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).