Fig. 4

Genome-wide association study (GWAS) of leaf anthocyanin content in L. sativa using filtered SVs. a Manhattan plots of GWAS across nine lettuce chromosomes. b Read alignment on the genomic regions flanking the RLL2 gene shown in the IGV interface. The accessions with high anthocyanin content were colored in red. The RLL2 gene structure is shown at the bottom. c Sequencing depth ratio within the association region in six representative accessions. The 600-kb deletion is indicated by the orange box, and RLL2 is indicated by the arrow. The orange and blue lines indicate the relative sequencing depth (read coverage within a 100-kb window with 10-kb step divided by the average depth across the genome) in three representative accessions with high and low anthocyanin content, respectively. d A Maximum-likelihood phylogenetic tree of RLL2 protein sequences from six representative accessions. The accessions with high anthocyanin content were colored in red. e The frequency of the 600-kb deletion in L. sativa accessions with high and low anthocyanin content