Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/29/2011
Publication Date: 6/4/2012
Citation: Kwon, S.J., Truco, M., Hu, J. 2012. LSGermOPA, a custom OPA of 384 EST-derived SNPs for high-throughput lettuce (Lactuca sativa L.) germplasm fingerprinting. Molecular Breeding. Volume 29, Issue 4, Page 887-901. Interpretive Summary: SNP (single nucleotide polymorphism) is the most abundant genetic variation among individuals and populations of animals and plants. To investigate the genetic diversity and relationship among the accessions of the USDA lettuce germplasm collection, we are fingerprinting the approximately 1,600 lettuce accessions with the Illumina’s GoldenGate SNP assay. We used the service of the UC Davis Genome Center for SNP genotyping. A custom OPA (oligo pool all), LSGermOPA, targeting 384 SNP loci was designed from the lettuce EST (expressed sequence tag) sequences from the US Compositae Genome Project database. This paper reports the results on 148 cultivated lettuce accessions, which demonstrated that LSGermOPA is capable of disclosing adequate levels of polymorphism among lettuce cultivars and is appropriate to be used for assessment of genetic diversity and population structure of the lettuce germplasm collection.
Technical Abstract: We assessed the genetic diversity and population structure among 148 cultivated lettuce (Lactuca sativa L.) accessions using the high-throughput GoldenGate assay and 384 EST (Expressed Sequence Tag)-derived SNP (single nucleotide polymorphism) markers. A custom OPA (Oligo Pool All), LSGermOPA was formed by choosing validated SNPs from the Compositae Genome Project Database of UC Davis. High quality genotype data were obtained from 354 of the 384 SNPs (success rate = 92.2%) for the148 lettuce accessions. The average of expected (He) and observed (Ho) heterozygosity were 0.371 and 0.066, repectively. The average polymorphic information content (PIC) was 0.293. The reproducibility was 99.8% as measured by four duplicated DNA samples in the assay. Analysis of molecular variance revealed that among the five horticultural types of lettuce cultivars, leaf type had highest variation (24.2%) and crisphead and stem types had lowest variation (2.4%). Pairwise comparisons showed that the lowest genetic distance (Fst = 0.065) was between the leaf and crisphead types, while the romaine and butterhead types were the most distant (Fst = 0.376) pairs. The phylogenetic relationship and population structure based upon the LSGermOPA-generated SNP data were consistent with previous results using other marker systems. These results demonstrated that LSGermOPA is capable of disclosing adequate levels of polymorphism among lettuce cultivars and is appropriate to be used for assessment of genetic diversity and population structure of the lettuce germplasm collection.