texts, in-person and small group meetings, publications, videos, and websites. Within the year, 36 newsletter announcements have been sent to 1,433 extension clientele and stakeholders with each delivery. A demonstration field planted with CLR-resistant trees at the Kona Research Station is being established for the purpose of providing outreach to industry of varietal and selection tree phenology, cross-pollination, propagation including grafting, coffee quality, and more as related to this project. This field includes 'Obata' and Catimor hybrids. Since September 2022, Kawabata and staff organized 21 recorded presentations with live Q&A sessions following the virtual presentations. These videos included topics such as "Progress on Coffee Breeding for CLR Resistance", "Coffee Germplasm and Rust Resistant Varieties", "Catimor Hybrid CLR-resistant Coffee Project at the Kona Research Station", and "Managing CLR: A Research Update". These recorded presentations can be viewed at the Kona Extension YouTube account and at HawaiiCoffeeEd.com. On average, these recorded presentations were viewed by 320 people each. A total of 86 farm visits have been made throughout the state to provide outreach directly to farmers. Kawabata and staff organized an educational booth displays at the Kona Coffee Cultural Festival Hoolaulea in Kona (Nov. 2023), at the Kona Coffee Farmers Association Symposium in Kona (Mar. 2024), the Hawaii Coffee Association's Annual Conference in Oahu (Jul. 2024), and at the Maui Coffee Association's Seed to Cup Festival in Maui (Aug. 2024). These industry and public events held in the past year reached over 290 coffee producers and stakeholders directly and exposed over 4,500 other participants to information provided.
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Progress 09/01/22 to 08/31/23
Outputs Target Audience:Hawaii's statewide coffee industry which includes producers and stakeholders. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?In addition to a post-doc and several technicians HARC, this project allows Wang lab to train 1 intern from Career Skills Program (US Army, Schofield Barrack) and 9 high school interns from Hawaii State Department of Education and HARC Internship Programs on coffee plant maintenance, CLR controls, pollinations, sample collections, etc. Two individuals from HARC on Oahu were trained in the leaf disk assay methodology in Keith lab at ARS in Hilo. The outcome of this knowledge transfer will be to have experiments being conducted at both ARS and HARC to increase throughput of the testing pipeline. Laboratory experience in general microbiology and plant pathology, data collection, and data analysis have been provided to full- and part-time biological technicians and students working on the project at ARS in Hilo. One undergraduate student from UH-Hilo is involved in the project and has been trained with general plant molecular biology (Yu), data collection and data analysis at ARS in Hilo. We anticipate greater interaction and training for Hawaii coffee producers in the next few years of the project as results are solidified and shared by project researchers. How have the results been disseminated to communities of interest?Research results and outreach is being disseminated via such methods as workshops, conferences, expos, field days, webinars, emails, newsletters, farm visits, phone calls, texts, in-person and small group meetings, publications, videos, and websites (Kawabata). Delivery methods such as newsletter announcements and conference and expo participation reach a broader audience. Whereas farm visits, phone calls, texts, emails, virtual and in-person events target the individual and small groups. Four PIs (Wang, Matsumoto, Keith, and Kawabata) participated in the webinar series organized by PI Kawabata on coffee leaf rust-related research. The videos can be found at Welcome Coffee Growers! - Home (hawaiicoffeeed.com). Same four PIs presented research progress at Hawaii Coffee Association 28th Annual Conference on June 215-17, 2023. The presentations can be found at Hawaii Coffee Association - 2023 Conference Presentations. What do you plan to do during the next reporting period to accomplish the goals?Objectives 1 and 2. We will ramp up the capacity to improve throughput of the CLR-screening pipeline (Wang, Keith). CLR-resistant Catimor hybrids, all Obata hybrids, and selected control plants will be DNA typed to verify the genetic backgrounds (Wang, Zhang). Objective 3. Complete NGS-based bulk segregant analysis (BSA) and comparative bulk transcriptome analysis (Yu). Objective 1-3. Kawabata and staff will work with project researchers to continue disseminating results and project updates on such topics as coffee leaf rust and its management, coffee breeding, germplasm, SNP and other molecular markers, coffee cupping and quality, tree phenotypic data, metabolomic information, principal component analyses, and new selections as related to the project. As appropriate, new data from this project will be incorporated into CLR integrated pest management recommendations for Hawaii producers. Project information will be shared with farmers, processors, industry professionals, researchers, and interested agencies and stakeholders through a wide variety of methods such as those mentioned. Output, participation, and impact will be recorded and measured by post-event and longer-term industry surveys. Summaries will be made available to the project and industry.
