conference schedule and program with abstracts - Horticulture ...

O-43
Genetic characterization of the USDA grape germplasm collection:
Challenges and lessons learned
S. Myles* 1 , and E. Buckler 1,2
1 Institute for Genomic Diversity, Cornell University, Ithaca, New York, USA; 2 United States
Department of Agriculture – Agricultural Research Service, Ithaca, New York, USA
Corresponding author: smm367@cornell.edu
Germplasm collections around the world contain an enormous amount of potentially useful
genetic variation that is only occasionally quantified and remains largely unexploited. The first
step towards harnessing the benefits of these collections involves a thorough survey of genetic
variation. Here we describe the use of modern DNA sequencing and genotyping technologies to
provide a detailed assessment of the grape germplasm collection of the United States Department
of Agriculture (USDA). We show that a custom genotyping array, the Vitis9kSNP array, is
useful for quantifying relationships among cultivars within V. vinifera and for distinguishing
between highly diverse wild Vitis species from around the world. In addition, with 6000 reliable
genetic markers, the resulting genetic data can be used to accurately estimate pedigree
relationships among cultivars; to identify regions of the genome that have experienced strong
positive selection during domestication and breeding; and to identify genotype-phenotype
associations. Accurately assaying genetic variation across an entire genus presents distinct
challenges, especially in highly diverse plant species like the grapevine. We discuss these
challenges and suggest that modern DNA sequencing technologies will enable us to overcome
many if not all of them.
63