Progress 10/01/12 to 09/30/13
Outputs
Progress Report Objectives (from AD-416): The objective of this research is to discover and characterize SNP-based genomic patterns of diversity in the apple germplasm collection maintained in the USDA-ARS Plant Genetic Resources Unit (PGRU) in Geneva, New York and backed up for long-term conservation at the USDA-ARS National Center for Genetic Resources Preservation (NCGRP). The information collected from this study will advance our knowledge and understanding of genomic diversity, domestication and breeding histories, gene flow and other evolutionary and adaptive changes in both cultivated and wild apples. The information will provide a critical foundation for future gene discovery and trait development through marker-trait association analysis and breeding. This will accelerate progress of utilizing Malus germplasm for apple improvement worldwide. Approach (from AD-416): The research will focus on the 2,500 accessions that comprise the USDA- ARS Malus collection maintained in Geneva, NY. Funds permitting, genomic analysis of additional apple varieties and collections from non-ARS sources may also be included. Genotyping-by-sequencing (GBS) techniques will be used to discover SNPs preserved genome-wide within Malus sp. accessions. DNA isolation and preparation will be done by ARS, but GBS library construction and sequencing will be performed at Cornell University core facility. GBS data will be processed and analyzed to address questions about the diversity of the USDA-ARS Malus collection, including diversity and differentiation, domestication and introgression history, signatures of selections and cultivar pedigree estimation. In addition, these data will serves as the basis for developing markers for use in breeding, and collection management. Discovered SNPs and genetic characterization of the apple collection will be made publicly available. The objective of this research is to discover and characterize SNP-based (single nucleotide polymorphism, a type of DNA marker)genomic patterns of diversity in the apple germplasm collection maintained in the USDA-ARS Plant Genetic Resources Unit (PGRU) in Geneva, New York. The information collected from this study will advance our knowledge and understanding of genomic diversity, domestication and breeding histories, gene flow and other evolutionary and adaptive changes in both cultivated and wild apples. The information will provide a critical foundation for future gene discovery and trait development through marker-trait association analysis and breeding. This will accelerate progress of utilizing Malus germplasm for apple improvement worldwide. The project is progressing well and all the major milestones/timelines have been met. Major accomplishments so far include: 1) raw sequence data (genotyping by sequencing or GBS) generated for about 2,000 apple DNA samples ; 2) a SNP calling pipeline developed; 3) summary statistics of sequencing and genotype quality and other useful metrics developed; and 4) LD (linkage disequilibrum - a type of statistics to measure how a DNA region is distributed in a population) on Malus domestica DNA samples calculated. We anticipate that we will begin developing tools for marker- assisted breeding in early 2014 once robust genotype calls have been made and a �clean� data set that has been extensively quality-filtered is provided to all collaborators.
Impacts
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Publications
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