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).