Genome-wide-association analyses
Additive genetic variance (VA) ranged from 0.10 for relative gut length to 0.62 for GRN and 0.69 for plate number (Table 4). SNP based heritability ranged from 0.42 (for relative gut length) to 0.62 (for plate number) and 0.65 (for GRL2) (Table 4). We found between five and 100 putatively causal SNPs associated with variation in each trait (Table 4). In nine cases, pairs of SNPs that were associated with trait variation were also closely linked (within 1kb) on the genome. All of these were between functionally similar traits. Specifically, one 1kb region (on chr VII) had SNPs associated with DS1 and DS2, seven regions (on chr I, IV, XIV and XVIII) had SNPs associated with GRL2 and GRL3, and one region (chr VI) had SNPs associated with both GRL3 and GRW. Genomic regions associated with the relative lengths of GRL2, GRL3 and the gut were linked to the same 10 QTLs for various feeding traits, and the relative length of GRL3 was linked to a further 28 QTLs for feeding traits, including gill raker length, spacing and number. Genomic regions associated with relative GRW overlapped with all those for GRL2 and GRL3, as well as a further 68 QTLs for feeding traits, including for lateral, medial and middle raker spacing. Regions of the genome associated with lateral plate number in our analysis were physically linked to 17 regions with QTLs previously identified for armour plating phenotypes, nine of which were for lateral plate number. Most notably, the major peak on the Manhattan plot for lateral plate number in our analyses (see Fig S5) fell on the major effect EDA gene on chr IV, which is known to control the recurrent plate loss in freshwater stickleback . All trait related SNPs were linked to regions on the genome with previously mapped QTLs for landmark positions of body shape (; Table S4).