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. 2020 Jan 1:2020:baaa060.
doi: 10.1093/database/baaa060.

CerealsDB-new tools for the analysis of the wheat genome: update 2020

Paul A Wilkinson  1   2 , Alexandra M Allen  1 , Simon Tyrrell  3 , Luzie U Wingen  4 , Xingdong Bian  3 , Mark O Winfield  1 , Amanda Burridge  1 , Daniel S Shaw  1 , Jan Zaucha  5 , Simon Griffiths  4 , Robert P Davey  3 , Keith J Edwards  1 , Gary L A Barker  1
Affiliations

CerealsDB-new tools for the analysis of the wheat genome: update 2020

Paul A Wilkinson et al. Database (Oxford). .

Abstract

CerealsDB (www.cerealsdb.uk.net) is an online repository of mainly hexaploid wheat (Triticum aestivum) single nucleotide polymorphisms (SNPs) and genotyping data. The CerealsDB website has been designed to enable wheat breeders and scientists to select the appropriate markers for research breeding tasks, such as marker-assisted selection. We report a large update of genotyping information for over 6000 wheat accessions and describe new webtools for exploring and visualizing the data. We also describe a new database of quantitative trait loci that links phenotypic traits to CerealsDB SNP markers and allelic scores for each of those markers. CerealsDB is an open-access website that hosts information on wheat SNPs considered useful for both plant breeders and research scientists. The latest CerealsDB database is available at https://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/indexNEW.php.

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Figures

Figure 1.
Figure 1.
Searching the QTL database for a particular phenotype generates a table (a) displaying all QTLs for that phenotype along with chromosomal positions, population information and LOD scores. Clicking on an individual QTL links to QTL maps (b) where markers are shown at the start and end of the confidence interval of the QTL along with the peak marker. An ideogram of the chromosome (c) is also displayed where available showing the QTL highlighted in red and the chromosomal position of important markers are also highlighted.
Figure 2.
Figure 2.
Colour-coded glyphs allow users to rapidly scroll through hundreds of results and identify cross-platform SNPs, which is a useful tool for plant breeders that often require ‘legacy’ markers for their breeding programmes.
Figure 3.
Figure 3.
A circular dendrogram rendered using phylocanvas shows Watkins lines highlighted in blue. Users can view relationships between wheat varieties genotyped on both the 820K and 35K arrays and display the data in a number of different styles of dendrogram.
Figure 4.
Figure 4.
The introgression plotter generates a heatmap and a circos plot in this example for the variety Brompton. The heatmap (a) plots total introgression size for each comparison with relatives ordered vertically by relatedness to bread wheat and chromosomes ordered horizontally. Users can zoom in on the heatmap for more detail. The circos plot (b) has a number of tracks: track 1 (innermost track), putative introgressed/deleted regions; track 2, SNP density for each wheat chromosome; track 3, CNV gain; track 4, CNV loss; track 5, minor allele frequency. The outermost track represents wheat chromosomes (500 = 500 Mbp). The Brompton wheat variety is known to have the 1B/1RS translocation and this can clearly be seen in the circos plot.
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References

    1. Gupta P.K., Rustgi S. and Mir R.R. (2008) Array-based high-throughput DNA markers for crop improvement. Heredity, 101, 5–18. - PubMed
    1. Wilkinson P.A., Winfield M.O., Barker G.L.A. et al. (2012) CerealsDB 2.0: an integrated resource for plant breeders and scientists. BMC Bioinformatics, 13, 219. - PMC - PubMed
    1. Wilkinson P.A., Winfield M.O., Barker G.L.A. et al. (2016) CerealsDB 3.0: expansion of resources and data integration. BMC Bioinformatics, 17: 256. - PMC - PubMed
    1. Winfield M., Allen A.M., Burridge A.J. et al. (2015) High density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool. Plant Biotechnol. J., 14, 1195–1206. - PMC - PubMed
    1. Burridge A.J., Wilkinson P.A., Winfield M.O. et al. (2018) Conversion of array-based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (Triticum aestivum). Plant Biotechnol. J., 16, 867–876. - PMC - PubMed

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