Location: Plant Genetic Resources Unit (PGRU)
2023 Annual Report
Objectives
Objective 1: Characterize important rootstock traits in apple using genetic and genomic approaches.
Sub-objective 1.A: Characterize genetic and gene expression components of dwarfing and early bearing induction traits
Sub-objective 1.B: Characterize genetic and gene expression components of rootstock connected tree decline caused by apple viruses.
Objective 2: Breed improved apple rootstocks that perform well in diverse apple growing environments while maintaining standards for rootstock induced dwarfing, early bearing, yield efficiency, disease resistance, and overall field performance.
Sub-objective 2.A: Perform all breeding and evaluation stages involved in the 15-35 year process of developing new rootstocks with the assistance of recently developed breeding tools, such as marker-assisted selection and micro-propagation.
Approach
Apples are the most consumed fruit in the United States, featuring more than 26,000 producers and a farm-gate value of about $3.2-4 billion for apples produced in the U.S (usapple.org). To keep up with the demand for traditional and novel apple cultivars, apple growers plant 15-30 million trees yearly to replace obsolete orchards and transition to new cultivars. Apple growers face increasing challenges with increased disease pressure (fire blight, viruses, and replant disease) and the effects of climate change (water availability, temperature fluctuations, etc.). A proven solution to these challenges has been to breed new types of apple trees that can overcome these challenges naturally. All newly planted apple trees are made of two different parts, the rootstock cultivar, which provides the foundation of the tree and interacts with soil, and the scion cultivar, which is joined to the rootstock by way of grafting. The research in this project involves breeding new apple rootstocks that feature improvements regarding disease resistance, productivity, and fruit quality; when compared to conventional rootstock technologies. Breeding new apple rootstocks requires a lengthy and intensive effort that utilizes some of the best genetic marker technologies and multiple rounds of decade-long replicated field trials that match the life span of intensive apple orchards (12-19 years). Apple rootstock productivity is the result of two-component traits which are not well understood: dwarfing (or vigor control) and early-bearing, which, when combined, allow apples to be produced efficiently. Another component that is not well understood is tolerance to apple viruses, which can cause the decline and death of apple trees. Research is needed to understand both traits. The approach includes several designed and already planted field and greenhouse experiments that will produce necessary performance data which, when combined with genomic and other molecular data, will be used to develop new solutions (including new apple rootstocks) that will provide stakeholders with improved options for increased productivity and profitability of apple orchards.
Progress Report
As the new project started mid fiscal year, all planned yearly processes involved in breeding, selection and evaluation of new apple rootstocks were successfully accomplished. In the fall we harvested apple rootstocks from our layering propagation beds for evaluation and part of the material was shared with ARS scientists for studying cold hardiness in the wintertime. Remaining material was used for nursery tree evaluations that will occur in the next two years. In late winter we processed approximately 4,000 seedlings from three different bi-parental crosses for inoculation with Phytophthora and Pythium disease particles causing crown and root rots and obtained kill ratios of 50-60%. The surviving seedlings are recovering and will enter the next stage of phenotypic selection (fire blight inoculation) coming next year. Inoculations with fire blight were performed on root and crown rot survivors from last season resulting in a 40-60% kill rate depending on parentage. In the meantime, we have collected DNAs from all survivors to test for the presence of several selection markers associated with important apple rootstock traits. New hybridizations (crosses) are needed in order to generate new gene combinations in the form of new seedlings – this is largely performed with the assistance of bees, which have been somewhat difficult to source in the past few years and in the Spring of 2023 we were able to access (rent) several beehives to pollinate 4 mother plant types under pollination tents to generate thousands of seed. Fruit containing the seed representing new combinations is harvested in late summer and prepared for planting in the winter time. In the Spring of 2023 we planted a new field trial representing several of the most advanced apple rootstocks in the breeding program and some that were recently released by the breeding program. This new field trial will be useful to show the potential of these rootstocks to do well in endemic fire blight conditions typical of many locations in the U.S.
We have repeated a major replicated experiment that was performed last summer to confirm the results obtained about rootstock resistance to woolly apple aphid infestations. This will help affirm new findings about the resistance/susceptibility of a number of advanced rootstock lines that are in the process of being released. It is also aiding in finding germplasm representing new sources of resistance.
Accomplishments
1. Description of allele interactions in genetic resistance to fire blight. One of the sources for genetic resistance to fire blight caused by Erwinia amylovora (a devastating bacterial disease that attacks apples) is found in the wild relative Malus ×robusta 5. This resistance seems to be dependent on the strain of bacteria causing the infection with some strains overcoming such resistance. As such, this crabapple has been mated with susceptible apple cultivars and rootstocks to obtain resistant combinations. One of the progenies was inoculated with several E. amylovora strains in order to study the genetics and mechanism of fire blight resistance and susceptibility. Two genetic factors have been discovered, one on chromosome 3 of apple which seems to be strain specific and another one chromosome 7. In a publication in the journal of plant pathology, we report the detection of the chromosome 7 genetic factor in different ‘Malling 9’ × M. ×robusta 5 population in Germany and confirm the its independence E. amylovora strains. This finding is important because broad genetic resistance that is not strain specific should be more durable and effective.
