Location: Plant Genetic Resources Unit (PGRU)
2023 Annual Report
Objectives
Objective 1: Develop and release improved apple rootstocks by leveraging advances in marker assisted breeding, including construction of genetic maps, establishing trait associations, gene discovery for important rootstock traits (dwarfing, early bearing, yield efficient, fire blight resistant), and screening for novel alleles for important rootstock traits.
Sub objective 1A: Perform all breeding and evaluation stages involved in the 15-30 year process (timeline depending on intensity of phenotyping and need to fast-track) of developing new rootstocks with the assistance of recently developed breeding tools, such as high throughput phenotyping and marker-assisted breeding.
Sub-objective 1B: Identify and characterize novel germplasm, genes, alleles and trait loci through quantitative trait analyses leveraging new genetic-physical maps.
Objective 2: Identify and dissect important rootstock traits that modify gene activity in the scion, toward enhancing drought tolerance, tree architecture, propagation by nurseries, root growth and physiology, nutrient use efficiency, and disease resistance; incorporate this knowledge into breeding and selection protocols.
Sub-objective 2A: Identify components of rootstock induced traits that modify gene expression and metabolic/physiological profiles of grafted scions to increase tolerance to abiotic stresses, improve fruit quality and storability, increase tree productivity, disease resistance and nutrient use efficiency.
Sub-objective 2B: Validate relationships between trait components and overall apple tree performance in different rootstock-scion combinations and incorporate new knowledge into breeding and selection protocols.
Approach
The objectives of this project will be met by applying a combination of conventional breeding techniques and marker assisted breeding to select for improved rootstocks. The project will also leverage the use of aeroponics to study components of root traits that aid in nutrient uptake and water use efficiency by monitoring gene expression and other metabolic componds in apple roots.
Progress Report
The process of breeding apple rootstocks involves certain yearly (cyclical) activities that are aimed at the generation, propagation, evaluation of new improved breeding lines. We were successful this year in the vernalization and germination of about 8,000 seed representing 5 different parental crosses. The seedlings were inoculated with spores of diseases associated with replant disease complex – this has been the most reliable method to select resistant material as the genetics of resistance to one of the components of replant disease (Pythium ultimum) has proven to be genetically complex. Other breeding operations including rootstock harvest, evaluation, propagation of test trees, etc. were also performed successfully.
The effect of viruses and viroids on G.935 and other apple rootstocks was assessed by testing for the presence of Apple Stem Pitting (ASPV), Apple Stem Groving (ASGV), Apple Chlorotic Leaf (ACLSV), Apple Mosaic (ApMV), Citrus Concave Gum (CCGAV) viruses in a cider variety apple trial featuring more than 50 different types of cider apples with different viral load combinations. Preliminary data shows that ApMV and CCGAV had the largest effect on tree stunting indicating a strong interaction with some genetic components on G.935 apple rootstocks. It is essential to know of the presence and to eradicate these viruses from scion varieties being grafted to Geneva rootstocks as some of the negative effects can take years to display.
In collaboration with scientists at Cornell University and Virginia Tech we have conducted an economic study about the effect of using fire blight resistant rootstocks on the net present value of apple plantings in low, moderate and high fire blight regions and compared them to using rootstocks that are sensitive to fire blight. Results that model the effects of increasing fire blight incidence to 40% incidence showcase strong evidence on the economic case to adopt Geneva rootstocks as insurance for the profitability of the orchard (coupled with the spray applications based on the fire blight prediction models).
As this report marks the end of a five-year project we reflect on the many major and impactful findings that were established in this period: 1. Where it was once thought that rootstocks had little to no impact to fruit quality parameters of apples, we found that by multiple mechanisms (nutrient absorption and translocation, hormone deployment, water relations, tree architecture modification) rootstocks can dramatically affect maturity, sugar content, mineral nutrient balances and associated disorders, postharvest storability and size of apple fruit. 2. We have elucidated the genetics of resistance to some of the components of the replant disease complex and continued to work on selecting new material that maintains that resistance in the field. 3. We have found that apple root systems are very diverse in the way they absorb nutrients, interact with different soil pH levels, develop different architectures, produce and exude complex metabolic compounds, generate different gene expression patterns, and interact with different soil types. 4. We have generated perhaps one of the largest root gene expression databases associated with different apple genomes which has allowed for the development of hypothesis associated with certain gene products and derived genetic markers. 5. We have released six new apple rootstocks all with high productivity and disease resistance standards which can be deployed for diverse orchard applications. 6. We have continued our award-winning technology transfer efforts by establishing multiple field trials in U.S. apple growing regions. 7. We have described and published the economics of rootstock choice with data spanning 20 years of rootstock specific production featuring different trellis (training) systems. These are some of the many impacts the apple rootstock has enjoyed in the past five years despite the slow downs caused by the pandemic.
Accomplishments
1. First report on the genetics of resistance to Pythium ultimum. Natural genetic resistance to components of the apple replant disease (ARD) complex syndrome is available in apple rootstocks developed by the Geneva apple rootstock breeding program. This very desirable genetic resistance is mostly derived from a wild apple species, Malus robusta, a common parent in Geneva apple rootstocks. This research was performed to discover the genetic factors associated with the resistance to Pythium ultimum one of the major components of the ARD syndrome. The experiments involved inoculating breeding lines derived from Malus robusta and measuring their resistance to Pythium ultimum, then using the resistance score to discover genetic markers associated with it. The results of the genetic analysis showed that this trait is more complex than initially thought of and that it responds to the combination of at least 5 genetic factors residing on different chromosomes of the apple genome. This information is being used to develop genetic markers to select rootstocks with improved resistance to apple replant disease.
Review Publications
Fazio, G., Mazzola, M., Zhu, Y. 2023. Genetic analysis of resistance to Pythium ultimum a major component of replant disease in apple rootstocks. Journal of the American Pomological Society. 77(1)28-37.
Gonzalez-Nieto, L., Reig, G., Lordan, J., Miranda-Sazo, M., Hoying, S., Fargione, M., Reginato, G., Donahue, D., Francescatto, P., Casagrande-Biasuz, E., Fazio, G., Robinson, T. 2023. Long-term effects of rootstock and tree type on the economic profitability of ‘Gala’, ‘Fuji’ and ‘Honeycrisp’ orchards performance. Scientia Horticulturae. https://doi.org/10.1016/j.scienta.2023.112129.
