Location: Crop Diseases, Pests and Genetics Research
2025 Annual Report
Objectives
Objective 1: Breed superior table grape and natural dried-on-vine raisin varieties with high fruit quality, consumer appeal, disease resistance, and reduced cultural input requirements.
Sub-objective 1.A: Develop a pipeline for commercial release of high-quality table grape and natural dried-on-vine raisin selections through field trials.
Sub-objective 1.B: Develop high-quality table and natural dried-on-vine raisin grape lines with two or more stacked loci for powdery mildew resistance.
Sub-objective 1.C: Develop high-quality table and natural dry-on-vine raisin grape lines with PdR1 and PdR2 locus for durable resistance to PD.
Sub-objective 1D: Establish trial of 12 reference cultivars with virus-free material and collect data on anthocyanin and flavonoid compounds.
Objective 2: Breed new Prunus selections including self-compatible almond varieties with Nonpareil like kernel characteristics.
Sub-objective 2.A: Develop, select, and evaluate new high-yielding self-compatible (SC) almonds.
Sub-objective 2.B: Develop, select, and evaluate new glabrous-skinned apricots.
Sub-objective 2.C: Test and validate Peach-Nectarine indelG marker in apricots to identify glabrous-skinned apricots.
Approach
The long-term goal of the project is to develop superior table grape and natural dried-on-vine raisin varieties that have high quality, consumer appeal, natural disease resistance to fungal and bacterial pathogens and requires reduced cultural input. Each year, crosses will be made among superior selections that has performed well in the field evaluations. Molecular markers will be used to discard disease susceptible lines and to combine different powdery mildew resistance genes for lasting protection. New improved lines will be selected and compared with the existing table grapes for quality and storage after cold treatments and fruit showings will be held during each season. New superior advance lines will be introduced as new cultivars with the table grape and raisin grape industry's approval. We aim to combine Xylella fastidiosa (Xf) resistance from Vitis arizonica into high-quality hybrids of both table and raisin grape cultivars. Xf is a bacterial disease that threatens grape production. Studies will be carried out to characterize the profile of anthocyanin (free and bound) and flavonoid compounds of 12 varieties under two different climate conditions. Same set of plants will be grown in the Parlier, and Coachella valley that is significantly warmer. Both anthocyanins and flavonoids are negatively impacted by high daily temperatures. This experiment will allow to study the impact of temperature on the stability of these compounds and identify varieties that perform better in hot climates to facilitate future breeding efforts to mitigate the impact of climate change. To create new self-compatible (SC) almonds with high yields and Nonpareil-like kernels, crosses will be made each year between SC lines. Seedlings will be genotyped with markers that target SC locus and only the lines with SC will be kept. Flowers will be bagged and only lines that would not require insects for pollinations will be selected. Phenological data will be collected annually and compared to the standard cultivars ‘Nonpareil’ and ‘Padre.’ Only lines that have most desirable combination of nut and tree characteristics will be selected and trialed further. New apricot varieties will be developed by crossing different types of smooth-skinned apricots. DNA-based marker assay will be developed to identify smooth skin apricots at earlier seedling stage to distinguish glabrous apricots from fuzzy apricots. Selected lines will be evaluated for their fruit quality and productivity.
Progress Report
This report documents FY 2025 progress for project 2034-21220-08-00D, "Breeding Prunus and Vitis to Improve Disease Resistance, Fruit Quality, and Climate Change Adaptation", which began in May 2023.
The project covers breeding research for table and raisin grapes, almonds, apricots, and citrus. Research is supported by the table grape, raisin grape, almond, and citrus industry stakeholders to develop new improved varieties and conduct trials. In FY 2025, a significant infrastructure overhaul was completed for both citrus and grape programs. To streamline phenotypic data collection, scannable QR code labels that store digital information such as field identification, genotype, or treatment details were utilized and the mobile tool Field Book app was deployed for data collection. A total of 3000 grapevine seedlings from crosses conducted in 2022 and 2024 representing unique lines and germplasm propagated from hardwood cuttings were planted in newly established field blocks. Collaborations and research support agreements were established to expand research capacity nationally with universities and scientists at other ARS facilities.
