3. ●
Help to design crosses
●
Be down to hearth
●
Leverage what we have
●
Leverage what we will have
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Target driven approach
Our targets
http://bioinformatics.tecnoparco.org/fruitbreedomics/
4. What do we have?
traits
amplicons
SNPs
commercial
essays
Linked to
Linked to
Contained by
Can detect
varieties
have
phenotypes
have
11. 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)
13. Essays & Papers
● Essays linked to SNPs
● Technology
● SNPchip
● Scientific papers linked to SNPs, amplicons, or
traits
14. ●
“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
15. ●
Independent segregation
●
AA x Aa → 100% dominant phenotype
●
Aa x Aa → 75% dominant, 25% recessive
●
More than one trait → probabilities multiply
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Target driven approach
●
Define desired result
●
Fix one parent?
Cross model
18. Target number of seedlings
●
Given a probability p of success
(e.g. p=0.5, or p=0.25)
●
We want x successful crosses
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How many seedlings (n)?
●
Depends on the target confidence level (α)
22. 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