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United States Department of Agriculture

Agricultural Research Service

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Location: Plant Genetic Resources Research

2010 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
Substantial progress was made on all 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 reached a major milestone under sub-objective 1.A with the release of four new apple rootstocks (G.214, G.969, G.890 and G.210) for the U.S. industry. The release was accompanied by the transfer of foundation propagation material in the form of thousands of micropropagated plants to all U.S. apple rootstock nurseries licensed to grow Geneva® apple rootstocks. These new apple rootstocks have shown tolerance to apple replant disease and resistance to fire blight, two diseases widely recognized as major threats to the long term viability of the U.S. apple industry. All of the newly released rootstocks are more productive than current industry standards and will serve the fresh market and processing apple industries. Apple rootstock production methods by stooling and layering beds have not changed in many years – improving the productivity of apple rootstock nurseries is relevant to sub-objective 1.B . In FY10 we completed a three year study into methods for improving the propagation of apple rootstocks comprising chemical treatments, planting methods and changes in other cultural practices. The result was the discovery of a chemical treatment (prohexadione-CA) that improved the quality/quantity of saleable apple rootstock liners significantly. This discovery is already being implemented by several apple rootstock nurseries in the U.S. and will have an impact on apple rootstock production worldwide. Substantial progress was made in all operations related to breeding apple rootstocks such as planting new orchards, measuring tree size and productivity, measuring tolerance to diseases such as fire blight, describing propagation properties, making new experimental trees in the nursery, making new crosses, harvesting and grading rootstock liners, etc. However, the project still suffered setbacks due to problems caused by the improper application in FY09 of a pre emergence herbicide by staff of the Field Research Unit of Cornell (the only people trained and equipped to apply the material) which caused death and stunting of nursery stool beds destined for propagation research. 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. We have made significant progress in characterizing the macro and micro-nutrient absorption potential of commercial and experimental apple rootstocks in different soils and pH conditions. Knowledge about how apple rootstocks roots absorb mineral nutrients can increase the efficiency of fertilizer treatments made by growers and curb runoff into streams.

4. Accomplishments
1. Release of new apple rootstocks G.214, G.210, G.969 and G.590. In March 2010, ARS researchers in Geneva, NY released four new apple rootstocks: G.214 a dwarfing (30-40% of seedling), precocious, productive rootstock resistant to fire blight. This rootstock went through rigorous testing for multiple disease resistance (fire blight, phytophthora root rot and wooly apple aphid) and has performed very well in replant trials under organic management. G.214 will is tailored for fresh market high density apple production amenable to mechanization. The second rootstock released G.890 is a semi-dwarfing (50-65% of seedling) productive plant resistant to fire blight that has performed well in difficult replant soils in Washington state and is tailored for fresh and processing apple production. The third rootstock G.210 is semi-dwarfing (50-60% seedling) and survived the series of inoculations with apple rootstock pathogens (Erwinia amylovora, Phytopthora cactorum, wooly apple aphid); it has been characterized as tolerant to the replant disease complex in several replicated studies. The fourth rootstock is G.969 a semi dwarfing (45-55% of seedling) productive plant, resistant to fire blight that lends itself as a good support for weaker or more difficult scion varieties like Honeycrisp. All these rootstocks were tested in the field for productivity and precocity and performed very well when compared to other rootstocks that have similar vigor characteristics. All of these rootstocks have been transferred to the nursery industry for large scale production and are expected to have a major role in sustainable apple production for years to come.

