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United States Department of Agriculture

Agricultural Research Service

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Research Project: Genetic Characterization of Fruit Quality Traits in the USDA Malus Germplasm Collection Maintained in Geneva, New York

Location: Plant Genetic Resources

2013 Annual Report


1a.Objectives (from AD-416):
The objective of this research is to characterize genomic and phenotypic variation patterns of fruit quality traits in the worldwide apple germplasm collection maintained in the USDA-ARS Plant Genetic Resources Unit (PGRU) in Geneva, New York. The information obtained from this study will provide a critical foundation for future development of fruit quality traits through marker-trait association analysis and breeding. It will help accelerate the progress of utilizing Malus germplasm for apple improvement worldwide.


1b.Approach (from AD-416):
Evaluate both fruit and biochemical quality traits in apples. The fruit traits include fruit size, firmness and stage of maturity; and the biochemical traits include sugar, organic acids, phenolic compounds and vitamin C. Focus on the core collection of Malus domestica maintained in the USDA-ARS Geneva Malus repository in this study. Genetic segregation populations and breeding lines from Cornell Apple Scion Breeding Program will also be included. Use HPLC and other analytical instruments to evaluate the phenotypic variation of primary and secondary metabolites. PGRU has an ongoing Malus GBS (genotyping-by-sequencing) Project from which tens of thousands of SNPs will be soon generated on the entire Malus collection preserved in PGRU. We will have access to the SNP information generated from the GBS Project. In this study, we will focus on generating SNP data from segregation populations and breeding lines which are not covered by the GBS Project. GBS library construction and sequencing will be done through a service at Cornell University. Investigate marker-trait association through association and linkage mapping analyses. Distribution of research results through publications and other means.


3.Progress Report:

The project goals of 2012-2013 have been successfully accomplished. We harvested ripe fruit samples from 166 apple accessions of the core collection during the growing season of 2012-2013. These samples were frozen in liquid nitrogen after harvest and then stored in a -80 freezer for further processing. Now all the samples have been grounded and are being analyzed for the composition and content of more than 30 polyphenolic compounds using HPLC. The data collection will continue for next several months. Second-year fruit samples will be harvested in September and October 2013. These phytochemical compounds being analyzed constitute the antioxidant capacity of apples and have many other attributes beneficial to human nutrition and health.


Last Modified: 11/20/2014
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