FB phenotypesand genotypes Database and Breeding Interface.What for? How to use them?

Eucarpia fruit breedingand genetics symposium

Nelson Nazzicari, Andrea Caprera, Laura Rossini, Stefano Tartarini, Luca Dondini, Andrea Patocchi, Luca Bianco, Alessandra Stella

Fruitbreedomics

Fruitbreedomics

● “improve the efficiency of current fruit breeding programs”

Fruitbreedomics

● “improve the efficiency of current fruit breeding programs”

● “bridge the gap between molecular genetic research and breeding”

Fruitbreedomics

● “improve the efficiency of current fruit breeding programs”

● “bridge the gap between molecular genetic research and breeding”

● Big & ambitious project

Fruitbreedomics

● “improve the efficiency of current fruit breeding programs”

● “bridge the gap between molecular genetic research and breeding”

● Big & ambitious project● From March 2011 to Aug 2015

Fruitbreedomics

● “improve the efficiency of current fruit breeding programs”

● “bridge the gap between molecular genetic research and breeding”

● Big & ambitious project● From March 2011 to Aug 2015

LOTS OF DATA PRODUCED!

Fruitbreedomics

● “improve the efficiency of current fruit breeding programs”

● “bridge the gap between molecular genetic research and breeding”

● Big & ambitious project● From March 2011 to Aug 2015

LOTS OF DATA PRODUCED! (+ tools)

Fruitbreedomics - WP7

Fruitbreedomics - WP7

Fruitbreedomics - WP7

● Bioinformatics infrastructure

Fruitbreedomics - WP7

● Bioinformatics infrastructure● Data hub & tool development

Fruitbreedomics - WP7

● Bioinformatics infrastructure● Data hub & tool development● Service project members

Fruitbreedomics - WP7

● Bioinformatics infrastructure● Data hub & tool development● Service project members● Release to the public

Fruitbreedomics - WP7

● Bioinformatics infrastructure● Data hub & tool development● Service project members● Release to the public

http://bioinformatics.tecnoparco.org/fruitbreedomics/

DB status: phenotypes

Apple● 9488 phenotype entries● 1665 varieties, 2488 trees● 36 traits, 8 collectionsPeach● 8945 phenotype entries● 2772 varieties, 2988 trees● 41 traits, 19 collections

DB status: genotypes

● SSR - Apple● 1619 varieties, 1689 trees ● 6 locations● 16 SSR (ch01f02, ch01f03b, ch01h01, ch01h10, ch02c06,

ch02c09, ch02c11, ch02d08, ch03d07, ch04c07, ch04e05, ch05f06, ch_vf1, gd12, gd147, hi02c07)

● (and more to come)● SNPchip - Peach

● 9k chip● 3301 individuals

● SNPchip - Apple● 20k chip● 1950 individuals● (import in progress)

DB status: traits & markers

34 traits

49 amplicons

365 SNPs

25 commercialessays

Linked to

Linked to

Contained by

Can detect

DB status: resequencing data

● SNPs from design of 20K SNP array● Sequence data aligned on the apple reference genome v2.0

(915 known scaffolds)● 16 cultivars, for 12 raw (unfiltered) data is available

● Dr Oldenburg● Fuji● Lady Williams● F2-26829-2-2● Macoun● Coxs Orange Pippin● Worchester Pearmain-USA● Jonathan

● Malus micromalus● McIntosh● Delicious● Braeburn● Common Antonovka● Priscilla-NL● X9748● X9273

On the shoulders of...

● Holistic approach● Easily present data● We became part of the dev community

● From 6 to 7 (big update!)

Peek view

Peek view

Peek view

JBrowse integration

● JBrowse is the HTML5GMOD successorof GBrowse

● Now a pwd protectedinstance on FB site

Breeder's Interface

A tool to help design crosses

BI: traits

● Monogenic traits● Primary source: BI meetings and discussions

● Peach: ~ 60 collected (~30 considered “high priority”)● Apple: 18 collected (mainly resistance)

● For each trait:● Description● Genotypes ↔ Phenotypes (e.g. G/- fuzzy, g/g glabrous)● Genetic position (when available)● References (when available)

● Secondary source: Task 1.2● “Development and mapping of SNP markers tightly associated

to selected traits/loci”● SNPs, amplicon, and essays

BI: genotypes

● For each trait● For each variety

● “mendelian” genotypes: A/A, A/a, or a/a● actually, a little more complicated...

● Sources● phenotype analysis (a lot of A/-)● apple SNP chip data

● Totals● APPLE: 456 varieties, 3 traits● PEACH: 343 varieties, 16 traits

BI: model● User input

● Desired phenotype● Free cross or fix parent● Target number of seedlings

● Translation● List of compatible genotypes

● Behind the scenes● Precomputed all possible crosses● 99255 apple crosses● 58653 peach crosses● Probabilities for each genotypic outcome

● Online● Cumulative probability● (Ordering)

BI: cross description

BI: limitations

● One theorethical limitation● non independend segregation● when two (or more) loci are “close”...● … and at least one parent is heterozigous for

both loci● User gets a warning

● One practical limitation● more data

LDExplorer

A tool to explore Linkage Disequilibrium

LDExplorer

● Linkage Disequilibrium (LD)● SNPchip data● Leverage well known tool: PLINK● Queue system● Input

● A subset of genotyped individuals● Analysis parameters

● Output● LD analysis results● .PED and .MAP files● TAG SNP info● LD decay plots (chromosomes and whole genome)

● Thanks to Luca Bianco

Thank you!