Molecular Breeding

, Volume 29, Issue 4, pp 887–901

LSGermOPA, a custom OPA of 384 EST-derived SNPs for high-throughput lettuce (Lactuca sativa L.) germplasm fingerprinting


DOI: 10.1007/s11032-011-9623-5

Cite this article as:
Kwon, SJ., Truco, MJ. & Hu, J. Mol Breeding (2012) 29: 887. doi:10.1007/s11032-011-9623-5


To deploy a high-throughput genotyping platform in germplasm management, we designed and tested a custom OPA (Oligo Pool All), LSGermOPA, for assessing the genetic diversity and population structure of the USDA cultivated lettuce (Lactuca sativa L.) germplasm collection using Illumina’s GoldenGate assay. This OPA contains 384 EST (expressed sequence tag)-derived SNP (single nucleotide polymorphism) markers selected from a large set of SNP markers experimentally validated and mapped by the Compositae Genome Project. Used for genotyping were DNA samples prepared from bulked leaves of five randomly-selected seedlings from each of 380 lettuce accessions. High-quality genotype data were obtained from 354 of the 384 SNPs. The reproducibility of automatic genotype calls was 99.8% as calculated from the four pairs of duplicated DNA samples in the assay. An unexpectedly high percentage of heterozygous genotypes at the polymorphic loci for most accessions indicated a high level of heterogeneity within accessions. Only 148 homogenous accessions, collectively comprising all five horticultural types, were used in subsequent analyses to demonstrate the usefulness of LSGermOPA. The results of phylogenetic relationship, population structure and genetic differentiation analyses were consistent with previous reports using other marker systems. This suggests that LSGermOPA is capable of revealing sufficient levels of polymorphism among lettuce cultivars and is appropriate for rapid assessment of genetic diversity and population structure in the lettuce germplasm collection. Challenges and strategies for effective genotyping and managing lettuce germplasm are discussed.


Lettuce Germplasm SNP marker Diversity 

Supplementary material

11032_2011_9623_MOESM1_ESM.xls (151 kb)
Supplementary material 1 (XLS 151 kb)
11032_2011_9623_MOESM2_ESM.xls (124 kb)
Supplementary material 2 (XLS 124 kb)

Copyright information

© Springer Science+Business Media B.V. (outside the USA) 2011

Authors and Affiliations

  1. 1.US Department of Agriculture-Agricultural Research Service, Western Regional Plant Introduction StationWashington State UniversityPullmanUSA
  2. 2.Genome CenterUniversity of California at DavisDavisUSA

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