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ARS Home » Northeast Area » Geneva, New York » Plant Genetic Resources Unit (PGRU) » Research » Research Project #434954

Research Project: Development of Biotic and Abiotic Stress Tolerance in Apple Rootstocks

Location: Plant Genetic Resources Unit (PGRU)

2018 Annual Report

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.

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
Significant progress was made on all fronts of this project 8060-21000-029-00D associated with National Program 301 (Crop Genetic Improvement). Apple rootstocks have a substantial influence on yield, fruit quality and profitability of a modern apple orchard. The beginning of the growing season was marked by a very late spring and a compressed bloom season which allowed the setup of 9 new crosses between elite apple rootstock germplasm and some Native American species of apples being preserved by the ARS Germplasm System apple collection in Geneva, New York. Cyclical operations occurring every year in the breeding program (planting of nursery stock, measuring tree size and productivity in experimental orchards, grading roots in nursery material, etc.) were successful. Progress was also made in the integration of newer molecular markers for selection of seedlings with improved performance qualities. The program established new trial plantings in Pennsylvania (Pennsylvania State University) and North Carolina (North Carolina State University) which are aimed at testing the performance of 12-15 experimental apple rootstocks in southern apple growing conditions – of particular importance for these plantings are the resistance to emerging diseases such as Apple Sudden Death Syndrome experienced in some orchards Pennsylvania and fire blight in North Carolina. Efforts for technology transfer were made by increasing the throughput of clonal propagules that the program has for elite rootstocks to be shared with nurseries and researchers worldwide. This efforts led to the transfer (through Cornell IP managers) of 15 elite apple rootstocks. The sharing of such material allows nurseries to experience the behavior of such rootstocks in their growing conditions, especially when such nurseries are using methods of sterile micro-propagation to multiply these apple rootstocks. The process of optimizing growth media recipes for micro-propagation may take months or years and the opportunity to do such work prior to public release decreases time of implementation of such valuable resources by apple growers. Most of the rootstock selection traits used to identify a superior rootstock are measured indirectly on grafted scions. Selection for improved apple rootstock qualities could be more efficient if we could peek at the underground root machinery directly instead of relying exclusively on scion measurements. Significant progress was made this year in order to observe root growth in vivo and measure morphological features with the aid of cameras and root imaging software. Timing and length of root growth is an example of a difficult to phenotype underground trait that is associated with whole tree source-sink metabolism and resulting yield potential. We used a system of clear tubes and cameras to visualize the growth of apple roots of 8 different rootstocks in soils that had been adjusted to three different pH levels. Preliminary data indicates that G.890 (a semi-dwarf rootstock) had roots that had a tendency to be deep rooted by reaching the deeper tubes well ahead of all other rootstocks. This tendency to grow downward (geotropism) was also confirmed in micropropagated material where roots would appear only at the bottom of rooting plugs in this rootstock. Additional root growth data was gathered by growing small apple trees in aeroponics systems (dark containers that spray a mist of nutrient solution onto the roots while suspended in air). Growing roots in air mist allowed imaging of branching tendencies of apple roots and harvesting roots for analysis of metabolic compounds and gene expression by RNA sequencing.