From core to target collections: genomic prioritization of trait-associated diversity

These are the supplementary data files of the research article titled "From core to target collections: genomic prioritization of trait-associated diversity". These files contain genetic, phenotypic and descriptive information about part of the lettuce collection of the Center for Genetic Resources Netherlands (CGN), the national Dutch genebank. As part of the research, a GWAS study was produced, as well as several collections optimized in diffferent ways. These results are added in these files. All genomic positions indicated in the different files are based on the genome sequence of Lactuca sativa Salinas_v8 . In more detail: Supplementary data 1 (Sup1) contains a full genotype table for all individuals in the collection. This includes >2M marker records for 1229 individuals. Supplementary data 2 (Sup2) contains descriptive data (species classification, origin, common name, date of collection) and aggregated phenotype data (30 traits) for 1229 individuals. Supplementary data 3 (Sup3) contains phased marker data for all individuals in the collection. This is >2M markers, phased in haplotypes 1 and 2 for each individual. Supplementary data 4 (Sup4) contains haplotype-tagged data for all individuals in the collection. Contiguous phased markers, defined by haploblock ranges, were tagged in codes of the type "H1", "H2", "H3", etc. Column definitions are as follows: chrom (chromosome), minpos (left edge of haploblock), maxpos (right edge of haploblock), nmark (number of markers within haploblock), mismatch.exp (expected number of mismatches between variants with the same haplotype label), haplos (number of haplotypes in that block). Supplementary data 5 (Sup5) locations of significant regions identified by GWAS for all traits with positive results. Supplementary data 6 (Sup6) zip file containing all collections (core and target collections) defined in this study. Supplementary data 7 (Sup7) script containing functions with an implementation of a greedy haplotype optimisation algorithm. Supplementary data 8 (Sup8) file containing additional supplementary figures to the research article. For further information do not hesitate to contact the corresponding author.