1. Backcross Breeding

2. History of Backcrossing
Harlan and Pope, 1922
Smooth vs. rough awn
Decided to backcross smooth awn
After 1 BC, progeny resembled Manchuria

3. Terminology
Recurrent parent (RP) - parent you are transferring trait to
Donor or nonrecurrent parent (DP) - source of desirable trait
Progeny test - when trait is recessive

4. Single dominant gene for disease resistance- pre flowering
Cross recurrent parent (rr) with resistant donor parent (RR) - all F1s are Rr
Cross F1 to RP to produce BC1 progeny which are 1 Rr: 1 rr
Evaluate BC1s before flowering and discard rr plants; cross Rr plants to RP

5. Single dominant gene for disease resistance- pre flowering
BC2 F1 plants evaluated, rr plants discarded, Rr plants crossed to RP
…. BC4 F1 plants evauated, rr plants discarded, Rr plants selfed to produce BC4 F2 seeds, which are 1RR: 2 Rr: 1rr
BC4 F2 plants evaluated before flowering, rr discarded, R_ selfed and harvested by plant, then progeny tested. Segregating rows discarded, homozygous RR rows kept and tested.

6. Single dominant gene - post flowering
Cross susceptible RP (rr) with resistant DP (RR) - all F1s are Rr
Cross F1 to RP to produce BC1 progeny which are 1 Rr: 1 rr
BC1F1 plants crossed to RP, trait evaluated before harvest, susceptible plants discarded
BC2F1 plants (1 Rr:1rr) are crossed to RP, trait evaluated before harvest, susceptible plants discarded

7. Single dominant gene - post flowering
Procedure followed through BC4
Seeds from each BC4 F2 individual are harvested by plant and planted in rows
Segregating rows are discarded, homozygous RR rows are maintained, harvested and tested further

8. Single recessive allele - progeny test in same season
Cross susceptible (RR) RP to resistant (rr) DP
F1 plants crossed to RP, BC 1 seeds are 1 RR:1Rr
All BC1 plants crossed to RP and selfed to provide seeds for progeny test
Screen BC1F2 plants before BC2F1 plants flower. BC1 F1 plants that are RR will have only RR progeny. BC1 F1 plants that are Rr will produce BC1F2 progeny that segregate for resistance.

9. Single recessive allele - progeny test in same season
BC2 F1 plants from heterozygous (Rr) BC1 plants are crossed to RP; those from susceptible (RR) BC1 plants are discarded
BC2 F2 selfed seed is harvested for progeny testing
Progeny tests are conducted before BC3F1 plants flower. Only plants from (Rr) BC2 plants are crossed to RP

10. Single recessive allele - progeny test in same season
Each BC4F1 plant is progeny tested. Progeny from susceptible BC3 plants are all susceptible and family is discarded
If progeny test completed before flowering, only homozygous resistant (rr) plants are selfed. Otherwise, all plants selfed and only seed from (rr) plants harvested.
Additional testing of resistant families required.

11. Single recessive allele - progeny test in different season
Cross susceptible (RR) RP to resistant (rr) DP
F1 plants crossed to RP, seeds are 1 RR:1Rr
BC1 plants selfed, seed harvested by plant
BC1F2 plants grown in progeny rows, evaluated, seed from resistant (rr) rows is harvested. BC1F3 progeny crossed to RP to produce BC2F1 seeds.

12. Single recessive allele - progeny test in different season
BC2F1 plants crossed to RP to obtain BC3F1 seeds which are 1Rr: 1 RR
BC3F1 plants are selfed, and progeny are planted in rows
BC3F2 seeds are harvested from resistant (rr) progeny rows
Resistant BC3F3 plants crossed to RP to produce BC4F1 seeds

13. Single recessive allele - progeny test in different season
BC4 F1 plants selfed and produce 1RR:2Rr:1rr progeny
BC4F2 plants selfed and resistant ones harvested by plant
Resistant families tested further

14. Importance of cytoplasm
For certain traits (e.g. male sterility) it is important that a certain cytoplasm be retained
In wheat, to convert a line to a male sterile version the first cross should be made as follows: Triticum timopheevi (male sterile) x male fertile wheat line. From that point on, the recurrent parent should always be used as the male.

15. Probability of transferring genes
How many backcross progeny should be evaluated?
Consult table in Fehr, p. 367; for example in backcrossing a recessive gene, to have a 95% probability of recovering at least 1 Rr plant, you need to grow 5 backcross progeny.

