Data overload – Breeding decision-support software to

the rescue!

S. Jung, Taein Lee, Kate Evans, Cameron Peace, Gennaro Fazio, Sushan Ru, Amy F. Iezzoni,

Doreen Main

Outline of Presentation

BIMS (Breeding Information Management System) – what is it?

Why BIMS?

What data does BIMS have?

What features are in BIMS?

Testimonials

BIMS for your crop!

RosBREED

RosBREED

What is BIMS?

• BIMS Breeding Information Management System

• FunctionalityWeb portal that leverage genomics information for maximum utility within the Marker-Assisted Breeding (MAB) Pipeline, including functions to aid breeding decision-making

• Where is it?Integrated with GDR (Genome database for Rosaceae) that contains genomic, genetic and breeding data

RosBREED

Why BIMS?Genotypic data, phenotypic data – Too much to handle!

Which parents to cross? Which seedlings to select?Which QTLs to try to adapt to my breeding program?

RosBREED

With BIMS

we can help you with what trees to cross

RosBREED

What data does BIMS have?

• Breeding Data from participating RosBREED breeders (apple, strawberry, tart cherry, sweet cherry and peach)Phenotypic data, genotypic data, pedigree data, germplasm data, etc

• Integrated with other GDR genetics and genomics datamarkers, QTL, genetic map, whole genome sequences, trait ontology

RosBREED

What features are in BIMS?

• Comprehensive search site for breeding data• Modules to support MAB pipeline

Database for breeding data

• Browse by dataset• Search phenotypic data• Search genotypic data• Generate input file for software (Pedimap,

FlexQTL)

Phenotypic data search

9

10

Variety Detail Page

Genotypic data search

12

Tools – Generate Input files for Pedimap, a breeding software

RosBREED

Modules to support MAB pipeline

Trait Locus Warehouse

Selection Target Identifier

Choose market class

•Fresh market•Processing market…

See SE Valuesmock-

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Acidity

BF 21.3

SweetnessTrait 2Trait 1

Market Type

Select Target Identifier

Choices Made

Trait Name

Statistical Significance of QTL

LOD 7.6

Fresh Fresh

QTL name

Trait Effect Stat. signif.

Population/germplasm

Source Genomic location

Market type

Range Priority index/EWLocusV

Glu7.1 sweetness

±4⁰Brix BF 23.1 RosBREED CR Set

Tex134 2:37-43 Fresh 1.4-2.4

11 ±3

MDH3 acidity ± 0.32 mea

LOD 7.6

Con × Bolinha

Bolinha 1:21.4 Fresh 8-10 5 ±1

Search Result Print

Reset

User can rewrite these values

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Technology Portfolio

Genome Database Resources

LG1 LG2 LG3 LG4 LG5

Graphical location of chosen QTL

Zoom in on QTL interval and discover what markers are there to be utilized for MAS

x

QTL name Trait Effect Range Genomic Location/Interval QTL origin info Genomic Resources available near QTL

SSC 4.5 SSC LG4 – 45-55 cM Apple RosBREED flexQTL SSR1, SNP12343, SCAR abcd, ….

TA 1.4 TA LG1 – 30-32 cM FiestaxDiscovery cross

SSC 4.2 SSC LG4 – 15-21 cMo

o

If better marker is necessary, look up to find SSRs and SNPS around QTL and design primers using online software

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RosBREED

Reference Germplasm Database

• A module to help a breeder to become convinced or otherwise that an unproven DNA test of interest indeed holds predictive power for germplasm of interest.

Simple Validation Functional genotype effects

Cross AssistGenerates a list of parents and the number of seedlings to

get the progeny with desired traits

RosBREED

A RosBREED Tart Cherry breeder

Amy Iezzoni says..

“I really like having my breeding data searchable from a web portal. No more pouring over spreadsheets hoping I have the latest one, looking for a particular data point! With the toolbox, I can just log in and search for the data point and have it in a matter of minutes.”

RosBREED

A RosBREED Apple breeder

Jim Luby says..

“I like the searchable database format for my potential parents and the ability to get a Pedimap-ready output without the worry about format is really efficient for visualizing phenotypes in our breeding program.”

RosBREED

A RosBREED Strawberry breeder

Jim Hancock says..

“To date, I have done all my evaluations and parent selection by shuffling through spread sheets and hand written notes. I hope to streamline my whole operation with BIMS.”

RosBREED

A RosBREED Apple breeder

Kate Evans says..

“Being able to search through multiple years of phenotypic data as well as link in genotypic data is wonderful. I can easily make selections and chose potential parents using the Toolbox format.”

RosBREED

BIMS for your crop group

• Underlying database for BIMS is constructed using Chado, an open-source, generic, modular, ontology-based database for biological data

• BIMS is developed by the collaboration between breeders, geneticists, genomicists, and bioinformaticists

Can be applicable for any other crops, not just for Rosaceae

Acknowledgement

• BIMS team• Team Leader: Gennaro Fazio• BIMS module design team: Cameron Peace, Gennaro Fazio, Sushan Ru• BIMS database designer: Sook Jung• BIMS Database developer: Taein Lee• BIMS Trainee: Sushan Ru• Genomics Team Leader/ GDR : Dorrie Main• MAP Pipeline Team Leader: Cameron Peace

• Other RosBREED Team Members• PD: Amy Iezzoni• Kate Evans (Design of breeding database)• Breeding team who provided data

This project is supported by the Specialty Crop Research Initiative of USDA’s National Institute of Food and Agriculture