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United States Department of Agriculture

Agricultural Research Service

Research Project: MANAGEMENT OF TEMPERATE FRUIT NUT AND SPECIALTY CROP GENETIC RESOURCES Title: Genome-wide SNP detection, validation, and development of an 8K SNP array for apple

item Chagne, David -
item Corwhurst, Ross -
item Troggio, Michela -
item Davey, Mark -
item Gilmore, Barbara
item Lawley, Cindy -
item Vanderzande, Stijn -
item Hellens, Roger -
item Kumar, Satish -
item Cestaro, Alessandro -
item Velasco, Riccardo -
item Main, Dorrie -
item Rees, Jasper -
item Iezzoni, Amy -
item Mockler, Todd -
item Wilhelm, Larry -
item Van DE Weg, Eric -
item Gardiner, Susan -
item Bassil, Nahla
item Peace, Cameron -

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 12, 2012
Publication Date: February 21, 2012
Citation: Chagne, D., Corwhurst, R., Troggio, M., Davey, M.W., Gilmore, B.S., Lawley, C., Vanderzande, S., Hellens, R.P., Kumar, S., Cestaro, A., Velasco, R., Main, D., Rees, J., Iezzoni, A., Mockler, T., Wilhelm, L., Van De Weg, E., Gardiner, S., Bassil, N.V., Peace, C. 2012. Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS One. 7(2): e31745. doi:10.1371/journal.pone.0031745.

Interpretive Summary: An international team of scientists and researchers called the International RosBREED Apple SNP Consortium collaborated on developing and charaterizing thousands of important markers in apple. We determined the DNA code information for 27 apple cultivars chosen to represent worldwide breeding programs. Comparison of the DNA code information to that of the 17 chromosomes of ‘Golden Delicious’ resulted in detection of 2,113,120 single base pair changes. A subset of 144 of these markers were validated using 160 apples. This validation assay enabled fine-tuning of the final subset of markers to place on a microcomputer chip.These markers were located on all 17 chromosomes of apple. This chip allows assaying a large number of DNA regions simultaneously and is essential for a range of genetics studies and plant breeding applications. Evaluation of this chip in families and an apple collection identified 5,554 of 7,867 useful markers. This chip is publicly available and will provide an unprecedented resolution of genetic variation in apple.

Technical Abstract: As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus × domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of ‘Golden Delicious’, SNPs were identified using SoapSNP. A total of 2,113,120 SNPs was detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but were also located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes that will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple.

Last Modified: 10/7/2015
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