SNP Genotyping of Brassica napus Cultivars

Four young leaves from different individuals of each variety were planted in Wuhan and were sampled. DNA was extracted using a modified CTAB method²⁷ and then adjusted to 50 ng μl⁻¹. The 60K Brassica Infinium SNP array was employed and the SNP data were analyzed using Illumina BeadStudio (Illumina Inc. San Diego, California, USA).¹⁴ (link)^,²⁰ (link)^,²¹ (link) The SNPs with call frequencies > 0.8 or minor allele frequencies (MAF) > 0.05 and homozygous genotype frequency > 0 were selected for association mapping analysis.²⁰ (link) The physical position of the SNPs was identified by aligning the sequence of a 50 bp SNP probe attached to each SNP with the genome sequences of B. napus²⁸ (link) using local BLASTn (BLAST: Basic Local Alignment Search Tool, http://blast.ncbi.nlm.nih.gov/Blast.cgi). If the SNP probe matched two or more locations in the reference genome, the SNPs were regarded as non-specific markers and abandoned.²⁰ (link)

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Wang X., Chen Y., Thomas C.L., Ding G., Xu P., Shi D., Grandke F., Jin K., Cai H., Xu F., Yi B., Broadley M.R, & Shi L. (2017). Genetic variants associated with the root system architecture of oilseed rape (Brassica napus L.) under contrasting phosphate supply. DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, 24(4), 407-417.

Publication 2017

Illumina BeadStudio

Brassica Ctab Genome Genotype Homozygous Physical Snps

Corresponding Organization :

Other organizations : Huazhong Agricultural University, University of Nottingham, University of Giessen

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Protocol cited in 3 other protocols

Variable analysis

independent variables

Different varieties of Brassica plants

dependent variables

DNA extracted from the leaf samples
SNP data obtained from the 60K Brassica Infinium SNP array

control variables

Four young leaves from different individuals of each variety were planted in Wuhan and sampled
DNA was extracted using a modified CTAB method and adjusted to 50 ng μl^-1
SNPs with call frequencies > 0.8 or minor allele frequencies (MAF) > 0.05 and homozygous genotype frequency > 0 were selected for association mapping analysis
The physical position of the SNPs was identified by aligning the sequence of a 50 bp SNP probe attached to each SNP with the genome sequences of B. napus using local BLASTn

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