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

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

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.

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

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

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.

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

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.

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.

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

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

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.

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.

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

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.

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

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

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

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

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

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

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.

Gametes produced by an F1 heterozygous at both QTL and marker locus. Frequency M1 Q1 1/2(1-r) M1 Q2 1/2( r ) M2 Q1 M2 Q2

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

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

is to have marker loci flanking it 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

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

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=0.024. The probability Of losing the gene after 5 generations is P=0.1182

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

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