Location: Plant Genetic Resources Unit (PGRU)
2021 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
Our process of breeding apple rootstocks has field and laboratory components that occur cyclically every year and some that occur every few years because of the nature of how apple trees grow. We adapted our scientific effort to be compatible to the maximum telework requirements as much as possible and were able to perform most field and greenhouse operations needed to keep the breeding material in good condition. In the fall we were able to harvest rootstock liners from our stool bed nursery and plant a new research orchard that featured plants that had been growing in containers and needed transplanting. We were able to collect first growth and flowering data on these trees this spring and summer. While we had the best plans to perform controlled crosses in the spring using bees and pollination cages, we were unable to do so because of a shortage of pollination beehives that our unit rents every year. We successfully planted new seeds representing six different crosses and were able to inoculate them with crown and root rot causing fungal agents like phythium, rhizoctonia and phytopthora. Survivors were transplanted for the next iteration of inoculations featuring fire blight causing bacteria. Major efforts were placed into making our new greenhouse operational given that it was delivered at the height of the pandemic and lacked several day-to-day components needed for proper operation (like placing and organizing cookware in a new kitchen). The first experiment to go into the new greenhouses resulted from a request by a nursery and an ag robotics group in the western part of the U.S. to inoculate Gala apple trees grafted on one of our rootstocks (G.41) with fire blight bacteria and then taking hyperspectral images of the progression of the disease. Despite the heavy infection, all trees survived thanks to our resistant rootstocks, and we were able to collect important data before flowering and fire blight season occurred on the west coast where the experiments were repeated on outdoor trees. We refitted our aeroponics system in the new greenhouse and planted a new experiment featuring two breeding populations to study root formation and transcriptomics. One of these populations features plants that are shy-rooters (they produce few adventitious roots) when rooting is an important component of our breeding program – finding the genetic reasons underlying this trait will enable us to select better rootstocks.
Apple viruses and viroids are a cause for concern in our breeding program and for the apple industry. In a collaboration with Animal and Plant Health Inspection, Plant Protection and Quarantine (APHIS PPQ), Beltsville, and ARS Fort Collins, scientists we continued the evaluation of a new series of laboratory protocols aimed at eliminating the presence of viruses from our clonal stock that is destined for release to the industry. We seem to have developed a combination of treatments that are able to eliminate even the most recalcitrant of viruses. In addition, last season we planted a new orchard designed to study sensitivity of our rootstocks to viruses and viroids and this season we began to collect molecular (RNAseq and RT-PCR) and morphological data on sensitive and tolerant rootstocks with the aim of developing more tolerant rootstocks.
The genetics laboratory component of our breeding program suffered a one-year hiatus due to the lab closure but was able to restart in the spring for some essential “time sensitive” and “grower-needed” results like the molecular components of virus testing and the proper identification of soon to be released clonal stock material. We were also able to run a much-needed marker assisted selection protocol for plants that needed rogued before they are planted in the field. There is no question that some of the milestones in the project plan involving laboratory and subsequent bio-informatic procedures were impacted with a delay of one or more years and we continue to work on re-prioritization and implementation of those procedures as efficiently as possible.
Accomplishments
