Fig. 4: GbM variation enables efficient identification of new functional genes.

a,b, Association of FLC epiallelic states with FT_16 °C (a) and FLC expression (b) in 13 FLC haplogroups invariant for SNPs and known SVs. Only accessions without TE polymorphism around FLC are considered. The number of accessions corresponding to each haplogroup are indicated. P values correspond to two-tailed Student’s t-test. c,d, Fitness (c) or shoot dry weight (d) of prot1 mutants (two independent alleles) relative to Col-0 under heat or joint heat and drought stress. Numbers of independent experiments are indicated for fitness (c), and plant numbers are indicated for shoot weight (d). Different letters signify P < 0.05, one-way analysis of variance, Tukey’s test. e, Flowering time of Col-0 and knockout mutants of AT1G51820, AT2G18210, AT3G43860, AT3G09530, AT1G26795 and AT4G33560. Plants were grown at 16 °C. P values were calculated using a two-tailed t-test. f–i, Magnesium (f), manganese (g), potassium (h) and zinc (i) levels of Col-0 and knockout mutants of LEAFY, AT2G16200, AT1G50470, AT2G13570, AT4G22910, AT1G28650, AT2G40815, AT1G09725, AT4G02550 and AT1G28135. The number of biological replicates is 4. P values were calculated using a two-tailed t-test. Sample medians are represented by centre lines within the box plots (a–i). Box limits indicate the 25th and 75th percentiles; whiskers extend to 1.5 times the interquartile range. DW, dry weight. j, Distance (number of genes) of validated gene from the top SNP (SNP displaying the lowest association P value) in GWA analyses of various complex traits. Inset shows the frequency of top SNP located within the validated gene (encompassing the region from the end of the upstream gene to the beginning of the downstream gene) and the validation frequency for genes containing associated gbM variants. P values from the two-tailed Student’s t-test comparing the two groups are shown.