Progress 09/01/23 to 08/31/24
Outputs
Target Audience:Three PIs on this project (Brown, Ferguson, Goodrich) presented at the Statewide Pistachio Day in January 2024, which attracted over 600 attendees. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?For Objectives 3 and 4, a PhD student mentored by Brown and Ferguson has collected data on dormant sticks and begun refining chill and heat accumulation models for pistachio. For Objective 7, aPhD student mentored by Tolhurstand Goodrich has begun data collection, literature review and learning about yield-weather and yield distribution models. For Objectives 4 and10, an MS student mentored by Heeremawas is optimizing the dormant stick assay and monitoring the cotton root rot plantings. How have the results been disseminated to communities of interest?Three PIs on this project (Brown, Ferguson, Goodrich) presented at the Statewide Pistachio Day in January 2024. For Objective 5, all genome assembly data will be deposited onhttps://pistachiomics.sf.ucdavis.edu/, alongside the existing 'Kerman' genomic data. For Objective 7, we are working with UC Davis SiteFarm and FNRIC to develop an interactive decision tool to allow the user to individualize parameters to help with management and investment decisions. What do you plan to do during the next reporting period to accomplish the goals?Two PIs on this project (Marino, Trouillas) will present at the Statewide Pistachio Day in January 2025. For Objective 1, we will identify an additional site to monitor the effects of deficit irrigation. For Objective 2, we will deploy our yield monitoring system in orchards being used for Objectives 1 and 3. For Objective 3, though we have genotyped ~1000 rootstocks at the Davis location, we now have several thousand more trees that have been phenotyped and not genotyped. We will launch a major effort to genotype these trees in early spring 2025. For Objective 4, another year of data collection is planned this upcoming spring with particular focus on collection datesbetween 47 and 55 Chill portions. For Objective 5, once the HiFi sequencing of six additional speciesiscompleted, we will a constructPistaciasuper-pangenome with extensive analyses of structure and gene presence-absence variation, which will be utilized to refine and improve the GWAS results as well as serve as an essential and valuable resource, capturing the full spectrum of genomic variation across the genus. For Objective 6, we will impute genome-wide SNPs discovered in Objective 5 across all individuals in the breeding program, and rerun the GWAS. For Objective 7, our next steps are to develop a benchmark model of pistachio yields to be used for projecting yields under different climate scenarios, and to integrate the benchmark model into net present value framework to evaluate management and investment decisions under climate change scenarios. For Objective 8, while a transformation protocol has been established, it is not yet fully optimized. Key factors, such as the duration of immersion in Agrobacterium suspension and the cocultivation time, still require further testing and refinement. For Objective 9, A repetition of the mycelial plug inoculations in additionnal UCB1 seedling plants in Davis will be conducted in February 2025, using P. niederhauserii. For Objective 10, an additional trialwill be planted in another infested location near Lordburg, NM.
Impacts
What was accomplished under these goals?
Objective 1: Quantify impacts of deficit irrigation treatments on pistachio yield and quality over multiple years. In a deficit-irrigation trial in Woodland, CA, wereduced irrigation by 20-60%, which led to decreases insoil water contentand tree water status without impacting yield and actually improving nut quality. Specifically, two different deficit-irrigation treatments (spring deficit and sustained deficit) both significantly increased the proportion of in-shell split nuts relative to a normal irrigation control. This was the second year of the deficit irrigation experiment; similar results were obtained last year. Objective 2: Develop yield monitoring systems for incorporation into existing harvesting equipment.Over the past two yearswe have made significant efforts to develop an efficient yield monitoring system that can precisely measure the flow rate of pistachios as they are being harvested with harvesting equipment for each tree. Our research focused on designing a reliable and durable device that operates under severe field conditions, considering its reliability, durability, and minimal wiring requirements. In 2024, after finalizing the sensor assembly based on its width and distance from the conveyor belt surface, we tested the belt at various speeds with a known volume of nuts to investigate the effect of speed on the accuracy of our volume calculation technique. Objective 3.Discover alleles that increase pistachio yield under deficit irrigation, salinity, and disease pressure.This objective relies on high-throughput phenotyping and genotyping to discover rootstock alleles associated with superior performance under different growing conditions, including salinity, deficit irrigation, and disease pressure.RGB/Lidar scans of three orchards were performed during the 2024 growing season by a third party (Dropcopter, licensing GreenAtlas technology). These include the orchard near Davis, CA being used for the deficit irrigation experiment in Objective 1, which was also scanned last year, and two orchards that were scanned for the first time: an orchard with highly saline soil near Mendota, CA, and an orchard with mildly saline soil near Yuba City, CA. Analysis of GreenAtlas data from 2023 is ongoing. Objective 4. Refine existing chill models to better predict chill