Computational protocol: Genetic Linkage Map Construction and QTL Mapping of Salt Tolerance Traits in Zoysiagrass (Zoysia japonica)

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Protocol publication

[…] MapQTL 5.0 was used to map the QTLs for LF and SCW using the MapQTL interval mapping method. LOD thresholds at a significance level of P = 0.05 were determined using 1000 permutations. A QTL was declared when the LOD value was higher than the threshold. The maximum LOD score in the interval determined the QTL positions. Confidence intervals associated with QTL locations were set as the map intervals corresponding to 1 LOD either side of the maximum LOD. The detected QTLs were located on LGs using the MAPChart software . QTLs were named starting with ‘q’, followed by the abbreviated trait name (LF or SCW), and the number assigned to the QTL.Additive(A) and dominant (D) effects of the QTLs were estimated from an output of the program MapQTL 5.0 as A f = [(µ ac+µ ad)−(µ bc+µ bd)]/4 for female additivity, A m = [(µ ac+µ bc)−(µ ad+µ bd)]/4 for male additivity, and D = [(µ ac+µ bd)−(µ ad+µ bc)]/4 for dominance, where µ ac, µ ad, µ bc, and µ bd are the estimated phenotypic means associated with each of the four possible genotypic classes, ac, bc, ad, and bd, derived from a cross –. […]

Pipeline specifications

Software tools MapQTL, JoinMap
Application WGS analysis