Breeding Potato with BreeDB

31 January 2013, Richard Finkers (@rfinkers)

Heleen de Weerd, Benoit Carreres, et al.

Outline

Project flow

Developed tools

Where are we now

Genotyping•Genotyping-by-sequencing

•SNP arrays

Dosage information•fitTetra

Optional: Population Structure correction

LD analysis Marker selection

Future: in sillico

cultivar design

BreeDB Flowchart

Field trial•Observations•~omics analysis

Estimate means

Allele dosage estimation

Example: SNP genotyping array (20.000 loci)

Calculate Allele dosage (R: fitTetra)

Prefer: haplotype reconstruction

doi:10.1186/1471-2105-12-172

Population structure

Software: structure

Segments: old varieties/ American varieties / Fresh consumption / Starch

Pedigree

Potato pedigree

Phenotypic observations

Association analysis

Predictive models

Models based on 5-10 markers

Genotyping•Genotyping-by-sequencing

•SNP arrays

Dosage information•fitTetra

Optional: Population Structure correction

LD analysis Marker selection

Future: in sillico

cultivar design

BreeDB Flowchart

Field trial•Observations•~omics analysis

Estimate means

Questions?