June 19, 2015 – CIV - Comacchio

FB database and the Breeder's interface

Nelson Nazzicari, PTP (Lodi)

● Breeders' interface● Tool aim● Available data: traits, markers, essays, genotypes● Model assuptions

● The other parts of the DB

Agenda

● Help to design crosses● Be down to hearth● Leverage what we have● Leverage what we will have ● Target driven approach

Our targets

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

What do we have?

traits

amplicons

SNPs

commercialessays

Linked to

Linked to

Contained by

Can detect

varieties

have

phenotypes

have

Traits

Words

● Monogenic● Peach: ~ 60 collected (~30 considered “high

priority”)● Apple: 18 collected (mainly resistance)● For each trait:

● Description● Section (flower, resistance, ...)● Genotypes ↔ Phenotypes (e.g. Hd/- standard,

hd/hd stony hard)● Genetic position (when available)● Scientific references (when available)

Traits

Markers

● SNPs● Flanking regions● Position on genome

● Relation to trait locus● Distance (genetic/phisical)● Allele in phase

● Identification information● Primers● Amplicons● Founders sequences (apple only)

Markers

Essays & Papers

● Essays linked to SNPs● Technology● SNPchip

● Scientific papers linked to SNPs, amplicons, or traits

● “Mendelian” genotypes● For each variety:

● Ideal: A/A or A/a or a/a● These come from SNP chips and molecular tests

● Reality: a lot of A/-● These come from phenotype observation

Genotypes

● Independent segregation● AA x Aa → 100% dominant phenotype● Aa x Aa → 75% dominant, 25% recessive● More than one trait → probabilities multiply● Target driven approach

● Define desired result● Fix one parent?

Cross model

Describe cross

Target number of seedlings

● Given a probability p of success(e.g. p=0.5, or p=0.25)

● We want x successful crosses● How many seedlings (n)?● Depends on the target confidence level (α)

Target number of seedlings

Target number of seedlings

Exception: more than two alleles

Exception: loci are “close”

● Non independent segregation● Problems when:

● one parent is het on both● “close”

● We cannot really do anything without complete haplotypes● BI shows a warning

Phenotypes

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

Phenotypes

That's all, folks!