In support of Sub-objective 1.A, progress was made in breeding superior table grapes and natural dried-on-vine raisin varieties with high fruit quality and disease resistance. Specifically, field evaluations were completed on grapevines from two blocks for fruit quality traits including berry size, skin, texture, color, seed trace, and powdery mildew disease resistance. All lines with desirable characteristics were propagated from hardwood cuttings and planted in a library block to serve as mother vines for future crosses. Field maps, new planting and removal, history of parents used in crosses, and previous and new field evaluation data were updated regularly with new information to maintain the breeding program information database in Microsoft Access. A total of 16 table grapes and four raisin grapes breeding lines that were sent to Micro Paradox in FY 2024 for shoot tip culture propagation became available in FY 2025. About 700 vines from these lines were obtained from Micro Paradox and are currently being tested for grapevine leafroll associated virus–3 and other viruses. In addition, virus-free grapevines from two raisin lines and seven table grape lines that had been submitted for virus clearing to the Foundation Plant Services at the University of California, Davis, and Micro Paradox were retrieved, propagated, and planted in the field to generate tissue for grafting and planting in spring 2026. Interactions with the California Table Grape Commission facilitated the development of a field trial layout for reference lines on appropriate rootstocks. Similarly, interactions with representatives from the Raisin Administrative Committee resulted in the expansion of research aimed to understand the genetics of naturally-dry-on-vine (NDOV) raisin grapes and preharvest shattering in the raisin variety ‘Sunpreme’. A mapping population to understand the genetics of NDOV and preharvest shattering was developed and DNA genotyping was completed to rule out off-types. A marker-assisted screening method was developed to identify and discard susceptible seedlings from the populations before being planted in the field.
Under Sub-objectives 1.B and 1.C, hybridizations were conducted for both table and raisin grapes using advanced selections from the University of California, Davis, and the ARS Parlier, California, location to develop lines with durable resistance to powdery mildew and Pierce’s disease. Reflex-flowered vines with a combination of Run1Ren1Ren4 loci, which confers resistance to powdery mildew, were used as females in backcrosses with high-quality table grapes and natural dry-on-vine raisin selections. Pollen from hybrids carrying the Run1Ren1Ren4 loci was also used in hybridizations with powdery mildew resistant selections of Vitis amurensis, where a new locus for powdery mildew resistance was recently identified and named Ren12. Following these crosses, seeds were germinated, embryo rescue was conducted, and approximately 2,600 seedlings were planted in new seedling blocks in the field. Four genetically-diverse grapevine populations are currently maintained to identify loci associated with powdery mildew resistance. These populations were also selected for computer vision-based phenotyping to determine powdery mildew disease severity. Two of the four populations are part of a cold hardiness genomic mapping project in collaboration with North Dakota State University. Plant material was provided to the university collaborators for training of a PhD student.
For Sub-objective 1.D, efforts focused on the characterization and comparison of anthocyanin (free and bound) and flavonoid profiles across 12 grape varieties (seven red, three black, and two green). Trials were established at two locations: ARS Parlier, California, and Coachella Valley, California. Both sites were maintained, and grapevines were trained to support future evaluations of fruit produced under commercial conditions.
