Computational protocol: Panicle blast 1 (Pb1) resistance is dependent on at least four QTLs in the rice genome

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Protocol publication

[…] We constructed a genetic map using MAPMAKER/EXP v. 3.0 software (Lander et al. ). QTL analysis for grain length and grain width was performed using version 2.5 of QTL Cartographer software (Basten et al. ), and the threshold was obtained by using 1000 permutations. The progeny lines of F4 or F5 plants were grown to select recombinants within the QTL in order to develop inbred lines with recombinations within and around QTL7. Plants with independent recombination events were selected from on the basis of genotypes around the QTL region determined by using simple-sequence repeat (SSR) markers. The primers for SSR markers were listed in Additional file : Table S1. […]

Pipeline specifications

Software tools MAPMAKER, QTL Cartographer
Application WGS analysis
Organisms Oryza sativa