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Backcross Breeding

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

Backcross Breeding

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

History of Backcrossing

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

Page 3: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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

Page 4: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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

Page 5: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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.

Page 6: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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

Page 7: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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

Page 8: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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.

Page 9: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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

Page 10: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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.

Page 11: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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.

Page 12: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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

Page 13: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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

Page 14: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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.

Page 15: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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.

Page 16: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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

Page 17: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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.

Page 18: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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

Page 19: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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

Page 20: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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

Page 21: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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

Page 22: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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

Page 23: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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

Page 24: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

Model

Two alleles at marker locus M1 and M2Two alleles at target gene, Q1 and Q2

M1 Q1

M2 Q2r

Q2 is the target allele we want to backcrossinto recurrent parent, which has Q1 to beginwith.

Page 25: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

Gametes produced by an F1 heterozygous at both QTL and marker locus.

Gamete Frequency

M1 Q1

1/2(1-r)

M1 Q2

1/2( r )

M2 Q1

1/2( r )

M2 Q2

1/2(1-r)

Page 26: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

BC1F1 Genotype frequencies for a marker locus linked to a target gene.

Genotype Frequency

M1M1Q1Q1 1/2(1-r)

M1M1Q1Q2 1/2( r )

M1M2Q1Q1 1/2( r )

M1M2Q2Q2 1/2(1-r)

Page 27: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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

Page 28: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

Flanking Markers

• Best way to avoid losing the target geneis to have marker loci flanking it

MA1 rA Q1 rB MB1

MA2 Q1 MB2

Page 29: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

BC1F1 genotype frequencies using marker lociFlanking the target gene

Genotype Frequency

MA1MA1Q1Q1MB1MB1 1/2(1-rA)(1-rB)

MA1MA1Q1Q2MB1MB1 1/2rArB

MA1MA2Q1Q1MB1MB1 1/2rA(1-rB)

MA1MA1Q1Q2MB1MB1 1/2(1-rA)rB

MA1MA1Q1Q1MB1MB2 1/2(1-rA)rB

MA1MA1Q1Q2MB1MB2 1/2rA(1-rB)

MA1MA2Q1Q1MB1MB2 1/2rArB

MA1MA2Q1Q2MB1MB2 1/2(1-rA)(1-rB)

Total 1

Page 30: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

Flanking Markers

Probabilityof losing the target gene after selectingOn flanking markers:

P(MA1MA2Q1Q1MB1MB2|MA1MA2MB1MB2)

Example: If the flanking markers have 10% recombinationFrequency with the target gene:, the probability of losing The gene after 1 generation is P=0.024. The probabilityOf losing the gene after 5 generations is P=0.1182

Page 31: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

Other Considerations

• Backcross breeding is viewed as a conservative approach

• The goal is to improve an existing cultivar

• Meanwhile, the competition moves past

Page 32: Backcross Breeding. History of Backcrossing Harlan and Pope, 1922 Smooth vs. rough awn Decided to backcross smooth awn After 1 BC, progeny resembled Manchuria

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