DuWTill

DuWTill is a simple Web client for the database of mutations in the South Australian Durum Wheat Tilling (DuWTill) collection created as part of a joint project between Australian Centre for Plant Functional Genomics (ACPFG), University of Saskatchewan and Università degli Studi della Tuscia for the project “A Molecular Diversity Drive for Precision-Engineered Wheat”.

Data content

Seeds of an advanced durum breeding line, UAD0951096_F2:5 (which has given rise to the commercially grown cultivar DBA-Aurora), were mutagenized with 0.7% EMS and 500 mutant plants were grown through one further generation to seed. In the next generation (M2) DNA from 100 of these plants and the unmutagenized control (UAD0951096_F2:5) were sequenced (Illumina, 2x150 bp) following reduction by exome capture using the 106.9 Mb Roche NimbleGen SeqCap Wheat Exome Design.

To improve variant calling, a novel consolidated Durum Exome Capture Reference (DECaR) was built: reads from the unmutagenized control sample were mapped into two publically available durum wheat whole genome assemblies of Svevo and Kronos EI v1, and then combined with assembled unmapped control reads. The resulting reference was 484.5 Mbp. The pipeline is described here.

Reads of the 100 exome-captured samples were aligned to DECaR. Any variation from DECaR was considered a mutation if it was present in only one mutant sample and non-polymorphic between the control and DECaR. We also demanded a mutation to be covered by at least three reads, and had sufficient coverage for the control allele in at least 50 other mutant samples. DECaR also allowed us to predict zygosity of the mutations discovered.

For further details and to cite:

Mario Fruzangohar, Elena Kalashyan, Priyanka Kalambettu, Jennifer Ens, Krysta Wiebe, Curtis J. Pozniak, Penny J. Tricker, Ute Baumann "Novel Informatics Tools to Support Functional Annotation of the durum wheat genome." Frontiers in Plant Science (In review)

DuWTill Web Server

The identified mutations are accessible on a public DuWTill Web server http://duwtill.acpfg.com.au.

Local Build (Windows)

We included two projects in this distribution: DuWTill itself and the YourDB console application, which is useful if you want to investigate your own data. For further instructions, please refer a README in each project.

Prerequisites

1. Internet Information Services (IIS). Turn this Windows feature on from here: Control Panel->Turn Windows features on or off. There are good instructions on how to do it here. We used IIS 8.0 Express for development and IIS 10.0 on DuWTill Web server.
2. Visual Studio 2015 or later, downloadable from the official Web site.

Build

1. Download and unzip the DuWTill release.
2. Open the WebTilling.sln file in Visual Studio.
3. Follow the instruction in README in each project.
4. Build the solution.

These steps should resolve dependencies and download the required packages. You are then ready to publish the application to IIS.