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.