Impacts What was accomplished under these goals?
Objective 1. Select CLR-resistant coffee cultivars with high beverage quality from the existing populations derived from the crosses between Catimor and Hawaiian commercial cultivars. Objective 2. Produce and select new cultivars through crosses of new sources of CLR-resistant varieties (eg. Obata) with Hawaiian commercial cultivars to anticipate arrival of new CLR races. Objective 3. Develop marker assisted breeding systems for CLR-resistance and high beverage quality. Objectives 1 and 2. A total of more than 5100 seedlings are currently grown at HARC facilities (PI Wang). More than 3000 3rd generation seedlings were produced via self-pollination of 57 existing hybrid coffee trees from 15 different crosses of Hawaiian commercial cultivars with Catimor (Objective 1). Approximately 650 2nd generation hybrids were generated from 63 cross-pollination between Obata and 16 cultivars (Objective 2). More than 1500 parent plants will be used as controls for both objectives. A lab was set up at HARC to increase CLR-resistance screening capacity, in addition to CoPI Keith Lab at PBARC, ARS, Hilo. Two-hundred-and-nine seedlings have been or are currently being tested for CLR-resistance at the two locations. Of the 73 individuals that have completed testing, 49 were found to be resistant to CLR. Furthermore, 82 previously produced field-grown hybrid plants were tested and 30 were found to be resistant (Keith). DNA extraction has been completed on this field-grown population (CoPI Yu). All the DNA samples have been quantified and are ready for RAD-Seq library construction. A contract was also signed with LGC Bioreseach Technologies for DNA typing of 2000 newly-produced seedlings (Wang and CoPI Zhang). Objective 3 (Yu). NGS-based bulk segregant analysis (BSA): The genome sequencing of the parental lines of the mapping populations, including T5175, T8667, Typica, and short Mokka, has been done at CoPI Zhang lab. The genome sequences have been assembled to chromosomes using our optimized protocol. The extreme segregants have been selected based on the leaf disc assays. Due to CLR infection, the trees have been stumped. Genome sequencing of the extreme segregants will be done as soon as new growth leaf tissues are available. Comparative bulk transcriptome analysis: To determine time points of sampling, we analyzed gene expression patterns of the immune response gene PR1 at 6 time points (12hr, 1 day, 2 days, 3 days, 1 week, and 2 weeks post-inoculation) in 6 F2 individuals (3 resistant and 3 susceptible). Three points have been selected for comparative bulk transcriptome analysis. Outreach for Objectives 1 to 3 (CoPI Kawabata): As research results become available, the dissemination of these science-based results and new project updates are being communicated to Hawaii's coffee industry by the UH-CTAHR Cooperative Extension Service. Outreach is being provided via such methods as workshops, conferences, expos, field days, webinars, emails, newsletters, farm visits, phone calls, texts, in-person and small group meetings, publications, videos, and websites. Within the year, 32 newsletter announcements have been sent to 1,435 extension clientele and stakeholders with each delivery. A demonstration field planted with CLR-resistant trees at the Kona Research Station is being established for the purpose of providing outreach to industry of varietal and selection tree phenology, cross-pollination, propagation including grafting, coffee quality, and more as related to this project. This field includes 'Obata', 'False Tupi', and Catimor hybrids. From February to March 2023, Kawabata and staff organized 11 recorded presentations with live Q&A sessions following the virtual presentations. These videos included topics such as "Coffee Breeding for CLR - Resistance at HARC", "Evaluation of Coffee Varieties for Hawaii", "Catimor Hybrid CLR-resistant Coffee Project at the Kona Research Station", and "Managing CLR: A Research Update". These recorded presentations can be viewed at the Kona Extension YouTube account and at HawaiiCoffeeEd.com. On average, these recorded presentations were viewed by 150 people each. Since September 2022, 47 farm visits have been made throughout the state to provide outreach directly to farmers. In November 2022, Kawabata and staff organized an educational booth display at the Kona Coffee Cultural Festival Hoolaulea in Kona. In February 2023, they also participated in the Kona Coffee Farmers Association Conference in Kona with an educational booth display. In June, they attended the Hawaii Coffee Association's Annual Conference in Kauai and provided outreach with an educational booth display and CTAHR research and extension update presentation. Further, Kawabata participated in a coffee tasting in Hilo hosted by Matsumoto of USDA PBARC to learn about and provide feedback for 25+ different varieties of coffee for cup quality. In July, staff participated in the Maui Coffee Association's Seed to Cup Festival with an educational booth display. These such events held in the past year reached over 430 coffee producers and stakeholders directly and exposed over 2,000 other participants to information provided.
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