QTL mapping
The high-quality reads were aligned to the reference genomic sequences (HDEM (http://www.genoscope.cns.fr/externe/plants/chromosomes.html ) by BWA (0.7.12-r1039) (Li and Durbin, 2009). The reads near InDel variant sites were realigned by Indel Realigner of GATK to improve the precision of SNP acquiring. Precise and reliable SNPs were obtained by Unified Genotyper and filtering atypical SNPs. Then, SNP-index was calculated and mapped after SNP calling. The SNP-index in the p-pool and g-pool and their subtraction were mapped to show their distribution on the chromosome. The candidate region for the target trait was selected based on the subtraction value of the p-pool and g-pool. Precise phenotyping is a fundamental requirement for accurate QTL mapping, so the bud color trait was investigated after experiencing cold for ten days.