BnVIR Brassica napus variation information resource
eg: AT5G10140
 or FLC
————Bridging the genotype–phenotype gap to accelerate mining candidate variation of traits in Brassica napus

// Brief introduction of Evolution module

To explore the candidate regions potentially effected by selection, nucleotide diversity (π) and population fixation statistics (FST). π was calculated with expected heterozygosity per site derived from the average number of sequence differences in three subpopulations (winter, spring and semi-winter) with VCFtools (v0.1.13) [1] in a 500-kb sliding window with a step size of 50 kb. FST, which indicates genomic differentiation between populations, was calculated for each pair of subpopulations using VCFtools (v0.1.13) [1] in a same windows size as that of π. The outlier of FST were determined as windows with the top 5% of FST values, indicating divergent selection of the regions. To explore the selection pressure of genes in B. napus genome during domestication, Ka, Ks and Ka/Ks ratio were calculated for orthologous gene pairs of B. napus and its ancestors, B. rapa and B. oleracea, with Ka/Ks_Calculator (v 2.0) [2]. Selection signals were calculated based on ZS11 and Darmor-bzh reference genome, respectively.

// Reference

[1] Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T., et al. (2011). The variant call format and VCFtools. Bioinformatics 27:2156-2158.
[2] Wang, D., Zhang, Y., Zhang, Z., Zhu, J., and Yu, J. (2010). KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinformatics 8: 77-80.

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