- Backcross breeding is used to transfer one or few genes from a donor plant to an elite cultivar, while recovering the genome of the elite cultivar. It involves repeated crossing of an F1 hybrid to one of the parental lines. - Six backcrosses are typically required using conventional methods to recover 99.2% of the elite cultivar's genome. Marker assisted selection can reduce the number of backcrosses needed. - During backcrossing, recombination and crossing over occurs, resulting in gametes with different combinations of parental genomes. Marker assisted selection uses co-dominant markers to identify plants in early backcross generations with higher percentages of the elite cultivar's genome recovered. This allows for more

1. Backcross Breeding
• Also referred as line conversion or Varietal enhancement
• Repeated crossing of F1 progeny to its one of the parent
• To transfer one or few genes (even OTLs) from a donor to an
elite cultivar (Recurrent parent)
• Repeated backcrossing is done to recover complete genome
of the recurrent parent in addition to the target gene
Example: Introgression of transgenes from a transgenic
plant into elite varieties or Parents of hybrids
Breeder Blogs

2. Breeder Blogs
Markers are used for the
early recovery of the
Recurrent plant genome in
BC1 and BC2 generations

3. Back cross
generations
% of RPG
recovered
after each
backcross
BC1 75.0%
BC2 87.5%
BC3 93.8%
BC4 96.9%
BC5 98.4%
BC6 99.2%
Recovery of the recurrent parent genome (RPG) is important to retain the
originality of the parent in addition to the target trait
Six backcrosses are required to get
99.2% of recurrent parent genome
(RPG) through conventional method
A formula for the calculation of RP genome
recovered after each backcross
Breeder Blogs

4. Marker assisted backcross (MABC) reduces the number of backcrosses
required for the recovery of RP genome. To understand the genetics behind
the early recovery of RPG through MABC, the basics of genes and markers are
important
Genes and markers are segments of DNA on chromosomes. A gene has a known function but unknown
location. A marker has a known location on chromosome, but no apparentfunction. If the location of
the gene is known, that gene can be used as marker
Breeder Blogs

5. Gene 1
Gene 1
Centimorgans(CM)
Kilometers(KM)
Markers and genes on
chromosome are analogue
to road map with cities and
towns. If the genes are
considered as the two major
cities here, the towns in
between them are markers.
The exact distance between
them is known in both maps.
Distance on chromosomes
are measured in Centi
morgans units as like
Kilometres in a road map
Kilomaters(KM)
Analogue of Chromosomes and road map
Breeder Blogs

6. Monomorphic markers.
Present on chromosomes of
both the parents. This
markers cannot be used for
differentiating the parents
Genes shows allelic variations and express different phenotypes. Markers
too has allelic variations, that can be detected using PCR or other methods.
The different types of markers are given below
Polymorphic dominant
markers. Present either one
of the parent. Differentiates
the parents. But cannot be
used for differentiating the
heterozygous state
Polymorphic Co dominant
markers. Present on both
parents but differs in DNA
sequence and size. This class
of markers can differentiate
both the parents and
heterozygous state
Chromosome of Recurrent Chromosome of Donor
Breeder Blogs

7. Marker assisted backcross programme requires large number of Polymorphic co-dominant
markers distributed evenly throughout all the chromosomes.
(If polymorphic dominant markers are used, markers should be selected for both donor and
recurrent parent chromosomes)
Chromosomeof Recurrent Chromosomeof Donor
Polymorphicmarkers
Breeder Blogs

8. The pollination & fertilization process involves fusion of pollen and ovule.
During the gametes formation, two important process takes place
1. Reduction of chromosome number to half in gametes
 Each gametes represents only 50% of the parental
genome
2. Recombination and crossing over occurs between
homologous chromosomes of male and female, followed
by independent assortment of chromosome to gametes
 In F1 or any segregating population, each gamete
acquires the different combination of parental
chromosomes
Breeder Blogs

9. Now consider what happens during the backcross process at chromosome level, by looking at
one chromosome. This illustrations are applicable to all chromosomes and the genotypic and
phenotypic expression is the collective of all chromosomes
Recurrent parent
100 % RP - TG
Target gene (TG)
Donorparent
0 % RP + TG
50 % RP - TG
Ovule
50 % RP + TG
Pollen
0 % RP + TG
F1 Progenies are Heterozygous and Homogenous
Crossing
Breeder Blogs

10. Recombination takes place in the F1 pollen mother cells (PMC),
generates cross over chromosomes in pollens
Mostly 50 % the chromosomes are
exchanged between homologous
chromosomes and the amount of
chromosomes exchanged also equal
between two chromosomes
Crossing over is not always 50%
between chromosomes. In rare instances
more proportions of chromosomes are
exchanged between homologous
chromosomes
This forms the basic for the
marker assisted selection
Breeder Blogs

11. 1. Pollens with target gene and 50% of each parental chromosomes
2. Pollens without target gene and 50% each parental chromosomes
3. Pollens with target gene and more proportion of either one parental chromosomes
4. Pollens without target gene and more proportion of either one parental chromosomes
F1 produces following kinds of pollens
This two kind of pollens are
predominant in the flowers
These pollens are
Limited in numbers
Breeder Blogs

12. Segregation of F1 gametes and the genotype of BC1F1 populations
Recurrent parent F1
0 % RP + TG
Crossing
25 % RP + TG
Ovule Pollens
100 % RP - TG
50 % RP - TG 25 % RP - TG ~10 % RP - TG ~40 % RP +TG
75 % RP + TG 75 % RP - TG ~60 % RP - TG ~90 % RP + TG
These types of gametes also produced though not
mentioned in pollen genotypes
~60 % RP + TG ~90% RP - TG
Breeder Blogs
BC1F1 generation

13. 75 % RP - TG ~60 % RP - TG ~90 % RP + TG ~60 % RP + TG ~90 % RP - TG
Selection in BC1F1 populations (Foreground selection) for target gene
Foreground selection of target gene (TG) eliminates 50% of the plants without target gene
75 % RP + TG
75 % RP + TG~60 % RP + TG ~90 % RP + TG
Selected BC1F1 plants will be screened for Recurrent plan type characters (Background selection)
Phenotypically
distinguishable
Cannot be differentiated phenotypically.
Breeder Blogs

14. 75 % RP + TG~60 % RP + TG ~90 % RP + TG
Population distribution of BC1F1 population
50% RP 100% RP
The mean of the BC1F1 population is 75% of RPG. Though high RPG plants appears in the
population, selecting high RP plants by phenotypic selection is difficult. This leads to the
selection of 75% RP plants through conventional method, due to the fact that 75% plants
represent the more proportion in the population
No.ofPlants
% of RP Genome
Breeder Blogs

15. Genotyping of the of BC1F1 population with polymorphic Co-dominant markers
Will differentiate plants with different % RPG
The parallel lines indicates the position of the markers on the chromosomes. The co-dominant markers
identifies the male and female portions of chromosomes even at heterozygous state
3 /10 markers
Homozygous for RPG
If 10 Co-Dominant markers/ chromosome were used for genotyping the BC1F1 Population, the
three types of genotypes can be differentiated by the following technique
5 /10 markers
Homozygous for RPG
8 /10 markers
Homozygous for RPG
Number of markers homozygous for RPG was calculated for all chromosomes. The plants with
more number of RPG homozygous markers were selected and advanced to BC2F1.
Breeder Blogs

16. Genotyping will be done at BC2F1 populations with same set of markers. Plants with
more RPG Homozygous markers will be advanced
Comparison of conventional phenotypic selection vs. Marker based genotypic
selection
Breeder Blogs