Location: Plant Genetic Resources Unit (PGRU)
2019 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
This project addresses NP 301 Action Plan, Component 1 – Crop Genetic Improvement; Problem Statement 1A: Trait discovery, analysis, and superior breeding methods; Problem Statement 1B: New crops, new varieties, and enhanced germplasm with superior traits.
Significant progress was attained under 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); and 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). The implementation of new apple rootstocks by apple growers throughout the U.S. is dependent on field testing and field performance at or near the location where the rootstocks will be utilized. This year we propagated more than 5,000 apple trees that will be planted in field trials in Washington State, California, New York, Pennsylvania, Maine and Michigan in Spring and Fall of 2020. These field trials which include five to thirty different rootstocks feature traditional scion varieties like Gala and Granny Smith as well as new varieties like Cosmic Crisp® and SnapDragon®. Data from these trials will feed into a localized database which enables apple growers to make informed decisions about which apple rootstocks to plant on their farms.
All breeding cyclical operations which need to occur every year for successful operations (planting of nursery stock, measuring tree size and productivity in experimental orchards, grading roots in nursery material, etc.) were accomplished. The growing season was marked by a very late and cool Spring which brought an unusually high amount of rain causing some flooding and water logging in the field and subsequent death of several test trees. The wet ground also prevented timely planting of our new nursery material and delayed it well into July, whereas normally we should be finished planting in May. All other operations during the rest of the growing season were successful and yielded important data for the selection of new rootstocks for the apple industry.
Honeycrisp was the most planted variety in the U.S. in 2018. While it is a very desirable eating apple, it suffers from quality issues that sometimes prevent more than 50% of the apples to be sold in the fresh and more lucrative market – in high value varieties like Honeycrisp, over the life of an orchard such losses can amount to at least $50K per acre. The major reason for such losses is bitter pitting (small black indentations on the surface of the apple) which is caused largely by a nutrient imbalance of calcium, potassium, nitrogen and boron. ARS researchers in Geneva, New York analyzed X-Ray diffraction (XRF) patterns obtained from 6,000 apples picked from 600 Honeycrisp apple trees grown on 200 different rootstocks to predict the tendency of certain apple rootstocks to produce good quality apples. The data definitively showed that the ratio of potassium/calcium (K/Ca) was the best predictor of the tendency of the apples to develop bitter pit. Rootstocks that favored calcium in that ratio produced apples free of bitter pit. Other yield components like crop load and tree vigor also played a role in production of bitter pit free Honeycrisp apples. This experiment also yielded a genetic model for rootstock modulated calcium and potassium content in Honeycrisp.
Soil pH is one of the most important orchard land features that affect nutrient availability and fertility. Apple growers go to great length to optimize soil pH to improve the productivity of the orchard. ARS and Cornell University scientists in Geneva, New York completed three experiments performed in aeroponic, potted soil and rhizotron boxes to study the interaction of six apple rootstocks (G.41, G.11, G.214, G.969, G.890 and M.9) with three pH levels (5.5, 6.5 and 8). While the data is still being processed, preliminary results show that certain rootstocks seem to have a preferred pH level for optimal growth and performance. Once completed, this data will aid apple growers in the choice of a better rootstock for their soil conditions and increase the yield potential of their farms.
Accomplishments
1. Genetic control of boron uptake in apple rootstocks. Boron is an important nutrient that contributes to successful flowering and fruit set of apple trees. Lack of boron causes major physiological disorders. Excess of boron causes toxicity and increases the occurrence of bitter pit in apples. ARS and Cornell scientists in Geneva, New York and Fargo, North Dakota, found three rootstocks (G935, G.222 and CG. 4004) that naturally increase the boron content in scions, and three lowest boron absorbers in older and commonly planted rootstocks (M.9, B.9 and M.26). The data collected over the period of five growing seasons on mature trees shows that boron absorption is under tight genetic control. This discovery will improve fertilizer recommendations utilized throughout the U.S. and the world.
Review Publications
Reig, G., Lordan, J., Sazio, M.M., Hoying, S., Fargione, M., Reginato, G., Donahue, D., Francescatto, P., Fazio, G., Robinson, T. 2018. Effect of tree type and rootstock on the long-term performance of 'Gala', 'Fuji' and 'Honeycrisp' apple trees in a Tall Spindle production system under New York State climatic conditions. Scientia Horticulturae. 246:506-517.
Peace, C.P., Bianco, L., Troggio, M., Van De Weg, E., Howard, N.P., Cornille, A., Durel, C., Myles, S., Migicovskv, Z., Schaffer, R., Costes, E., Fazio, G., Yamane, H., Van Nocker, S., Gottschalk, C., Costa, F., Chagne, D., Zhang, X., Patocchi, A., Gardiner, S.E., Hardner, C., Kumar, S., Laurens, F., Bucher, E., Main, D., Jung, S., Vanderzande, S. 2019. Apple whole genome sequences: recent advances and new prospects. Horticulture Research. 6:59.
Reig, G., Lordan, J., Sazo, M.M., Hoying, S., Fargione, M., Reginato, G., Donahue, D.J., Francescatto, P., Fazio, G., Robinson, T. 2019. Long-term performance of 'Gala', 'Fuji' and'Honeycrisp' apple trees grafted on Geneva rootstocks and trained to four production systems under New York State climatic conditions. Scientia Horticulturae. 244:277-293. https://doi.org/10.1016/j.scienta.2018.09.025.
Fazio, G., Lordan, J., Grusak, M.A., Francescatto, P., Robinson, T. 2019. Mineral nutrient profiles and relationships of ‘Honeycrisp’ grown on a genetically diverse set of rootstocks under Western New York climatic conditions. Horticulture Scientia. https://doi.org/10.1016/j.scienta.2019.05.004.
Moran, R.E., Peterson, B.J., Fazio, G., Cline, J. 2018. Genotypic variation in apple rootstock cold temperature tolerance during spring and fall. Journal of the American Society for Horticultural Science. 143:319-332.
