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United States Department of Agriculture

Agricultural Research Service

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Location: Plant Genetic Resources Research

2011 Annual Report

1a. Objectives (from AD-416)
1. Develop and release improved apple rootstocks. 2. Develop and apply genomic and bioinformatic tools to marker-assisted selection of apple rootstocks.

1b. Approach (from AD-416)
Develop and release improved apple rootstocks. Perform all breeding and evaluation stages involved in the 15-25 year process of developing new rootstocks with the assistance of recently developed breeding tools, such as marker-assisted selection. Develop improved propagation methods that speed the distribution of selected material to customers through established networks of cooperating nurseries. Exogenous treatments of layering propagation stool beds will increase adventitious root formation and quality of nursery liners. Incorporate innovative concepts of orchard establishment and management including mechanization. Existing experimental rootstocks in the breeding pipeline possess adaptations for novel orchard concepts and mechanization. Develop and apply genomic and bioinformatic tools to marker-assisted selection of apple rootstocks. Develop algorithms to assist with identifying specific markers for priority horticultural traits from the large body of expressed sequence tags (EST) and genomic sequence data now available.

3. Progress Report
Significant advancements were made in all the objectives of project 1910-21000-023-00D relevant to National Program 301 “Genetic Improvement” component and National Program 305 Component 1 “Integrated Sustainable Crop Production Systems”. The project is working on increasing plant material for advanced testing of CG.3001, a new disease resistant rootstock that is showing good potential for release to the industry in the near future. This rootstock maintains the standards of dwarfing, high productivity, fire blight and crown rot resistance, and immunity to wooly apple aphids that have been known to characterize Geneva rootstocks. A major effort was placed on the development of DNA markers that are linked to the most important selection traits for apple rootstocks. The effort was aimed at refining the type of markers that were to be used for Marker Assisted Breeding for dwarfing, precocity, wooly apple aphid resistance, and fire blight resistance. We used an approach that combined the analysis of the genomic sequence of G.41 (a dwarfing , precocious, wooly apple aphid immune and fire blight immune rootstock) and the analysis of the expression of candidate genes to discover specific mutations in the regions affecting those traits that could be used to design new more efficient markers. The application of these new markers will allow the reduction of costly field plots for the evaluation of new generations of apple rootstocks. The project suffered another major setback due to improper application of herbicides on propagation material. This was a similar but more drastic incident than the one reported for FY09. Several new experimental rootstocks were killed and lost after many years of testing and selection. Furthermore the propagation beds that would have been used as the basis for the incorporation of new types of orchard production systems were decimated. We are in the process of assessing long term damage to the project and determining viable alternatives to the research that was destroyed. It is likely that this setback will affect accomplishment of milestones related to propagation research. Fortunately, most of the elite material is also kept in a secondary test location in Washington State and will be used to recover some of the lost genotypes in Geneva. Despite these setbacks there was considerable progress in the breeding program with new evaluation trees planted, the measurement of tree size and productivity, the measurement of tolerance to diseases such as fire blight, the making new experimental trees in the nursery, the making new crosses, the harvesting and grading rootstock liners and the identification of a set of new elite testing lines took place during the course of the year. We continued a major effort into diagnostic DNA fingerprinting of apple rootstocks for proper identification of misidentified rootstocks and avoidance of potential downstream planting and propagation problems. This effort supports apple rootstock nurseries that propagate Geneva rootstocks.

4. Accomplishments
1. Identified rootstock mediated gene transcription that affect fire blight disease susceptibility of apple trees. Apple rootstocks affect expression of genes related fire blight disease severity in apple scions. Fire blight is a devastating disease that decimates apple orchards throughout the U.S. All commercial apple trees are made up by a variety scion (like Gala) grafted onto a rootstock. Among the rootstocks available to the U.S. apple industry several have been shown to drastically affect productivity and other properties of the scion/orchard. In the publication that describes research collaboration between ARS researchers at Geneva, NY with scientists at Penn State University we reported on effects different rootstocks have on susceptibility of the apple variety Gala and connected that information to gene transcription changes caused by rootstocks. This study measured that the severity of fire blight on Gala trees differs depending on what rootstock they are grafted on and found significant differences among rootstocks. The same is true for several genes that are expressed differentially in Gala trees depending on what rootstock they are grafted on. The expression pattern of some of these genes modified by the rootstocks might be associated with fire blight severity. Several new apple varieties are very susceptible to fire blight which causes severe losses in apple production. The information in this scientific report is useful in the development of new disease resistant apple rootstocks and cultural strategies to minimize the losses due to this disease.

2. Evaluated cold hardiness of newly released apple rootstocks. Cold hardy apple rootstocks are an essential component for survival and productivity of trees in orchards planted in regions that can be subject to severe cold stress. ARS researchers at Geneva, NY in collaboration with scientists at the University of Maine we conducted a series of experiments aimed at testing the cold hardiness properties of several rootstocks recently released by our program and compared it to well established commercial controls. In the scientific report resulting from this research we describe that under the testing conditions of the experiment apple rootstock G.935 is the most cold hardy of the group tested, performing much better than the cold hardy control M.26. Also under the testing conditions of this experiment apple rootstock G.41 is just as cold hardy as M.26 depending on experiments and quality of the material. This research is important because it will provide technical recommendations for U.S. apple growers in northern climates.

3. Identified candidate genes for dwarfing, precocity and rooting traits. Dwarfing, precocity are very important apple rootstock traits that impart per acre productivity increases and cost savings worth $0.5-0.7B annually to the U.S. apple industry. If genes responsible for these traits were to be identified, they might be able to be applied on several other tree crops that might benefit from dwarfing and precocious rootstocks. During this research ARS researchers at Geneva, NY identified several gene sequences and related mutations that could confer the dwarfing and precocity phenotypes. These sequences were identified in the regions of the apple genome that have been discovered to control these important traits. We accomplished creating several molecular markers that can tag these DNA regions. The next step involves validating the expression profiles of these genes in breeding populations and the identification of the mutations responsible for the phenotype they confer to the apple trees.

Last Modified: 06/27/2017
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