Location: Plant Genetic Resources Unit (PGRU)
2020 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.
The main objective of the project (Objective 1) is to 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. A secondary objective (Objective 2) is to 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. While ARS researchers in Geneva, New York, made significant advances in both objectives, the transition to essential activities due to the pandemic has meant that much of data collection and lab activities planned for the 2020 growing season had to be canceled or postponed for next season. ARS researchers in Geneva, New York, were able to plant their rootstock and tree nursery, plant a new orchard meant to test sensitivity to viruses in their breeding lines, and to plant new seedlings (representing six new crosses and the beginning of a new breeding cycle). The field season has been characterized by an unusually long period of drought during the month of June and beginning of July – which has affected fruit set and fruit size in some of our plantings. ARS researchers in Geneva, New York, were fortunate that some of their grower collaborators and university research collaborators in California and Washington, New York and Maine were able to plant their field experiments. These field plantings are the best method to show the impact of rootstocks on productivity and disease resistance. More nursery field trials will be planted in Oregon and Washington this fall and winter.
The quest to discover more about how roots interact with the soil microbiome is progressing as ARS researchers in Geneva, New York, analyze the genetic factors influencing the presence and concentration of phenolic and other organic molecules in root tissues of breeding populations. Published collaborative research with the USDA ARS Wenatchee location showed that some organic molecules found in certain rootstock root systems are bio-active and are associated with differential development of microbial communities in a diverse set of apple roots and these molecules seem to be leached into the rhizosphere. Genetic analyses of root metabolite concentration in rootstock breeding populations revealed the presence of major genetic factors controlling the abundance of substances like caffeic acid (chromosome 6), isoquercitrin and rutin (chromosome 17) and noraucuparin (chromosome 2). More research needs to be performed that connects the abundance of these metabolites to the composition of the root microbiome (rhizobiome) – the important thing is that we have a set of contrasting root systems that display high and low levels of these compounds which enable sound statistical comparison to discover associations with microbial communities.
Accomplishments
1. Ten-year rootstock field experiment with Red Delicious Scion is completed. The primary role of our breeding program is to produce new apple rootstock that are commercially viable. In order to realize their commercial potential, it important to test this material in an “apple grower” field setting and compare it to existing commercial material. These types of field experiments sometimes include other components like orchard system design to understand how such rootstocks behave in different systems. Cornell University and USDA ARS investigators concluded and reported on a 2-acre field experiment planted in 2007 in the Hudson Valley apple growing region (New York) to test orchard systems and apple rootstocks, using Super Chief Delicious apple as cultivar. This research compared six Geneva® rootstocks (G.11, G.16, G.210, G.30, G.41 and G.935) with one Budagovsky (B.118) and three Malling rootstocks (M.7EMLA, M.9T337 and M.26EMLA). Trees on each rootstock were trained to four high-density systems: Super Spindle (SS) (5,382 apple trees/ha), Tall Spindle (TS) (3,262 trees/ha), Triple Axis Spindle (TAS) (2,243 trees/ha), and Vertical Axis (VA) (1,656 trees/ha). Analysis of yield and fruit quality data showed that rootstock and training system interacted to influence tree growth, productivity, and fruit quality. When comparing orchard systems, SS trees were the least vigorous but much more productive than any other system on a per-acre basis. The lowest yield values were for all training systems with B.118 and M.7EMLA and very often, apple growers are tempted to plant weak growing “spur-type” apples like Red Delicious on vigorous rootstocks like M.7 and B.118 – a choice that would likely result in disastrous yields. The outcome of this experiment gives viable rootstock alternatives than traditional commercial options and shows that the type of orchard system can be leveraged to achieve optimal commercial yields.
