agReg-SNPdb Plants






Georg-August-Universität Göttingen
CiBreed

Overview for Brassica napus (Rapeseed)

Brassica napus (also called rapeseed, oilseed rape or canola) is grown and used worldwide, with the oil used mainly for human consumption and biofuel production, while the meal remaining after oil extraction can be used as high-protein animal feed. In intensive breeding programs focusing on the reduction of nutritionally undesirable components, it was possible to create varieties with both low erucic acid and glucosinolate content. Rapeseed is the only plant species in agReg-SNPdb Plants for which no genome-wide SNP collection is available in Ensembl Plants. In our previous study, we created a genome-wide collection of rSNPs based on SNPs from the cultivars Zhongshuang11 and Zhongyou821 (280 and 133 samples, respectively) collected and published by Lu et al. (2019) . Based on this data, we could include rapeseed in agReg-SNPdb Plants.


rapeseed

Statistics

(Last updated on 08.02.2022)

Number of chromosomes 19
Number of genes 406,325
Number of SNPs 670,028

Click on a chromosome to download the data stored in agReg-SNPdb for the complete chromosome

Chromosome Number of SNPs Number of Genes
A01 31,838 18,043
A02 27,614 17,324
A03 40,967 28,964
A04 33,598 13,251
A05 25,921 18,479
A06 29,579 20,420
A07 40,043 19,028
A08 19,124 14,945
A09 41,367 26,611
A10 23,743 14,884
C01 37,751 19,996
C02 62,747 20,216
C03 49,236 35,338
C04 37,270 23,925
C05 26,912 24,795
C06 30,532 19,871
C07 52,797 23,362
C08 29,232 22,408
C09 29,757 24,465



Distribution of rSNPs relative to the TSS

SNP distance to TSS barley
Distribution of SNPs around the TSS of rapeseed. The upper plot shows the counts for the whole promoter region (-7.5 kb to +2.5 kb) in 500 bp intervals. The enlargement shows the proximal promoter region (-750 bp to +250 bp) in 50 bp intervals. The red asterisk annotates the position of the TSS.


Input data

Plant Assembly version Download links
Brassica napus (rapeseed) Brassica_napus_v4.1 Reference genome (also see Chalhoub et al.)
SNPs
Genes