On-farm Plant Breeding I

1. Michael Mazourek Cornell University

2. Plant Breeding General Schemes
– Recurrent Selection
• Straightforward
• Many alleles possible in population
– Pedigree –creates new combinations of traits
• See all permutations
• Few alleles
– Backcross – good for introgressing trait into elite
plant
• Dominant source
– Easy – phenotypic difference in progeny
• Recessive source
– Laborious – no phenotypic difference

3. Population Breeding
• Mass Selection – simple recurrent selection
– Works best when environmental influence is
minimal
– Plant Intercrossed or random mated population
– Select best 5-10% of plants
– Allow to intercross
– Repeat
– Slowly but surely

4. Mendel
• Alleles – different forms for a gene that control a
trait
• Dominant allele – written in CAPITAL LETTERS
• Recesive allele – written in smalls
• True Breeding = Homozygous
• Cross dominant plant x recessive plant
– Heterozygous offspring
–AA x aa => Aa F1

5. Breeding with Hybrids
Dominant traits
•only needs to be inherited from one parent to appear in
progeny – see it in the F1
•visible if present
Recessive traits
•needs to be inherited from both parents to appear in progeny
•plant can be an invisible carrier
Hybrid with dominant trait
•may or may not be true breeding
•Common for disease resistance
Hybrid with recessive trait
•progeny will be true breeding
•Common for domestication traits

6. Pedigree Breeding
• Make crosses to produce F2 population
– Sow large F2 (50-5,000 individuals)
– Select best individuals and self-pollinate
• Plant F3 families
– Select best individuals and self-pollinate
• Plant F4 families
– Select best individuals and self-pollinate
• Plant F5 families
– Select best families
– Increase for replicated trials
• Generations to replicated trials variable

7. ‘Amber Delight’
‘Bugle’ (Rupp Seeds) ‘Honeynut’ (High Mowing Seeds)
‘Amber Delight’
X

8. ‘Amber Delight’
‘Bugle’ (Rupp Seeds) ‘Honeynut’ (High Mowing Seeds)
‘Amber Delight’
Hybrid
Heterozygote for:
PMR
Some other genes
Not many others

9. ‘Amber Delight’
‘Bugle’ (Rupp Seeds)
‘Amber Delight’
PVP
Restricts:
Saved seed for commercial use
Sale of seed of first gen hybrids
Further generations non-restricted

10. From ‘Amber Delight’ to ‘898’
‘Bugle’ ‘Honeynut’
‘Amber Delight’
X
Select plants in field for
Powdery mildew resistance
Productivity
Test harvested fruit for
Brix
Color
Dry matter
F2 150 plants
F5 10 plants x 3 reps
F4 10 plants
F3 10 plants
898

11. How Many Seed Should I Plant?
• Crosses between uniform hybrids or inbreds
– at least 3 plants, not more than 6-10 plants
– More if low seed yield crop
• Self pollinations of uniform hybrids or F1’s
– At least 3 plants, not more than 6-10 plants
– More if low seed yield crop
• F2 plants from selfing F1
– At least 16 plants
– sweet spot between 75 and 150
– Depends on complexity of cross (x 5 rule)

12. Heterozygotes and Selection
• Anthocyanins in jalapeño
• Dominant
• Issue:
– Cross green with purple
– Discard green
– Select best purple plant
– Plant progeny
– Most segregate for green
A a
A AA Aa
a Aa aa

13. ‘Habanada’
X
F1
F2
P1 P2
3/4 1/4

14. X‘Habanada’
F1
P1 P2
X P2
BC1F1 population
BC1F2

15. Goal: Develop a sweet, striped (variegated) snacking
pepper

16. Developing a sweet, striped (variegated) snacking pepper
Starting Parents:
‘Fish’:
spicy, variegated
‘Lipstick’
sweet, non-variegated

17. Variegated
(recessive)
Non-
variegated
(dominant)
X
1/4 of F2 progeny will be variegated
F1

18. Pungent
(dominant)
Non-pungent
(recessive)
X
1/4 of F2 progeny will be non-pungent
F1

19. Variegated (recessive)
Pungent (dominant)
X
1/16 of F2 progeny will be non-pungent and variegated
F1
Non-variegated
(dominant)
Non-pungent (recessive)
1/16
16 x 5 = 80

21. Backcross Method (Dominant)
aa x AA
aa x Aa
1 aa
aa x 1 Aa
F1
BC1F1
BC2F1
1 aa
1 AaBC3F1
BC3F2 1AA:2Aa:1aa
•Relatively simple
•Population size small
•(~10 plants)
•Not much gained
50% P1
75% P1
87.5% P1
93.25% P1
93.25% P1, 96.875% homozygous,
1 aa
aa x 1 Aa
93.25% P1, 98.4375% homozygous,1AABC3F3

22. Slow Backcross Method (Recessive)
AA x aa
AaF1
“BC1F1”
F2
1AA
2Aa
AA x 1aa
X
Aa
1AA
2Aa
AA x 1aa
X
“BC2F1” Aa
“BC1F2”
Purposeful
Works great if you
can stand the wait

23. Population Sizes for Single Genes
• Important formula:
ln(1-Probability)/ln(1-frequency) = # plants
Ex how many plants do you need to be 99% sure to
find aa in F2 of AAxaa?
ln (1-0.99)/ln (1-0.25) = 16
How sure are you that you will find 1%
contamination if you check 100 samples?
ln(1-P)/ln(1-0.01) = 100
P=63%
Warning: formula for # to phenotype, does not
include germination losses, deer damage, etc

24. Early Red Bell Pepper Project
• EFAO, KASSI, Bauta Family Initiative
on Canadian Seed Security and more
• Goal of developing an early red bell
pepper that thrives on participating
grower farms

25. Ace
-very early
but pointy
Aristotle
-cubic, broadly adapted, many
disease resistances
but late
F1 – several pollinated due to variation
from crossing two hybrids
F2 – seed from earliest plants shared
Early Red Bell Pepper Project

26. One Generation of Selection
• Cornell
– planted progeny from individual plants
separately. (F3 families)
– chose best plants from best families.
– Pruned and dug up selections
– Self-pollinating greenhouse
• Ontario
– Planted mix of F3 seed at multiple farms
– Selected best individuals
– Saved open pollinated seed
– Dug up selections for self-pollination
– Will recombine seed between farms for
2017

27. Acknowledgements
• ACORN ECOSGN
• Lauren Brzozowski & Rachel Hultengren
• New Ontario seed friends
– KASSI, EFAO, Bauta Family Initiative
• Chris Hernandez, Bill Holdsworth, Brian
Leckie, Kyle LaPlant, Rachel Hultengren,
Lindsay Wyatt
• Maryann Fink, Paige Reeves, Emily
Rodekohr, Sara Shapleigh
• NOVIC Team
• ESO-Cuc Team
Northern Organic Vegetable Improvement Collaborative
USDA-OREI 2009-51300-05585
2014-51300-22223
ESO-Cuc: Addressing Critical Pest Management Challenges in
Organic Cucurbit Production
USDA-OREI 2012-51300-20006
Breeding, Research, And Education Needs Assessment For
Organic Vegetable Growers In The Northeast
USDA-AFRI 2014-67013-22409
Toward Sustainability Foundation
David Rockefeller Fund