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Tools for Genomics-Assisted Breeding in Polyploids

Funded by the National Institute of Food and Agriculture, USDA Specialty Crop Research Institute (2020-02585)

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Introduction: Tools for Genomics-Assisted Breeding in Polyploids

  • David Byrne
    • Professor
    • Basye Endowed Chair in Rose Genetics
    • Rosa and Prunus Breeding
  • Texas A&M University
    • Horticultural Sciences
    • College Station, TX
  • Toolsforpolyploids@tamu.edu

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OBJECTIVE 1

Develop computational tools for genomics-assisted breeding in polyploid crops

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  • Enhanced methods for genome-wide association studies
  • Linkage and QTL analysis in multi-parent populations
  • Polyploid haplotype assembly from short reads

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OBJECTIVE 2

Validate computational tools in public breeding programs

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  • Allele dosage assignment
  • Genome-wide association
  • Linkage and QTL analysis
  • Genomic selection
  • Sequence-based haplotyping

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OBJECTIVE 3

Train polyploid crop breeders to use and validate computational tools

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  • Documentation for computational tools
  • Workshops and short-courses for polyploid crop breeders
  • Polyploid Breeding Community Resource website

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Training and Outreach

Research and Development

Use and Validation

Polyploid Crops Community of Stakeholders

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​

​

OBJECTIVE 1

Develop computational tools for genomics-assisted breeding in polyploid crops

​

  • Enhanced methods for genome-wide association studies
  • Linkage and QTL analysis in multi-parent populations
  • Polyploid haplotype assembly from short reads

​

​

​

OBJECTIVE 2

Validate computational tools in public breeding programs

​

  • Allele dosage assignment
  • Genome-wide association
  • Linkage and QTL analysis
  • Genomic selection
  • Sequence-based haplotyping

​

​

OBJECTIVE 3

Train polyploid crop breeders to use and validate computational tools

​

  • Documentation for computational tools
  • Workshops and short-courses for polyploid crop breeders
  • Polyploid Breeding Community Resource website

​

Training and Outreach

Research and Development

Use and Validation

Polyploid Crops Community of Stakeholders

​

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Who is participating?

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Participants in the Training Workshop�46% from International Locations

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Participants in the Training Workshop�46% from International Locations

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Participants in the Training Workshop�21% Private, 36% Public, 43% Students

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Participants in the Training Workshop�Most in 20s and 30s

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Participants in the Training Workshop�58% Breeders and Support�45% Students

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Participants in the Training Workshop�Expertise

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Characteristics of Polyploid Crops

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Participants in the Training Workshop�Crops Represented

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Participants in the Training Workshop�Ploidy Levels Worked �Many programs work on multiple ploidy levels

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Participants in the Training Workshop�Size of Breeding Programs – Number of Seedlings

51%

26%

23%

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Summary – Plant characteristics

  • Groups of crops
    • Fruit
    • Root-tuber
    • Ornamentals
    • Turf/forage/sugar cane
    • Vegetables
    • Grain crops
  • Ploidy and genome size
    • 300 mb to 36,000 mb
    • 3x, 4x, 6x, 8x, 10x and higher
    • Allo to segmental to autopolyploid to unknown

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Summary – Breeding characteristics

  • Breeding characteristics
    • Interspecific/ploidy common
    • Medium to large size
    • Most perennial, clonal
    • Outcrossing or both
    • Inbreeding depression
    • Incompatibility, self/interspecific

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    • Length of breeding cycle
      • Most 1-4 years
    • Breeding approaches
      • Interspecific crosses
      • Recurrent selection
      • Backcrossing
      • Pedigree

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Use of Genomics-Assisted Breeding

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Participants in the Training Workshop�Use of Parental, Seedling, and Genomic Selection�

Most common use is sometimes or never

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Impediments �Number of times mentioned

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Participants in the Training Workshop�Previous experience with software

Most participants have not used the software

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Confidence of Significant Effect on Breeding Program: 10 years

