Location: Crop Diseases, Pests and Genetics Research
2024 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 2024 progress for project 2034-21220-08-000D, ‘Breeding Prunus and Vitis to Improve Disease Resistance, Fruit Quality, and Climate Change Adaptation', which began in May 2023.
The project is supported by the table and raisin grape industry stakeholders to develop new varieties with improved quality, yield, and natural disease resistance to pathogens. Between 2018 and 2023, progress was hampered by a vector-transmitted virus, and aging infrastructure. Infrastructure renovations conducted in FY 2024 included soil preparation and installation of new irrigation and trellis system in 25 acres of research and breeding blocks. A walk-in controlled environment chamber was built to house embryo rescued grape seedling plants, and other updates were made to the existing infrastructure in the labs and greenhouses for both Prunus and Vitis operations. A total of 1500 seedling plants from 2022 and 2023 crosses were planted in newly established blocks in FY24. A new Vitis germplasm library block was established and plants of 700 unique lines propagated from hardwood cuttings were planted. This germplasm collection represents lines that could potentially be moved into advanced trials for variety release after virus clean up, and lines that will be used as parents for future crosses.
In support of Sub-objective 1A, field evaluations were completed on 3000 plants growing in five blocks for fruit quality traits including berry size, skin, texture, color, seed trace, and disease resistance. Field maps, history of parents used in crosses and where possible previous field evaluation data were combined with new information to develop the breeding program information database, which was maintained in electronically. Based on field evaluations, 850 lines representing potential new cultivars and parental germplasm were selected for propagation to be planted in the germplasm library block. Twenty lines that include both table and raisin grapes were selected for virus cleanup via shoot tip culture. Virus-free plants of two raisin lines and seven table grape lines received from the Foundation Plant Services (FPS) at the University of California, Davis, and Micro Paradox (MP) are under propagation to develop tissue for chip budding on the freedom rootstock in Spring 2025. In support of Sub-objectives 1B and 1C, hybridizations were carried out for both table and raisin grapes, with advance selections from U.C. Davis to develop lines with more than one resistance locus, which could provide durable resistances to both powdery mildew and Pierce’s disease. Reflex-flowered vines with combination of Run1Ren1Ren4 loci were used as females in backcrosses with high quality table grapes and natural dry-on-vine raisin selections. Pollen from Run1Ren1Ren4 hybrids was used in hybridizations with powdery mildew resistant selections of Vitis amurensis, where a new locus for powdery mildew resistance was identified and named Ren12. Resultant seeds from these hybridizations were germinated, and 1500 seedlings were planted in newly established seedling blocks. Four populations with different genetic background were maintained to identify potential loci associated with resistance to powdery mildew. These four populations were also selected for computer vision phenotypic analysis to estimate powdery mildew infection. Two of these populations are part of the research project to identify genomic regions for cold hardiness in collaboration with North Dakota State University. A replicated trial involves characterization and comparison of anthocyanin (free and bound) and flavonoid compounds of 12 varieties (seven red, three black, and two white) under two different climate conditions at the USDA-ARS site in Parlier and the Coachella valley. Cuttings of virus free plant material were propagated. Plants are maintained and trained at both sites to bear fruit for evaluations in commercial setting.
In support of Objective 2, all almond breeding populations were maintained in the fields, however new crosses were not made due to lack of personnel in FY24. In support of Sub-objective 2B, multiple populations planted by the previous breeder were evaluated for skin pubescence, blush and flesh color, stone adherence, variation in pit burn, and ripening date when fruit was available. These crosses were made between parents that have late fruit maturity and glabrous skin type and other important fruit features. From these, fruit maturity trait was determined to segregate two breeding populations. Most plants planted in 2021 are still in the juvenile phase and do not have fruit. Evaluations will continue in 2025 and beyond to identify superior quality late maturing line that could be released as new variety to expand the apricot harvest season. In support of Sub-objective 2C, test material populations were selected based on the parental background for fuzzy and glabrous skin phenotype. Young leaf tissue for DNA extractions were collected for 323 lines including parents of breeding populations. Additional known reference peach and nectarine cultivars were added as control from the USDA-ARS National Clonal Germplasm Repository in Davis. Preliminary results on subset of samples showed that the peach-nectarine indelG marker consistently differentiates between peaches and nectarines; however, more testing and sequence comparison of the genomic region is required to make it a useful marker to distinguish fuzzy and glabrous apricots.
Accomplishments
Review Publications
Aguero, C.B., Riaz, S., Tenscher, A.C., Bistue, C., Walker, M.A. 2022. Molecular and functional characterization of two RGA type genes in the PdR1b locus for Pierce’s disease resistance in Vitis arizonica/ candicans. Plant Cell Tissue and Organ Culture. 151:497-510. https://doi.org/10.1007/s11240-022-02366-6.
Huerta-Acosta, K., Riaz, S., Tenscher, A., Walker, M.A. 2022. Genetic characterization of Pierce’s disease resistance in a Vitis arizonica/monticola wild grapevine. American Journal of Enology and Viticulture. 74(1). Article 0740003. https://doi.org/10.5344/ajev.2022.22021.
Massonnet, M., Riaz, S., Pap, D., Figueroa-Balderas, R., Walker, M.A., Cantu, D. 2022. The grape powdery mildew resistance loci Ren2, Ren3, Ren4D, Ren4U, Run1, Run1.2b, Run2.1, and Run2.2 activate different transcriptional responses to Erysiphe necator. Frontiers in Plant Science. 13. Article 1096862. https://doi.org/10.3389/fpls.2022.1096862.
Massonnet, M., Vondras, A.M., Cochetel, N., Riaz, S., Pap, D., Minio, A., Figueroa-Balderas, R., Walker, M.A., Cantu, D. 2022. Haplotype-resolved powdery mildew resistance loci reveal the impact of heterozygous structural variation on NLR genes in Muscadinia rotundifolia. G3, Genes/Genomes/Genetics. 12(8). Article jkac148. https://doi.org/10.1093/g3journal/jkac148.
Morales-Cruz, A., Aguirre-Liguori, J., Massonnet, M., Minio, A., Zaccheo, M., Cochetel, N., Walker, A., Riaz, S., Zhou, Y., Cantu, D., Gaut, B.S. 2023. Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate. Communications Biology. 6. Article 580. https://doi.org/10.1038/s42003-023-04938-4.
Xiao, H., Liu, Z., Wang, N., Long, Q., Cao, S., Huang, G., Liu, W., Peng, Y., Riaz, S., Walker, M.A., Gaut, B.S., Zhou, Y. 2023. Adaptive and maladaptive introgression in grapevine domestication. Proceedings of the National Academy of Sciences (PNAS). 120(24). Article e2222041120. https://doi.org/10.1073/pnas.2222041120.