Genotyping and Population Structure Analysis of Rapeseed Accessions

A selected set of 136 rapeseed accessions were genotyped using the Brassica 60K Illumina Infinium^@ SNP array (Illumina) as described previously (Liu et al., 2016 (link)). After quality control (minor allele frequency>0.05 and missing data<20%) (Liu and Muse, 2005 (link)), a total of 21426 SNPs were selected for subsequent GWAS analysis. SNP density map was drawn using the CMplot package (Yin et al., 2021 (link)) in R3.3.3 (Team RC, 2013 ) to gauge the marker coverage across the B. napus genome. Principal component analysis was performed using Tassel v5.0 software (Bradbury et al., 2007 (link)). Only the first two principal components were plotted by the ggplot2 package (Wickham, 2011 (link)) in R3.3.3 (Team RC, 2013 ). MEGA-X software (Kumar et al., 2018 (link)) was used to draw the phylogenetic tree and show the genetic relationship among GWAS accessions. Both principal component analysis and phylogenetic tree are used to reveal the distribution of population structure. LD (linkage disequilibrium) attenuation was estimated to demonstrate the degree of genetic linkage, and it is drawn by PopLDdecay software (max decay distant = 2500, break = 6000bp, bin1 = 1000, bin2 = 6000) as described previously (Zhang et al., 2019 (link)).

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Yang Y., Wang W., Hu Q., Raman H, & Liu J. (2023). Genome-wide association and RNA-seq analyses identify loci for pod orientation in rapeseed (Brassica napus). Frontiers in Plant Science, 13, 1097534.

Publication 2022

Brassica 60K Illumina Infinium@ SNP array

Brassica Genetic linkage Genome Gwas Muse Relationship Tassel

Corresponding Organization : Ministry of Agriculture and Rural Affairs

Other organizations : New South Wales Department of Primary Industries

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Variable analysis

independent variables

Genotyping of 136 rapeseed accessions using the Brassica 60K Illumina Infinium SNP array

dependent variables

Selection of 21,426 SNPs after quality control (minor allele frequency > 0.05 and missing data < 20%)
Principal component analysis to reveal population structure
Phylogenetic tree to show genetic relationship among GWAS accessions
Linkage disequilibrium (LD) attenuation to demonstrate the degree of genetic linkage

control variables

Minor allele frequency threshold (> 0.05)
Missing data threshold (< 20%)
LD decay distance (max = 2500, break = 6000 bp, bin1 = 1000, bin2 = 6000)

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