16. Probability of transferring genes
To increase the probability to 99% and the number of Rr plants to 3, you must grow 14 progeny
If germination is only 80%, you must grow 14/0.8 = 18 progeny

17. Recovery of genes from RP
Ave. recovery of RP = 1-(1/2)n+1, where n is the number of backcrosses to RP
The percentage recovery of RP varies among the backcross progeny
For example, in the BC3, if the DP and RP differ by 10 loci, 26% of the plants will be homozygous for the 10 alleles of the RP; remainder will vary.

18. Recovery of genes from RP
Selection for the RP phenotype can hasten the recovery of the RP
If the number of BC progeny is increased, selection for RP can be effective

19. Linkage Drag
Backcrossing provides opportunity for recombination between the favorable gene(s) from the RP and the unfavorable genes that may be linked
Recombination fraction has a profound impact: with c=0.5, P(undesirable gene will be eliminated) with 5 BC is 0.98
with c=0.02, P(undesirable gene will be eliminated) with 5 BC is 0.11

20. Backcrossing for Quantitative Characters
Choose DPs that differ greatly from RP to increase the likelihood of recovery of desired trait (earliness example)
Effect of environment on expression of trait can be a problem in BC quantitative traits

21. Backcrossing for Quantitative Characters
Consider selfing after each BC
Expression of differences among plants will be greater
May be possible to practice selection
Single plant progeny test will not be worthwhile; must use replicated plots

22. Other Considerations Marker assisted backcrossing
Assume that you have a saturated genetic map
Make cross and backcross
To hasten the backcrossing process, select against the donor genotype (except for the marker(s) linked to the gene of interest) in backcross progeny

23. Marker-Assisted Backcrossing
May improve efficiency in three ways:
1) If phenotyping is difficult
2) Markers can be used to select against the donor parent in the region outside the target
3) Markers can be used to select rare progeny that result from recombinations near the target gene

24. Model r Two alleles at marker locus M1 and M2
Two alleles at target gene, Q1 and Q2 M1 Q1 r Q2 M2
Q2 is the target allele we want to backcross
into recurrent parent, which has Q1 to begin
with.

25. Gametes produced by an F1 heterozygous at both QTL and marker locus.
Frequency
M Q1
1/2(1-r)
M Q2
1/2( r )
M Q1
M Q2

26. BC1F1 Genotype frequencies for a marker locus linked to a target gene.
Frequency
M1M1Q1Q1
1/2(1-r)
M1M1Q1Q2
1/2( r )
M1M2Q1Q1
M1M2Q2Q2

27. Recombination P(Q1Q1|M1M2)=r Assume r=10%
Select one plant based on marker genotype alone, 10% chance of losing target gene
Probability of not losing gene=(1-r)
For t generations, P=1-( 1-r )t
For 5 BC generations, probability of losing the target gene is P=1-(.9)5=0.41

28. is to have marker loci flanking it
Flanking Markers
• Best way to avoid losing the target gene
is to have marker loci flanking it
MA rA Q rB MB1
MA Q MB2

29. BC1F1 genotype frequencies using marker loci Flanking the target gene
Frequency
MA1MA1Q1Q1MB1MB1
1/2(1-rA)(1-rB)
MA1MA1Q1Q2MB1MB1
1/2rArB
MA1MA2Q1Q1MB1MB1
1/2rA(1-rB)
1/2(1-rA)rB
MA1MA1Q1Q1MB1MB2
MA1MA1Q1Q2MB1MB2
MA1MA2Q1Q1MB1MB2
MA1MA2Q1Q2MB1MB2
Total 1

30. Probabilityof losing the target gene after selecting
Flanking Markers
Probabilityof losing the target gene after selecting
On flanking markers:
P(MA1MA2Q1Q1MB1MB2|MA1MA2MB1MB2)
Example: If the flanking markers have 10% recombination
Frequency with the target gene:, the probability of losing
The gene after 1 generation is P= The probability
Of losing the gene after 5 generations is P=0.1182

31. Other Considerations
Backcross breeding is viewed as a conservative approach
The goal is to improve an existing cultivar
Meanwhile, the competition moves past

32. Backcross Populations
May be used as breeding populations instead of F2, for example
Studies have shown that the variance in a backcross population can exceed that of an F2
Many breeders use 3-way crosses, which are similar to backcrosses