Computational protocol: Isolation and fine mapping of Rps6: an intermediate host resistance gene in barley to wheat stripe rust

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Protocol publication

[…] A genetic map was constructed using 589 markers including 535 barley OPA (Close et al. ), 26 CAPS markers, and 28 Sequenom markers. JoinMap v4 was used using default parameters and an independence LOD threshold of 4.0 (van Ooijen ). Genetic distances were estimated using the Kosambi mapping function. Integrity of the genetic map was evaluated through comparison with the current OPA consensus genetic map of barley (Muñoz-Amatriaín et al. ) and with two-point linkage tests using R/qtl (v1.33-7). [...] Composite interval mapping was performed with QTL Cartographer (v1.17j) using model 6, the selection of five background markers, a step size of 2 cM, and a window size of 10 cM (Basten et al. ). Significant QTLs were extracted using the Eqtl module under the H0:H3 model using experiment-wide thresholds (EWT) that were calculated using 1000 permutations with the reselection of background markers using a threshold of α < 0.05 (Doerge and Churchill ; Lauter et al. ). ANOVA analyses for testing the linkage of individual markers were performed with R/qtl. […]

Pipeline specifications

Software tools JoinMap, R/qtl, QTL Cartographer
Application WGS analysis
Organisms Hordeum vulgare, Triticum aestivum, Flavobacterium sp.