2. Apple Rootstock Breeding and Genetics for Improved Mineral Absorption. Nutrient and micronutrient absorption and translocation are important apple rootstock traits that have been largely ignored in breeding programs due to the high cost connected to testing tissue samples for mineral absorption. Developing a methodology that would allow the discovery, breeding and selection of efficient absorbers and translocators of mineral nutrients would greatly improve the overall impact on sustainable apple production worldwide. Furthermore, it could improve the concentration of essential dietary minerals for humans. The Geneva® apple rootstock breeding program possesses one of the widest germplasm pools for the development of yield-efficient, disease-resistant apple rootstocks. ARS research in Geneva, NY in collaboration with Cornell University, Lithuanian Institute of Horticulture and USDA-ARS Children's Nutrition Research Center grafted an array of apple rootstock genotypes representing this germplasm pool with the same scion (Gala) and tested for genetic influence on the uptake of macro- and micronutrient minerals at different soil pH levels. As a general trend, absorption of molybdenum (Mo), calcium (Ca) and phosphorous (P) increased with higher pH levels while absorption of iron (Fe), manganese (Mn) and nickel (Ni) decreased with increasing pH. Absorption of potassium (K), copper (Cu), sodium (Na), zinc (Zn), magnesium (Mg) and sulfur (S) did not seem to be affected by soil pH. We discovered significant differences among rootstocks for leaf concentration for all macro and micronutrients tested. These differences also transferred to a subset of a segregating population used for the discovery of genes related to nutrient metabolism. Long term plans include incorporating such knowledge into the Marker Assisted Breeding scheme of our breeding program and improving our phenotypic selection pipeline.

3. Discovery of Treatments that Improve Nursery Apple Rootstock Production. Poor rooting is a common problem in apple rootstock propagation. ARS researchers in Geneva, NY established four field experiments in Ephrata, Washington; Angers, France; and Canby, Oregon and tested three approaches to increase rooting in apple rootstock stool beds. The first approach tested chemical applications (prohexadione-CA, IBA and NAA) at various times of the year on B.9, M.9 T337, M.9 EMLA and G.41 rootstock stool beds. The second approach tested the effects of dark preconditioning on B.9 and M.9 T 337 stool beds. The second approach combined the effects of chemical treatments and dark preconditioning on G.41 stool beds. The third approach examined the effects of planting style and density on B.9, M.9 T337 and G.935. Results showed that upright planting styles are the most productive, with a high density spacing give the best overall results. Prohexadione-CA (Apogee) significantly increased rooting, improved caliper of the rootstocks the control and caused a shift in production by 10-30% (depending on rootstock genotype) from non-saleable grades (C and D) to saleable (A and B). This increase in marketable production resulted in a net increase in profitability of the nursery operation. Application of this technology by apple rootstock nurseries that produce 3-4 million rootstocks a year results in substantial efficiencies and additional profits. This technology was transferred to U.S. apple rootstock nurseries in 2010.

4. Elucidation of the Genetic Control of Very Important Apple Rootstock Traits. Dwarfing, precocity are very important apple rootstock traits that require lengthy periods (3-9 years) of field testing for the purposes of breeding and selection of new rootstocks. The discovery of the genetic control of these traits allows us to select dwarfing/precocious plant material before it is planted in the field thus creating substantial efficiencies in the breeding and selection of new rootstocks. As a result of a six year endeavor in this research, we elucidated the inheritance and location in the apple genome of these multi-gene traits as well as their effect. ARS researchers in Geneva, NY are utilizing this information to implement marker assisted selection in our breeding program. Further studies are being conducted to increase the precision and predictability of the genetic markers in various apple rootstock breeding populations.

5. Characterization and Genetic Mapping of Expression Profiles of Apple Genes. The discovery of gene sequences that are associated with important phenotypes in apple rootstocks will impact the long term efficiency of the breeding program. ARS researchers in Geneva, NY in collaboration with Penn State University, gene expression of 26,000 unique gene sequences was measured on a full sib population to discover genes that were associated with fire blight resistance and other important apple rootstock traits. We utilized the expression profiles for these genes to map expression QTLs (e-QTLs) for all 26,000 unigenes and recorded the location in the apple genome of the genes/control regions that modulate the production of RNA for these genes. A sub-sample of these genes was submitted to scientists in Italy (IASMA) that have produced a full apple genomic DNA sequence and we found good correspondence with the location of the e-QTLs and the physical location of the genes or transcription factors that control them. We are assembling a network map that will elucidate associations with important apple rootstock traits.

Last Modified: 06/23/2017
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