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. 2015 Jun 2;200(4):1313–1326. doi: 10.1534/genetics.115.175406

Figure 5.

Figure 5

Haplotypes in QTL-heterozygous mapping parents. (A) Chi-square test for independence between SNP alleles and QTL alleles, performed on phased genotype data coming from 117 QTL-heterozygous mapping parents. Blue dots, SNPs identified in the “scan,” based on Illumina sequence data; orange dots, SNPs identified by targeted Sanger-based resequencing of the “core” QTL region. (B) Position of polymorphisms within the reference sequence, the ICSASG scaffold, ccf1000000016_0_0. (C) Alleles at haplotypes. Blue, one allele; gray, the other allele; green, haplotypes containing QQTL; red, haplotypes containing qQTL; Q*, copies of the haplotype having the alternate linkage phase between SNP4 and the QTL.