2013 ASHS Annual Conference

The U.S. lettuce (Lactuca sativa. L.) germplasm collection is managed by the USDA–ARS Western Regional Plant Introduction Station in Pullman, WA. We recently genotyped approximately 1,200 accessions of cultivated lettuce with the Illumina’s GoldenGate assay for 384 SNP markers and created a special collection of 298 lines, each of which is derived from a single plant homozygous at 322 genotyped loci. This collection contains 122 butterhead, 63 crisphead, 53 romaine, 53 leaf, and 7 stem types. There are only 258 unique genotypes among the 298 lines since there are 26 pairs or small groups (a total of 66 lines) sharing identical genotypes. The average genetic similarity coefficient (GS) among the 258 unique genotypes was 63.9% with a range from 40.6% to 99.8%. Population structure analysis revealed that there are most likely six subpopulations corresponding more or less to the horticultural types with the crisphead types divided into two. We evaluated 10 phenotypic traits of these lines and conducted a preliminary genome-wide marker-trait association analysis using three different methods: single factor analysis, general linear model analysis and mixed linear model analysis. Nine significant marker-trait associations (SMTA) were revealed at P < 0.0001 level with all three methods and also when considering kinship and/or population structure for this collection. These marker-trait associations include five SMTAs for seed coat color, one for leaf margin undulation, two for leaf anthocyanin and one for stem anthocyanin. These marker-trait associations await validation with segregating populations before being used for marker-assisted selection.