DNA for the 4,245 trees was isolated from needles and twig buds with the Qiagen DNeasy Plant Kit and quantified with PicoGreen fluorescent dye (Invitrogen). Trees were genotyped using an Infinium iSelect SNP array (Illumina, San Diego, CA) as described in Lenz et al. (2020a) (link). After applying several filters for retaining high-quality data, imputing only a small proportion of genotypes (0.9%), and correcting the registered pedigree using marker data (see Suppl. Methods), a total 4,066 trees from 146 families, genotyped on 4,092 SNPs, were retained for quantitative genetic analyses. The retained SNPs had an average call rate of 99.1%, an average genotyping reproducibility rate of 99.99% as assessed by replicated control genotypes, an average minor allele frequency MAF = 0.211, and an average fixation index Fe = 0.022.
Genetic diversity within each BG was estimated with the status effective number (Ns):
where θ is the group coancestry (Lindgren et al., 1996 ), as estimated from the corrected full-sib pedigree. Descriptive statistics of BGs and phenotypes are presented inTables 1 2 Figure S2
Genetic diversity within each BG was estimated with the status effective number (Ns):
where θ is the group coancestry (Lindgren et al., 1996 ), as estimated from the corrected full-sib pedigree. Descriptive statistics of BGs and phenotypes are presented in
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