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

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Abstract

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.

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Acknowledgments

We greatly appreciate the generosity of Richard Michelmore for allowing us to access and use the unpublished data in selecting SNPs for LSGermOPA, and two anonymous reviewers for helpful and constructive comments on the manuscript. We thank Barbara Hellier, Pavelka, Maria, and Corey Whale for technical assistance in the greenhouse and thank Charles Nicolet and Vanessa Rashbrook for performing the SNP genotyping and helping us in using the GenomeStudio software. This research was supported by USDA-ARS CRIS 5438-21000-026-00D and by the Hatch Act funds to Multistate Research Project W006.

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Authors and Affiliations

  1. US Department of Agriculture-Agricultural Research Service, Western Regional Plant Introduction Station, Washington State University, 59 Johnson Hall, Pullman, WA, 99164, USA

    Soon-Jae Kwon & Jinguo Hu

  2. Genome Center, University of California at Davis, GBSF 451 Health Sciences Drive, Davis, CA, 95620, USA

    Maria-Jose Truco

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  1. Soon-Jae Kwon
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  2. Maria-Jose Truco
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  3. Jinguo Hu
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Correspondence to Jinguo Hu.

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Kwon, SJ., Truco, MJ. & Hu, J. LSGermOPA, a custom OPA of 384 EST-derived SNPs for high-throughput lettuce (Lactuca sativa L.) germplasm fingerprinting. Mol Breeding 29, 887–901 (2012). https://doi.org/10.1007/s11032-011-9623-5

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