requirements and phenology of existing US pistachio. cultivars.Models for common pistachio cultivars are being developed using a bud pushing assaycommonly used to quantify chill requirements in deciduous tree crops.Dormant sticks were sampled from 10 grower orchards at different points throughout the winter and placed in a warm greenhouse environment to stimulate bud development. Weekly evaluations were conducted in the greenhouse usinga 1-4 scale of bud development. Chill portions were assigned to each collection based on hourly temperature recordsat each orchard, and heat was quantified by applying the Asymcur growing degree hour model. This information is being used to develop models for different cultivars that describe the amount of heat required to reach a given bud stage based the amount of chill accumulated in the field. Leafing and bloom ratings were taken on all orchards during the spring for the purpose of model validation. Objective 5: Understand molecular mechanisms underlying chill requirement in Pistacia.We aim to understand the molecular genetics behind the winter chilling requirements in Pistacia species, focusing on variation in gene expression related to dormancy.Pan-genomeconstruction of six pistachio cultivars has been completed with primary assembly annotations, revealing gene content variation categorized into core, dispensable, and private genes. We are currently advancing the construction of P. vera pan-genome with 14 haplotypes, including 'GoldenHills' which was sequenced this year. Additionally, high-coverage HiFi sequencing has been successfully completed for four Pistacia species (P. khinjuk, P. terebinthus, P. palaestina, and P. weinmanifolia), and their genome assemblies were completed. Objective 6.Phenotype chill requirement for all scions in the breeding program.Dormant sticks from both the 2020, 2021, and 2022 seedling blocks were sampled in the winter of 2023-2024. In addition, we sampled germplasm blocks in Davis and Winters, CA. This year we scaled up and placed sticks in large sub-irrigation benches in the greenhouses, reducing labor compared to the individual plastic tubs used in previous years. Dormant stick phenotypes are being used for GWAS using a random regression model in sommer. Objective 7. Analyze economic impacts of improvements in management and genetics on net returns to pistachio production to inform orchard establishment and replacement decisions.We have collected gridded weather data from PRISM for the San Joaquin Valley going back to 1991. This data can be interpolated to the county-level or used for higher resolution depending on what pistachio yield data we are able to acquire. We will continue looking to acquire yield data to increase the relevance of the modelling efforts, potentially from variety trials, growers, and/or historical objective measurement reports from USDA NASS. Objective 8: Accelerate the breeding cycle using rapid-cycling pistachio rootstocks.Stabbing experiments successfully induced galls in pistachio tissue, though none of the resulting galls produced shoots. Concurrently, trials were conducted to evaluate the effects of different concentrations of the antibiotics, timentin and carbenicillin, on pistachio tissue cultures. Neither antibiotic exhibited any negative effects on the plant tissues, and carbenicillin alone was effective in controlling Agrobacterium overgrowth. Several types of explants have been tested for transformation, including shoots, calli, germinated seeds, epicotyls, hypocotyls, and embryos. Thus far, embryos and calli have shown the most promise. Objective 9: Screen UCB-1 seedlings for resistance to Phytophthora under field conditions.Two experiments were conducted to identify UCB1 seedlings tolerant to Phytophthora crown and root rot. The first experiment was initiated on April 25th, 2024, using 269 4-year-old field planted UCB-1 seedlings. A single branch for each plant was inoculated with a 1 cm mycelial plug of P. niederhauserii, isolate KARE2555, under natural conditions in a field at UC Davis and left to incubate for 5 months. Differences in seedling susceptibility/tolerance were assessed by measuring and comparing the canker (lesion) length among the various inoculated plants. The second experiment was conducted on May 23rd, 2024, using 220 potted UCB1 seedlings. Plants were inoculated with 50 cc P. niederhauserii infested 10%CV8-oat-vermiculite medium and kept under greenhouse conditions at Kearney Agriculture Extension Center. Plants were assessed for differences in root weight, crown rot development, and plant death in November 2024. Objective 10.ScreenP. mexicanaand its hybrids for resistance to cotton root rot.Seedlings of P. mexicana, along with similarly-sized seedlings of P. vera, P. weinmannifolia, and UCB-1 (P. atlantica x P integerrima) for comparison, were planted in a site near the New Mexico State University campus in Las Cruces, NM where cotton root rot infected pecan trees had been removed. The NMSU Plant diagnostic clinic confirmed that each of the dead pecan trees was infected by the cotton root rot fungus by microscopy. The Pistacia seedlings were planted at close spacing in a randomized complete block design centered on the point where the diseased/dead pecan tree had been before it was removed.
Publications
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2023
Citation:
Brown, P.J. 2023. Haplotyping interspecific hybrids by dual alignment to both parental genomes. Plant Genome 16(2).
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2023
Citation:
Sheikhi, A., M.M. Arab, M. Davis, W.J. Palmer, R. Michelmore, et al. 2023a. Contrasting allelic effects for pistachio salinity
tolerance in juvenile and mature trees. Sci. Rep. 13(1): 14391.
