Fig. 3: The 16S rRNA QTLs.

a A color coded summary of the number of 16S rRNA QTLs identified per chromosome to wild and modern alleles. b A summary of the number of 16S rRNA QTLs found by taxonomies, with the chromosome of each QTL represented within each square. The presence and absence of dark borders around each square are used to indicate a QTL linked to higher abundance for a wild allele and modern allele respectively. c A hierarchically structured network depicting the 16S rRNA QTLs identified in this study. From the top to bottom: the nodes in the first row represent tomato chromosomes, which are linked to specific ASV in the next row, which are linked to different families and classes of bacteria in subsequent rows. The size of the chromosome nodes is weighted by the number of outbound edges. The ASV, family, and class node sizes are weighted by the number of in-bound edges. The edges are color coded based on negative effect relative to the modern reference (e.g., wild allele), and positive effect relative to the modern reference (e.g., modern allele). The abundance of individual ASV, and at different taxonomic levels, is determined through a complex interaction of multiple alleles from both modern and wild origin. d A statistical analysis of the four lineages with 3 or greater QTLs shows that the absolute value of effect size for different lineages is different. Specifically, we find that the effect size for ASV within Massila (n = 4) was significantly larger than for the other lineages (Adhaeribacter, n = 3; Caulobacter, n = 4; Methylophylaceae, n = 9). The effect size was calculated as the percent change relative to the mean CSS abundance for each ASV. In addition to the scatter plot, data are presented with boxplots representing the median value, the interquartile range, and whiskers representing the minimal and maximal values excluding points greater than 1.5 times the interquartile range. Source data are provided as a Source Data file.