Computational protocol: QTL analysis of internode elongation in response to gibberellin in deepwater rice

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Protocol publication

[…] To construct a linkage map, genomic DNA was extracted from 84 individuals of the RIL using the isoplant method (). The extracted DNA samples were used for genotyping with single-nucleotide polymorphism (SNP) markers [see Supporting Information] using an Affymetrix customized SNP array for rice. Single-nucleotide polymorphisms were detected by the Golden Gate assay of BeadXpress (Illumina, Inc., San Diego, CA, USA). MAPMAKER/EXP, version 3.0 () was used to construct the linkage map. R/qtl () was used for the QTL analysis. Composite interval mapping (CIM) was used to detect the QTLs. The number of covariates was assumed to be 1. Quantitative trait loci were considered significant at P < 0.05, with the logarithm of odds (LOD) score given by 1000 permutation tests (; ). A two-QTL scan was performed for the detection of interacting QTLs. Quantitative trait loci were considered significant at P < 0.1 using the fitqtl method (). Candidate QTL regions were identified using the lodint method (). […]

Pipeline specifications

Software tools MAPMAKER, R/qtl
Application WGS analysis
Organisms Oryza sativa