Plant Breeding Calculator

A Go program that calculates trait inheritance probabilities in breeding projects. This tool helps breeders predict the distribution of traits across generations and plan their breeding programs effectively.

Command Line Flags

• -motherName: Name of the mother plant
• -motherTraits: Traits of the mother plant in the format Name:Dominant:GeneLabel,Name:Dominant:GeneLabel,...
• -fatherName: Name of the father plant
• -fatherTraits: Traits of the father plant in the same format as mother traits
• -totalPlants: Total number of plants (default: 64)
• -targetGenotypes: (Optional) List of target genotypes to filter for (e.g., "ll,cc" for mutant leaves and purple foliage)

Core Features

• Calculates F2 generation probabilities for multiple traits
• Handles both dominant and recessive inheritance patterns
• Provides probability ratios and expected plant numbers
• Filters combinations based on target genotypes
• Generates human-readable trait descriptions

Genetic Notation

The calculator supports two types of genotype notation for filtering:

Recessive Traits

Use doubled lowercase letters:

• ll for mutant traits
• cc for recessive color traits
• ff for recessive form traits

Dominant Traits

Use single uppercase letters:

• L for regular traits
• C for dominant color traits
• F for dominant form traits

Results Notation

• L_ indicates presence of dominant allele (LL or Ll)
• ll indicates homozygous recessive
• Space separated for multiple traits (e.g., L_ cc F_)

Sample Command Line Execution

go run main.go \
  -motherName="Purple Flash" \
  -motherTraits="Regular Leave Shape:true:L,Purple Foliage:false:C,Round Fruit Shape:false:F" \
  -fatherName="Candlelight Mutant" \
  -fatherTraits="Mutant Leave Shape:false:L,Green Foliage:true:C,Long Fruit Shape:true:F" \
  -totalPlants=64 \
  -targetGenotypes="ll,cc"  # Filter for mutant leaves and purple foliage

Additional Examples

Filter for dominant traits:

-targetGenotypes="L,F"  # Filter for regular leaves and long fruit

Mix of dominant and recessive:

-targetGenotypes="L,cc"  # Filter for regular leaves and purple foliage

Example Output

F2 Generation Probabilities for Purple Flash × Candlelight Mutant
Total plants: 64

Target traits:
- Regular Leave Shape (L)
- Purple Foliage (cc)

Matching Combinations:
=====================
9/64 (14.1%) = Regular Leave Shape, Purple Foliage, Long Fruit Shape
    Genotype: L_ cc F_
    Expected number of plants: 9.0

Summary Statistics:
==================
Total Probability: 12/64
Percentage: 18.8%
Expected Total Plants with Target Traits: 12.0

Program Structure

Key Types

type Trait struct {
    Name      string
    Dominant  bool
    GeneLabel string
}

type Plant struct {
    Name   string
    Traits []Trait
}

type TraitCombination struct {
    Traits       []bool
    Probability  int
    Denominator  int
    Description  string
    GeneNotation string
    Expected     float64
}

Limitations

• Assumes simple Mendelian inheritance
• Does not account for:
  • Incomplete dominance
  • Codominance
  • Complex gene interactions
  • Environmental effects

Future Improvements

• Support for incomplete dominance
• Visualization of results
• F3 generation predictions
• Confidence intervals
• Complex filtering patterns
• Visual trait distributions
• Batch processing capabilities

License

MIT License