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Progress 09/01/22 to 08/31/23
Outputs
Target Audience:Our target audience includes pistachio growers, researchers, processors, commodity board representatives, andnursery stakeholders. On-farm visits were paid to pistachio growers across California to initiate collaboration. The Statewide Pistachio Day 2023 meeting provided opportunity to contact additional stakeholders. We established a scientific advisory board (SAB) composed of diverse academic and industry representatives, and held our first annual meeting. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Project scientists, postdocs, graduate and undergraduate students are all involved with this project. Some are paid through project funds and others are paid through complementary CPRB-funded projects. Several graduate students presented their work at our first annual SAB meeting. How have the results been disseminated to communities of interest?So far much of our dissemination of results has been word-of-mouth or in small groups. Looking forward, several project PIs are scheduled to present at the 2024 Statewide Pistachio Day. What do you plan to do during the next reporting period to accomplish the goals?We plan to increase the number of orchards being monitored for yield GWAS, deficit irrigation trials, validation of the yield monitor, and chill model refinement. We plan to conduct extensive sequencing on diverse Pistacia, to monitor gene expression in buds over the dormant period, and to look at overlap between GWAS hits for chill requirement in the breeding program and genes expressed during bud dormancy. We plan to analyze large public and private datasets on pistachio yields across the growing region to help build economic models. We plan to transform embryogenic and/or organogenic cultures of Pistacia with 35S:FT to ease regeneration. A Phytophthora inoculation experiment is planned for spring 2024, as is a planting of diverse seedlings (including UCB-1 and open-pollinatedP. mexicana) into cotton root rot-infested soil in New Mexico.
Impacts
What was accomplished under these goals?
Objective 1 (Quantify impacts of deficit irrigation treatments): One deficit irrigation site was established in Yolo County, with a control treatment and two different deficit irrigation treatments. Yield and quality data from the first season suggest that yield is unchanged and quality somewhat improved under deficit irrigation. A second site was identified in Madera County that has been managed under different irrigation treatments for several years. Only physiological data were collected at this site. Initial results suggest that fully irrigated trees have higher stomatal conductance (gs) and higher stem water potential than deficit-irrigated trees, but that net assimilation (A) rates are similar between treatments, resulting in a huge increase in water use efficiency (A/gs) in the deficit irrigation treatment. These results will be shared at the 2024 Statewide Pistachio Day, but more years of data are needed. Objective 2 (Develop yield monitoring systems): An optical sensor for yield monitoring was developed and is being tested. The sensor is easy to install on existing harvesting equipment. A small 'umbrella-type' harvester was purchased from Italy with a 50% match from the California Pistachio Research Board. This harvester should arrive in Spring 2024 and will be invaluable for ground-truthing yield monitor measurements from individual trees. Objective 3 (Discover alleles): Initial GWAS efforts focused on a single site in Yolo County close to the site with the deficit irrigation treatments. A 43 x 40 block of trees (n=1720 trees total) were scored for yield and precocity on an ordinal (0-9) scale for the last two years. Genetic control of these traits changed between years as the trees matured. In July and September of 2023, these trees were scanned using the GreenAtlas platform, which provided RGB and Lidar-based estimates of nut count and canopy volume. GreenAtlas estimates of nut count in July and September were highly correlated with each other and with the ordinal yield estimates, and both methods detected the same QTL. Objective 4 (Refine existing chill models): Weather stations are being installed in 20 pistachio orchards statewide with funding from the California Pistachio Research Board (CPRB). These orchards will be targeted for future sampling. Objective 5 (Understand molecular mechanisms): DNA has been extracted from one tree of each Pistacia accession in the National Clonal Germplasm Repository (NCGR) and is being submitted for library prep and whole-genome sequencing on the Aviti platform at the UC Davis Genome Center. Objective 6 (Phenotype chill requirement): Sticks from the 2020 and 2021 seedling blocks of the breeding program (1099 trees total) were sampled 5 times during the winter of 2022-2023, forced in tubs of water in the greenhouse, and monitored for bud-break. Data will be used for GWAS and to refine chill models. Objective 7 (Quantify economic impacts): Acquisition of statewide pistachio yield data from public and private sources is underway. Objective 8 (Rapid-cycling rootstocks): Pistachio microshoots of scions and rootstocks were transformed with 35S:FT constructs and we are attempting to regenerate them. Objective 9 (Phytophthora resistance): An initial field inoculation was marginally successful because of hot weather, and a subsequent greenhouse inoculation was highly successful. We are planning a second field inoculation for early in the spring of 2024. Objective 10(cotton root rot resistance): Though germination of open-pollinated P. mexicana seeds from the NCGR was very low, we germinated 12 individuals and have them growing in the greenhouse. Sites for planting have been identified in New Mexico. We are testing stratification and promalin treatment to increase germination and are aiming to plant in spring 2024.
Publications
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