Genotyping and Linkage Mapping
Genotyping 229 mountain pine beetles produced 414 million reads and
22 242 SNPs after alignment of samples to the final female genome and
22 087 SNPs after alignment to the final male genome. Thirteen
individuals failed IBD testing in LepMap3, including one entire family
and three singletons from different families (Supp. Tab. 3). After
removing these individuals and imputing genotype information for the ten
missing F1 specimens, a total of 115 males and 111 females (N=226) in 13
families were used for linkage map construction.
A LOD score of 12 recovered all 11 autosomes and the neo-X chromosome in
each linkage map (Supp. Fig. 3 and Fig. 3). Increasing the LOD score to
values much higher than 12 in the male-aligned linkage maps and/or
adjusting the minimum number of SNPs required to form linkage groups
failed to recover a putative neo-Y chromosome, but did result in the
splitting of other autosomal linkage groups formed from single genomic
scaffolds. We were therefore unable to recover a neo-Y linkage group in
the male-aligned linkage map. Final female and male linkage maps
constructed from the final genome assemblies contained 2 795 and 2 910
SNPs, respectively. Linkage mapping results are shown in Supp. Tables
4-6.
The recovered linkage groups in the female-aligned linkage map were
consistent with those in the male map except for female chromosome 10,
which was equivalent to male chromosome 11 and vice versa (Fig. 3).
Genomic scaffold numbering in this study reflects assembled chromosome
size (with chromosome 1 being the largest scaffold) and is therefore not
necessarily consistent between the male and female assemblies. In this
instance, although male chromosome 11 and female chromosome 10 were
syntenous, the assembled size in base pairs of the male scaffold was
smaller than the female scaffold. The female-aligned linkage groups
ranged from approximately 50 to 90 cM in size, and the equivalent
male-aligned linkage map ranged from 50 to 70 cM. This size difference
can be attributed to the male and female neo-X linkage groups; the
female neo-X was approximately 20 cM larger than the male copy.
Chromosome 4 in both the male- and female-aligned linkage maps contained
a region approximately 30 cM in size with strong genetic linkage
(approximately 0.1 cM/locus), although the exact size and chromosomal
location of this region differed slightly between the maps (Fig. 3).