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. 2011 May 20;6(5):e19949. doi: 10.1371/journal.pone.0019949

Figure 1. QTL analysis for variation in vernalization response.

Figure 1

Composite interval mapping was used to identify genes contributing to the variation in vernalization response after treatment of Arabidopsis populations with different lengths of cold. (A) Lov-1 × Col-0, (B) Ull-2-5 × Col-0, (C) Var-2-6 × Col-0 and (D) Edi-0 × Col-0. Each chromosome with significant QTL (chromosome 1, 4 and 5) is shown separately and the positions (in cM) of the markers used are indicated as triangles. LOD (Logarithm of odds) scores were calculated by QTL Cartographer with a 5 % significance threshold (shown as dashed lines) determined from a 1000 permutation test. For (B) Ull-2-5 x Col this resulted in a high threshold due to segregation distortion, which is widespread in this cross (Figure S2). Each chromosome was tested individually and chromosome 3 identified as the cause of the high threshold. The permutation analysis was then performed excluding chromosome 3.