Computational protocol: Introgressing Subgenome Components from Brassica rapa and B. carinata to B. juncea for Broadening Its Genetic Base and Exploring Intersubgenomic Heterosis

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Protocol publication

[…] The genetic diversity and genetic distance between different plants was evaluated with molecular markers analyzed using Primer 6 software (Clarke and Gorley, ). The Shannon index was calculated using POPGENE 1.31 (Yeh et al., ). The phylogenetic tree was analyzed based on Nei's genetic distance (Nei et al., ) using the clustering method, employing a neighbor-joining tree with 1000 permutations, using POPTREE 2 (Takezaki et al., ). After eliminating improper markers with allelic frequencies less than 10 or >10% missing data, the population structure was analyzed by Bayesian clustering and the “admixture model” with STRUCTURE 2.2 (Pritchard et al., ; Falush et al., ). The length of burn-in time and replication number were both set to 100,000 in each run. To identify and determine the most probable population number (K), we calculated the ΔK values of K from 1 to 10 replicate runs for each K, and selected the K value corresponding to the peak of the ΔK graph after plotting (Evanno et al., ). […]

Pipeline specifications

Software tools POPGENE, POPTREEW
Application Population genetic analysis
Organisms Brassica juncea, Brassica rapa, Brassica carinata, Brassica nigra