3.2 | Host selection footprints
After combining the results of all the genome scan analyses, a total of
32 genomic regions with sizes ranging from 0.59 to 57 kb were detected
(Figure 2, Table 2). Among the 32 regions, 25 were only identified with
BayPass, two only with PoolFreqDiff, and three with both methods (Table
2). Fifteen genomic regions were detected using the six populations
sampled in 2011. Twelve of the regions had already been identified in
our previous study
(Carlier et al.,
2021b), including the five major and convergent regions: S1R2-Cu,
S2R1-Cu, S2R5-Cu, S12R1-Cu and S12R2-Cu. The detection of three new
regions in the present study was certainly because a larger number of
SNPs were found using the latest more efficient version of the software
used for the mapping step. We ran the same analysis on the eight
additional populations sampled in 2013 and a total of 19 genomic regions
were detected including two (S1R2-Cu, S12R1-Cu) already detected in the
2011 pool and 17 newly detected.
The genetic differentiation estimated between populations in the 32
candidate genomic regions (from 4 974 SNPs) was higher than that of the
whole genome (Figure S1, Table S1) with FST values
ranging from 0.003 to 0.226. Although none of the regions was found in
all seven population pairs analyzed, 29/32 were significantly
differentiated in at least two pairs, including three regions (S1R2-Cu,
S6R5-Cu, S12R1-Cu) in five pairs. A complex population structure was
observed with no apparent effect of the location, the sampling year, or
the variety of origin (Figure S1). Tajima’s D computed from 1-kb
non-overlapping window was significantly greater in the candidate
genomic regions than in the whole genome in all the study populations
and in either pool or individual sequencing in location 1 (Figure 3).