Computational protocol: Plant vigour QTLs co-map with an earlier reported QTL hotspot for drought tolerance while water saving QTLs map in other regions of the chickpea genome

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Protocol publication

[…] QTL analysis was conducted independently using three genetic maps developed earlier [, , ] and phenotyping data generated in this study. QTL Cartographer version 2.5, composite interval mapping (CIM) method was employed []. For ultra-high density bin markers, inclusive composite interval mapping-Additive mapping (ICIM-ADD) method was used for identification of QTLs using IciMapping software (v3.2; []). LOD threshold was set by using 1000 permutation and p value ≤0.05. Constructed linkage map was visualized using Mapchart 2.2 [] software. When the PVE (phenotypic variation explained) was above 10%, QTLs were considered major QTLs (M-QTLs) and PVE below 10% were minor QTLs. […]

Pipeline specifications

Software tools QTL Cartographer, JoinMap
Application WGS analysis
Organisms Cicer arietinum