The SNP database of Brassica napus L. (BnaSNPDB) is an interactive web-based platform and set of analytic tools for effcient retrieve and analysis of SNPs among 1007 rapeseed germplasm accessions based on the data reported by previous research( Wu et al., 2019 ).
High Quality SNPs
We here present 5 modules to retrieve and analyze the SNP dataset. Within each module, the user can select different parameters to retrieve and analyze the SNP dataset. You can find some example figures that these modules can generate in the manuscript Wu et al. Whole-Genome Resequencing of a Worldwide Collection of Rapeseed Accessions Reveals the Genetic Basis of Ecotype Divergence, Molecular Plant (2019) and manuscript Xuan et al. Genome-wide association study reveals new genes involved in leaf trichome formation in polyploid oilseed rape (Brassica napus L.), Plant, Cell & Environment (2019).
This module provides a pipeline to retrieve SNPs and display pairwise linkage disequilibria between SNPs and allows the user select different parameters.
This module compares the conserved SNPs specific to different groups of rapeseed.
This module implements the functionality to perform phylogenetic analysis in user-specified genomic regions.
This module provides the functionality to calculate nucleotide diversity among groups of rapeseed germplasm accessions in user-specified genomic regions.
This module allows user to extract the detail informations of SNPs, annotation of genes and essential information on the 1007 rapeseed germplasm accessions used in the BnaSNPDB.
More about of the SNP Dataset
Exploring the rapeseed (Brassica napus L.) genomic variation dataset
Rapeseed (Brassica napus L.), an important oilseed crop, has adapted to diverse climate zones and latitudes by forming three main ecotype groups, namely winyer, semi-winter, and spring types. In this database, We collected a worldwide collection of 1,007 B .napus germplasms accessions, including 658 winetr types, 145 semi-winter types, and 188 spring types, from 39 countries (Fig. 1).
Fig. 1 The geographic distribution of rapeseed accessions
We generated a total of 7.82 Tb of clean reads from whole-genome resequencing of the world collection from 39 countries across the world with an average of ~6.6-fold-coverage. We used the following pipeline (Fig. 2) to process the data:
Fig. 2 The pipeline for data processing procedures
- All raw paired-end reads were trimmed for quality control using Trimmomatic
- The remaining high-quality reads were aligned to the genome of Darmor-bzh with BWA software
- BAM alignments files were sorted and duplicated reads were marked subsequently generated with SAMtools and Picard
- SNPs were identified and filtering using GATK. SNPs annotation was performed using SnpEFF software.
Finally, 5.56 million SNPs were detected. The distribution of polymorphisms in B. napus genomic regions showed that 202,323, 62,834, 939,553, 899,982, and 2,778,189 SNPs were located within exons, introns, and upstream regions (within 5 kb upstream of transcription start sites), downstream regions (within 5 kb downstream of transcription stop sites), and intergenic regions, respectively (Fig. 3).
Fig. 3 The distribution of polymorphisms in B. napus genomic regions