Backcross Breeding

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Backcross Breeding
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History of Backcrossing

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

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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

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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

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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.

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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 Rr1rr) are crossed to RP, trait
  evaluated before harvest, susceptible plants
  discarded

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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

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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 RR1Rr
• 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.

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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

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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.

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Single recessive allele - progeny test in
different season

• Cross susceptible (RR) RP to resistant (rr) DP
• F1 plants crossed to RP, seeds are 1 RR1Rr
• 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.

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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

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Single recessive allele - progeny test in
different season

• BC4 F1 plants selfed and produce 1RR2Rr1rr
  progeny
• BC4F2 plants selfed and resistant ones harvested
  by plant
• Resistant families tested further

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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.

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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.

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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

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Recovery of genes from RP

• Ave. recovery of RP 1-(1/2)n1, 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.

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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

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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 c0.5, P(undesirable gene will be
  eliminated) with 5 BC is 0.98
• with c0.02, P(undesirable gene will be
  eliminated) with 5 BC is 0.11

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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

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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

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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

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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

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Model
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.
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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)
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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)
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Recombination

• P(Q1Q1M1M2)r
• Assume r10
• Select one plant based on marker genotype alone,
  10 chance of losing target gene
• Probability of not losing gene(1-r)
• For t generations, P1-( 1-r )t
• For 5 BC generations, probability of losing the
  target gene is P1-(.9)50.41

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Flanking Markers
Best way to avoid losing the target gene is to
have marker loci flanking it
MA1 rA Q1 rB
MB1
MA2 Q1
MB2
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BC1F1 genotype frequencies using marker
loci Flanking 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
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Flanking Markers
Probabilityof losing the target gene after
selecting On flanking markers
P(MA1MA2Q1Q1MB1MB2MA1MA2MB1MB2)
Example If the flanking markers have 10
recombination Frequency with the target gene,
the probability of losing The gene after 1
generation is P0.024. The probability Of losing
the gene after 5 generations is P0.1182
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Other Considerations

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

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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