In support of Objective 2, progress was made in breeding new self-compatible almond varieties with Nonpareil like kernel characteristics, and improved apricot varieties that expand harvest window. Specifically, all almond breeding populations were maintained in the fields and two new reciprocal crosses were made in FY 2025 using Y117-91-03 and ‘Yorizane’. A Research Geneticist was hired and onboarded in December 2024 to carry out almond breeding research, but shortly thereafter the incumbent opted for the Deferred Resignation Program 2.0. Under Sub-objective 2B, several apricot breeding populations established by the previous breeder were evaluated for key fruit traits such as skin pubescence, blush and flesh color, stone adherence, pit burn variation, and ripening date. Most of these materials originated from crosses of parents with late fruit maturity, glabrous skin, and other desirable characteristics. The fruit maturity trait segregates into two of the evaluated breeding populations. Many of the plants established in 2021 remain in the juvenile phase and have not yet fruited; evaluations will continue during the 2025–2026 seasons to identify late-maturing, high-quality lines for potential variety release to extend the apricot harvest window. For Sub-objective 2C, test populations of apricots were selected based on the parental background for fuzzy versus glabrous skin phenotypes. Young leaf tissue was collected, and DNA extractions were completed from 323 lines, including parents of the breeding populations. Additionally, known peach and nectarine cultivars were included as controls, sourced from the ARS National Clonal Germplasm Repository in Davis, California. Preliminary results from a subset of these samples indicate that the peach–nectarine indelG marker reliably differentiates between the two species. However, further sequence analysis and validation are needed to determine the marker's effectiveness in distinguishing between fuzzy and glabrous apricots. A majority of the Prunus germplasm trees (almond and apricot) are old, overgrown, and affected by diseases. To rejuvenate the collection, grafting was conducted for 57 select lines and two new plants of each were planted in the field to replace the old materials. Approximately 200 plants of rootstock ‘Nemaguard’ were planted for additional propagations in June.
In support of Objective 3, progress was made in building the basic infrastructure for the citrus breeding program. Construction of a new 2,000 square-foot greenhouse was completed and a land-lease agreement for 20 acres of research fields was established with Reedley College in Reedley, California. Citrus scions (eight mandarins, two oranges, and one grapefruit) developed by ARS in Fort Pierce, Florida, were cleared from quarantine and shipped to a local nursery in Dinuba, California, for propagation onto different rootstocks. Planting in the field is planned for spring 2026. ARS researchers in Parlier, California, maintained constant communication with the California Citrus Research Board and ARS researchers in Fort Pierce, Florida, on many aspects of the breeding research.
Accomplishments
1. Highly productive raisin variety strenghtens the U.S. raisin industry. American raisin growers are seeking new grapevine varieties that deliver high yields while requiring fewer resources. ARS scientists at Parlier, California, developed a seedless grape called ‘Murray Muscat’. This high-yielding variety produces premium muscat-flavored raisins and consistently outperforms current varieties under standard farming practices. With its superior productivity and quality, ‘Murray Muscat’ is poised to enhance the competitiveness of the U.S. raisin industry, which already supplies nearly half of the world’s raisins.
2. Grapevine resistance to mealybug prevents transmission of deadly viruses. The livelihood of American grape farmers is threatened by deadly grapevine diseases caused by viruses transmitted by the vine mealybug. In a major research breakthrough, ARS scientists at Parlier, California, discovered grape germplasm with natural resistance to vine mealybug. This is the first study to confirm that resistant grapevines can significantly hinder the growth and reproduction of vine mealybugs. These resistant genetic resources will support integrated pest management programs and drive new approaches to control virus-related diseases and advance sustainable grape production across the United States.
Review Publications
Xiao, H., Wang, Y., Liu, W., Shi, X., Huang, S., Cao, S., Long, Q., Wang, X., Liu, Z., Riaz, S., et al. 2025. Impacts of reproductive systems on grapevine genome and breeding. Nature Communications. 16. Article 2031. https://doi.org/10.1038/s41467-025-56817-7.
Riaz, S., Tenscher, A.C., Walker, M.A. 2023. Genetic mapping of Pierce’s disease resistance in germplasm collected from the Southwestern United States and Mexico. American Journal of Enology and Viticulture. 74(2). Article 0740026. https://doi.org/10.5344/ajev.2023.23006.