High

Medium

Low

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Training Workshop Agenda

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Workshop Agenda – January 12th�Computational Support Group

  • Introduction to SLACK and Docker
    • Filipe Inacio Matias
    • Gabriel Gesteira
    • Maria Caraza-Harter
    • Jeekin Lau
    • Cristiane Taniguti

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  • Question and Answers
    • Slack channel
    • Software installation
    • Docker application

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Workshop Agenda – January 13th

  • Introduction
    • David Byrne - Introduction
    • Dorrie Main – Polyploid Community Resource website

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  • Genotype Calls
    • Roeland Voorrips – Overview
    • Marcelo Mollinari – SuperMASSA
    • Lindsay Clark – polyRAD
    • Roeland Voorrips - fitPoly

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  • Question and Answers
    • Breakout Zoom sessions

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Workshop Agenda – January 14th

  • Linkage Maps and Haplotype Reconstruction
    • Marcelo Mollinari – Overview
    • Peter Bourke – polymapR
    • Marcelo Mollinari – MAPpoly
    • Chaozhi Zheng and Jeff Endelman - PolyOrigin

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  • Question and Answers
    • Breakout rooms

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Workshop Agenda – January 15th

  • Quantitative Trait Loci Analysis
    • Chris Maliepaard – Overview
    • Peter Bourke – polyqtlR
    • Guilherme Pereira – QTLpoly
    • Jeff Endelman – diaQTL
    • Jeff Endelman – GWASpoly

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  • Questions and Answers
    • Breakout rooms

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Expectations

  • Basic theory
  • Introduction of software
  • Demonstration of software
  • Ask questions via CHAT function

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  • Give confidence to use it
  • Best way to learn is by doing

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  • Develop a Network of Collaborators

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  • Followup
    • Recorded talks posted on web site
    • Questions via Slack Channel

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  • Surveys to get feedback
    • What works
    • What does not work
    • Features needed
    • Clarifications needed in manual
    • Suggestions for improvements

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  • Please respond to all surveys

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Tools for Genomics-Assisted Breeding in Polyploids

Funded by the National Institute of Food and Agriculture, USDA Specialty Crop Research Institute (2020-02585)

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Introduction: Tools for Polyploids Community Resource website

  • Dorrie Main
    • Professor of Bioinformatics
  • Washington State University
    • Department of Horticulture

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Genotype Calls

Funded by the National Institute of Food and Agriculture, USDA Specialty Crop Research Institute (2020-02585)

Tools for Genomics-Assisted Breeding in Polyploids:

Development of a Community Resource

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Genotype Calls: Overview of Dosage Calling

  • Roeland Voorrips
    • Senior Researcher
  • Wageningen Research – Plant Breeding
    • The Netherlands

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Genotype Calls: SuperMASSA

  • Marcelo Mollinari
    • Senior Research Scholar
  • North Carolina State University

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Genotype Calls: polyRAD: Bayesian genotype calling from sequence read depth

  • Lindsay Clark
    • Research Specialist in Life Sciences

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  • Roy J. Carver Biotechnology Center
  • University of Illinois, Urbana-Champaign

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Genotype Calls: fitPoly

  • Roeland Voorrips
    • Senior Researcher
  • Wageningen Research – Plant Breeding
    • The Netherlands

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Tools for Genomics-Assisted Breeding in Polyploids: Development of a Community Resource

  • Follow up questions about software use
    • SLACK channel

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  • General questions:
  • Toolsforpolyploids@tamu.edu

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  • Website
    • All recorded presentations
    • Links to all software

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Funded by the National Institute of Food and Agriculture, USDA Specialty Crop Research Institute (2020-02585)

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Please complete survey

Funded by the National Institute of Food and Agriculture, USDA Specialty Crop Research Institute (2020-02585)

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Genotype Calls: Question and Answers

  • General with Computational Support Group

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  • SuperMASSA with Marcelo Mollinari

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  • polyRAD with Lindsay Clark

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  • fitPoly with Roeland Voorrips