Computational protocol: Leaf morphology in Cowpea [Vigna unguiculata (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species

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Protocol publication

[…] The Kruskal-Wallis and Interval Mapping analysis packages of MapQTL 5.0 software were used to conduct the QTL analysis []. A QTL was considered significant if the same QTL was identified using both phenotypic datasets and if the statistical tests for the markers met significance thresholds for both Kruskal-Wallis and Interval Mapping analyses. A significance threshold was set to 0.05 for Kruskal-Wallis analysis and LOD thresholds for the Interval Mapping analysis were calculated using 1000 permutations at the 0.05 significance level. A 95% confidence interval was used to estimate the left and right margins of the QTL using 1-LOD and 2-LOD of the most likely position. QTLs were visualized using MapChart 2.2 software []. […]

Pipeline specifications

Software tools MapQTL, JoinMap
Application WGS analysis
Organisms Medicago truncatula, Glycine max, Vigna unguiculata