Association Study of Important Traits in Lettuce

Lettuce (Lactuca sativa) was domesticated from its wild ancestor L. serriola in the Mediterranean region. It was re-domesticated as a stem vegetable after it was introduced into China two thousand years ago. Besides the stem lettuce, leafy lettuce has been bred into four major types, romaine, butterhead, crisphead and loose-leaf. To perform association analysis, we selected 36 romaine, 40 butterhead, 35 crisphead, 19 loose-leaf, 41 stem lettuce cultivars, 28 intermediate ones, 43 wild genotypes as well as 40 inbred lines derived from a cross between a loose-leaf cultivar and a stem lettuce cultivar. RNAs were extracted from mature leaves and sequenced using Hiseq2500, and ~4 Gb sequence data were obtained for each sample. More than one million high-quality single-nucleotide polymorphisms were found among the sequenced genotypes. Lettuce is shown to have a strong population structure with cultivars of the same type grouped together. Furthermore, strong linkage disequilibrium (LD) exists in lettuce, hindering the application of association analysis. Nevertheless, comparative analysis identified a list of regions as putative domestication sweeps, including loci controlling stem thorn and seed shattering. Genome-wide association studies (GWAS) identified one locus for seed color, one locus for leaf shape and four loci for leaf color. These loci were confirmed using biparental segregating populations. RNAseq detected many genes that have presence/absence polymorphism or show dramatic expression patterns between wild genotypes and cultivars. Our data provide a good resource for lettuce genetics research and breeding programs and contribute to our understanding of lettuce evolution and domestication.