11 Plant vs Animal Breeding

11.1 Plant-Specific Features

11.1.1 Selfing

pop <- breeding.diploid(pop, selfing.mating = TRUE, breeding.size = c(200, 0))

11.1.2 Doubled Haploids (DH)

pop <- breeding.diploid(pop, dh.mating = TRUE, breeding.size = c(200, 0))

11.1.3 Cloning

pop <- breeding.diploid(pop, copy.individual.m = 10, breeding.size = c(1000, 0))

11.1.4 One-Sex Mode

pop <- creating.diploid(nsnp = 5000, nindi = 200, one.sex.mode = TRUE)

11.2 Animal-Specific Features

11.2.1 Litter Size Control

pop <- breeding.diploid(
  pop,
  selection.size = c(10, 20),
  litter.size = 8,              # 8 piglets per litter
  breeding.size = c(160, 160)   # 20 litters
)

11.2.2 Multiple Parities

# Sows have multiple litters
for (parity in 1:3) {
  pop <- breeding.diploid(
    pop,
    selection.f.gen = 5,        # Same females each time
    selection.m.gen = 6,        # New males
    breeding.size = c(100, 100)
  )
}

11.3 Summary

Plants: selfing, DH, cloning, no sex
Animals: litter size, multiple parities

Continue to Chapter 12: SNP Panels!

# Plant vs Animal Breeding {#sec-plant-vs-animal}

## Plant-Specific Features

### Selfing
```{r}
#| eval: false
pop <- breeding.diploid(pop, selfing.mating = TRUE, breeding.size = c(200, 0))
```

### Doubled Haploids (DH)
```{r}
#| eval: false
pop <- breeding.diploid(pop, dh.mating = TRUE, breeding.size = c(200, 0))
```

### Cloning
```{r}
#| eval: false
pop <- breeding.diploid(pop, copy.individual.m = 10, breeding.size = c(1000, 0))
```

### One-Sex Mode
```{r}
#| eval: false
pop <- creating.diploid(nsnp = 5000, nindi = 200, one.sex.mode = TRUE)
```

## Animal-Specific Features

### Litter Size Control
```{r}
#| eval: false
pop <- breeding.diploid(
  pop,
  selection.size = c(10, 20),
  litter.size = 8,              # 8 piglets per litter
  breeding.size = c(160, 160)   # 20 litters
)
```

### Multiple Parities
```{r}
#| eval: false
# Sows have multiple litters
for (parity in 1:3) {
  pop <- breeding.diploid(
    pop,
    selection.f.gen = 5,        # Same females each time
    selection.m.gen = 6,        # New males
    breeding.size = c(100, 100)
  )
}
```

## Summary
- Plants: selfing, DH, cloning, no sex
- Animals: litter size, multiple parities

Continue to [Chapter 12: SNP Panels](12-snp-panels.qmd)!