Genome-Wide Marker-Trait Association Among Ten Horticultural Traits and 322 SNP Markers in a Special Collection of 298 Homozygous Cultivated Lettuce Lines

We conducted a genome-wide marker-trait association analysis in a special collection of 298 homozygous lettuce (Lactuca sativa. L.) lines derived from individual plants sampled from 273 accessions. These plants were genotyped by the Illumina’s GoldenGate assay with 322 high quality SNP markers. Only 258 unique genotypes were identified among the 298 lines since there were 26 pairs or small groups (a total of 66 lines) sharing identical genotypes. These lines included 122 butterhead, 53 romaine, 63 crisphead, 53 leaf and 7 stem types. The average genetic similarity coefficient (GS) among the 258 unique genotypes was 63.9% with a range from 40.6 to 99.8%. A phylogenetic tree was constructed based on the genotype data. Population structure analysis revealed that the most likely number of subpopulations was six. For association analysis between the 322 SNP markers and the 10 phenotypic traits of the 258 homozygous lines, three different methods were performed: 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 markers will be useful in marker-assisted selection to breed lettuce cultivars with desirable agronomic traits and end-user qualities.