Genotyping of Brassica napus Accessions

Genotyping of the 520 B. napus accessions was carried out in Huazhong Agricultural University, Wuhan, China, using the Brassica 60 K Illumina Infinium SNP array. The SNP data were analyzed by Illumina BeadStudio genotyping software, as previously described11 (link). SNPs with minor allele frequencies (MAFs) of <0.05, or lacking a call higher than 0.9 were excluded from analysis. After processing, 31,839 SNP markers were retained for further analysis. To determine the physical localization of SNPs, flanking sequences were subjected to BLASTN searches against the B. napus genome, with an E-value cut-off of 1E-514 (link)47 (link). SNPs with a maximum Bit-Score were retained as unique SNPs, and subjected to further analysis.

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Lu K., Xiao Z., Jian H., Peng L., Qu C., Fu M., He B., Tie L., Liang Y., Xu X, & Li J. (2016). A combination of genome-wide association and transcriptome analysis reveals candidate genes controlling harvest index-related traits in Brassica napus. Scientific Reports, 6, 36452.

Publication 2016

Brassica 60 K Illumina Infinium SNP array BeadStudio genotyping software

Brassica Genome Physical Snps

Corresponding Organization :

Other organizations : Southwest University, Yunnan Academy of Agricultural Sciences

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Variable analysis

independent variables

Genotyping of the 520 B. napus accessions

dependent variables

SNP data

control variables

MAFs of <0.05 were excluded from analysis
SNPs lacking a call higher than 0.9 were excluded from analysis
Flanking sequences were subjected to BLASTN searches against the B. napus genome with an E-value cut-off of 1E-514
SNPs with a maximum Bit-Score were retained as unique SNPs

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