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United States Department of Agriculture

Agricultural Research Service

Research Project: CONSERVATION AND UTILIZATION OF THE GENETIC RESOURCES OF APPLES, GRAPES, AND TART CHERRIES Title: Genome-wide survey of genetic diversity of apple using genotyping-by-sequencing

Authors
item Gardner, Kyle -
item Schwaninger, Heidi
item Dann, Scott -
item Baldo, Angela
item Chao, C Thomas
item Fazio, Gennaro
item Volk, Gayle
item Richards, Christopher
item Zhong, Gan-Yuan
item Myles, Sean -

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: December 15, 2012
Publication Date: January 13, 2013
Citation: Gardner, K., Schwaninger, H.R., Dann, S., Baldo, A.M., Chao, C.T., Fazio, G., Volk, G.M., Richards, C.M., Zhong, G., Myles, S. 2013. Genome-wide survey of genetic diversity of apple using genotyping-by-sequencing [abstract]. Annual International Plant & Animal Genome Conference. W248.

Technical Abstract: With the advent of next-generation sequencing technologies it is now possible to generate large numbers of genetic markers without the need to rely on costly microarray platforms. Genotyping-by-Sequencing (GBS) enables the simultaneous identification and genotyping of single nucleotide polymorphisms (SNPs) in a highly multiplexed sample of multiple individuals. To investigate the domestication and breeding history of apples and to provide a foundation for marker-assisted breeding, we have used GBS to genotype about 2000 wild and cultivated apples from the USDA apple germplasm collection. From about 700 Gbp of sequence data generated from 42 lanes of the Illumina Hi-Seq platform, we have identified over 1,000,000 SNPs in the apple genome. Using these data, we demonstrate that patterns of population structure are in agreement with known relationships among apple species and cultivars. In addition, we present results of a preliminary genome scan for selection to identify the loci targeted during apple domestication and breeding.

Last Modified: 12/21/2014
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