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Tools for Polyploids - New Zealand meeting (RGC11)

Tools for Polyploids is going to New Zealand! Members of our team will be presenting at the 11th Annual Rosaceae Genomics Conference on March 17, 2023. In-person registration is closed but you can still attend virtually by emailing events@plantandfood.co.nz. 


Agenda for the Tools for Polyploids Training Workshop in New Zealand

March 17, 2023    
Time (NZDT) Topic Presenter
8:45 am Introduction and computer setup for session David Byrne, Susan Thomson, David Chagne
9:00 

Reads2Map software which assesses the various software to process sequence data to develop the best pipeline for data processing

Cris Taniguti
10:00 Break  
10:10 Reads2Map Cris Taniguti
11:00 Haplotyping from sequence data Tim Millar
12:00 noon Lunch and group photo  
1:00 pm Mapping software Jeekin Lau
2:00  QTL analysis Jeekin Lau
3:00

Break

 

3:10 QTL analysis Jeekin Lau
4:00 VIEWpoly, hidecan, App for BLUPs, and selection index

Cris Taniguti and Olivia Angelin-Bonnet

5:00 Adjourn  

 


Overview

SNP and dosage calling in polyploid genotyping-by-sequencing data

We will use a tetraploid rose example dataset to perform sequence quality control, alignment with the reference genome, SNP calling, and dosage calling. We will show how to perform the analysis step-by-step by using the Reads2Map workflows collection which is written with the automatized and reproducible workflow description language (WDL). 

 

Introduction to MCHap 

MCHap is a command line tool for micro-haplotype assembly in auto-polyploids and outputs standard VCF files. In this session, we will use MCHap to assemble micro-haplotypes in a bi-parental, tetraploid cross.

 

Linkage Mapping and QTL mapping 

We will take an example of either GBS-derived data (or array if the GBS one takes too long to run). We will go through the steps of linkage mapping using MAPpoly and will do QTL analysis in QTLpoly.

 

Updates in VIEWpoly: A visualization tool to integrate and explore polyploidy genetic analysis 

We will demonstrate an example of the usage of VIEWpoly, an R package, and a shiny app to mine results from MAPpoly, polymapR, QTLpoly, polyqtlR, and diaQTL. We will also show VIEWpoly new features such as its integration with HIDECAN package.