Location: Plant Germplasm Introduction and Testing
Title: High-throughput SNP genotyping of a subset of lettuce landraces for genetic diversity assessment Authors
Submitted to: Internationl Conference on Plant Molecular Breeding
Publication Type: Abstract Only
Publication Acceptance Date: August 25, 2010
Publication Date: September 5, 2010
Citation: Hu, J., Kwon, S.J., Hellier, B.C. 2010. High-throughput SNP genotyping of a subset of lettuce landraces for genetic diversity assessment. 3rd International Conference of Plant Molecular Breeding, September 5-9, 2010, Beijing, China P 104. Technical Abstract: Lettuce is one of the most popular vegetables grown commercially worldwide. It ranks as one of the top ten most valuable crops in the U.S. with an annual value of over two billion dollars since 2004. The USDA lettuce germplasm collection is maintained in seed form in the Western Regional Plant Introduction Station at Pullman, WA. We are in the process of fingerprinting the whole collection of approximately 1,600 accessions with the high-throughput SNP genotyping for genetic diversity assessment. We used the service provided by the DNA Technologies Core Facility of UC Davis Genome Center for SNP genotyping. The oligo pools (OPAs) targeting 384 SNP loci were designed from the high quality EST (expressed sequence tag) sequences generated by the US Compositae Genome Project (CGP) headed by Dr. Richard Michelmore of UC Davis. SNP genotyping was carried out by using the Illumina's custom VeraCode GoldenGate Genotyping Kits which can simultaneously genotype 384 loci in a single well of a standard 96-well microplate. The scanned data from BeadXpress Reader were analyzed with the GenomeStudio software to generate genotype data for individual accessions. Our initial result from 455 accessions demonstrated that this technique is very powerful in revealing genetic variation. Three hundred and thirty-five or 87% of the 384 SNP produced polymorphic genotype data and each of the 455 accessions could be discriminated by the dataset. Detail results from a subset of lettuce landrace germplasm will be presented.