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Wax production for each accession was completely consistent between the Fukui and Kobe environments.
There were five replications for each accession in a completely randomized design.
SOAPdenovo assembly for each accession was assessed by QUAST57 with Nipponbare RefSeq as the reference.
The variants were called for each accession by the GATK UnifiedGenotyper (release 3.2-2 48 with 'EMIT-ALL-SITES' option.
Through whole-genome sequence comparisons of W05 with Wm82_v2 and ZH13, we have identified ~2300 3000 TE insertions for each accession (Supplementary Table 10).
To further understand the evolutionary history of apple, we used a Bayesian clustering algorithm with admixed models13 to estimate ancestry proportions for each accession (Fig. 1c).
We then used the whole set of 4D SNPs to calculate the cluster membership for each accession with 10,000 iterations.
The QIAGEN DNeasy Plant Mini Kit was used to extract genomic DNA from the fresh leaves of a single plant for each accession.
For each accession, approximately 20 µg DNA was transferred to 96-well plates and freeze-dried for tGBS, which was completed by Data2Bio (USA).
Following mapping, genotypes were assigned to each genomic position for each accession based on the alignment mpileup files generated by SAMtools33.
All traits were measured from 5 randomly sampled plants for each accession after harvest.
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