G alaxy for G enomics-enabled B reeding Star Yanxin Gao - PowerPoint PPT Presentation

G alaxy for G enomics-enabled B reeding Star Yanxin Gao yg28@cornell.edu

Introduction • Application Specialist, IT • Enterprise Breeding System (2020+) • GOBii (2015-Present) • Breeding and Genetics • Corn, DAS (2008-2015) • Soybean, VT (2004-2008) • Vegetables, Cornell (1999-2004) Star Yanxin Gao, Ph.D., PMP

Outline 1. Project 2. Products 3. Partnership

GS-Galaxy Project (1st P ) GOBii Mission Genomic High Throughput selection Analysis and Transform breeding by enabling Decision Support genomic–assisted selection as Genotyping Management routine breeding applications Suitable Genotyping Platforms MAS High Throughput Sample Tracking Breeding Management Genomic-Assisted Selection Platform

GS-Galaxy Project (1st P ) People Cornell University IRRI • Venice Juanillas • Angel Villahoz-Baleta (Former ) • Ramil Mauleon (Former) • Star Yanxin Gao • Kelly Robbins • Ken McNally Collaborators • Liz Jones • Josh Cobb • Alexis Dereeper • Yaw Nti-addae • Carlos Ignacio • Michael Quinn • Dmytro Chebotarov • Paulino Perez • Nick Alexandrov Former) • Jose Crossa CIMMYT • Jessica Rutkoski (Former) • Clay Sneller • Juan Arbelaez (Former) • Victor Ulat • Kate Dreher • Susanne Dresigacker • Tom Hagen • Mike Olsen • Yoseph Beyene ICRISAT • Umesh Rosyara • Manje Gowda • Xuecai Zhang • Selvanayagam Siva • Nicholas Santantonio • Juan BURGUEÑO • Rajeev Varshney • Isaak Tecle • Fernado Toledo • Abhishek Rathor • Milcah Kigoni • Manish Roorkiwal • Iain Milne • Hima Kudapa • Gordon Stephen • Santosh Deshpande • Hiro Iwata • Dave Clements

GS-Galaxy Project (1st P ) Milestones 1st milestone: Minimum set of GS tools installed in Galaxy- June 2018: Ø GS workflow mapped for each crop and common minimum desirable tools and features identified. Ø Pipeline developed with minimum desirable features. Ø Basic and common tool components put in place. Ø Tested with well curated test datasets for each crop by product owners and testers 2nd milestone: Production server with published GS workflows-June 2019 Ø Customized workflows for each crop. Ø v1 for fully functioning GS pipeline. Ø Working pipeline available to centers. Ø Training and workshop to users other than product owners and more users start using pipeline and tools 3rd milestone: GOBII integrated as data source for Galaxy-June 2020 Ø Deliver a complete pipeline with no data manipulation required. Ø Access data extract for phenotypes and genotypes from Galaxy pipeline using remote Galaxy web servers. Ø Found a solution for storing the output data long term so it can easily be accessed. Ø Pipelines widely used within CG and outside CG in future.

GS-Galaxy Products (2nd P ) http://galaxy-demo.excellenceinbreeding.org/

GS-Galaxy Products (2nd P ) Enable routine genomic selection analysis v 2 v 3 v 4 v 6 v 5 v 7 v 8 Adopted Slide from Clay Sneller http://galaxy-demo.excellenceinbreeding.org/

GS-Galaxy Products (2nd P ) http://galaxy-demo.excellenceinbreeding.org/ Workflow 1: Predict GEBVs in untested lines Workflow 2: Clustering/population structure Workflow 3: Cross validation Workflow 4: Genome-wide association study

GS-Galaxy Products (2nd P ) GOBii-Galaxy Integration

GS-Galaxy Partnership (3rd P ) Partnership Models Adopt products Community development • Open-source and free • Implement new tools • Test with own datasets and use cases • Develop crop-specific workflows • Download from toolshed • Connect with databases

GS-Galaxy Partnership (3rd P ) Adoption Metrics • Number of registered users: 214 • Number of different crops/programs: 3 (rice, wheat, maize) • Number of analyses/jobs performed: 14200 • Total job file sizes stored: 148 Gb • Average file size: 4.2982 Mb

GS-Galaxy Partnership (3 rd P ) Vendors Genotyping Sample Analytics Breeding Management Management Management B4R Sample Data Service Data Tracking Loading Tracking Extract Breeding Data Decision Support Extract

Invite to Partner with GS-Galaxy EiB Demo Server: 1. Project http://galaxy-demo.excellenceinbreeding.org/ 2. Products Publish tools to Galaxy main toolshed 3. Partnership Galaxy workshop at Cornell/BTI April, 2020

Thanks