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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
commercial
essays
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
11 nazzicari
11 nazzicari
11 nazzicari
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
11 nazzicari
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 collections
Peach
● 8945 phenotype entries
● 2772 varieties, 2988 trees
● 41 traits, 19 collections
Phenotypes
That's all, folks!

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11 nazzicari

  • 1. June 19, 2015 – CIV - Comacchio FB database and the Breeder's interface Nelson Nazzicari, PTP (Lodi)
  • 2. ● Breeders' interface ● Tool aim ● Available data: traits, markers, essays, genotypes ● Model assuptions ● The other parts of the DB Agenda
  • 3. ● 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/
  • 4. What do we have? traits amplicons SNPs commercial essays Linked to Linked to Contained by Can detect varieties have phenotypes have
  • 7. ● 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
  • 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 ● 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 ● How many seedlings (n)? ● Depends on the target confidence level (α)
  • 19. Target number of seedlings
  • 20. Target number of seedlings
  • 21. Exception: more than two alleles
  • 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
  • 23. Phenotypes Apple ● 9488 phenotype entries ● 1665 varieties, 2488 trees ● 36 traits, 8 collections Peach ● 8945 phenotype entries ● 2772 varieties, 2988 trees ● 41 traits, 19 collections