Breeding methods in self-

pollinated crops
 Breeding in self-pollinated crops
• Self-pollinated crops are homozygous and hence true breeding.

– Do not suffer from inbreeding depression

– Hence we can fix genes to a genotype

• Breeding in self-pollinated crops involve:

– Creating genetic variability (generate an F2 pop.)

– Selection of the best recombinants

– Fixing the genes by making the plant homozygous

• Repeated for 7-8 generations
 Breeding in self-pollinated crops

• There are 5 different breeding strategies in self-pollinated crops.

– Pedigree breeding
– Bulk population breeding method
– Single seed descent method
– Haploid breeding: single and double haploids
– Backcross breeding

• Breeding in self-pollinated crops leads to creation of:

– Pureline variety- homozygous and homogenous
– Bulk variety
– Composite variety
– Multilines
PEDIGREE BREEDING
PEDIGREE BREEDING
 Pedigree breeding method
Method:
• Parental choice- choose genetically diverse true-breeding parents
with complementary characteristics
– F2 will be very diverse
– Chance of obtaining transgressive segregates is much higher
– Transgressives are superior to parents due to overdominance

• F1 generation is heterozygous but homogeneous

• Self the F1 to get the F2 (3000 to 10000 plants)

– Selection begins in the F2
– Select 1% to 10% of the plants that combine the best
characteristics based on independent culling or index selection
 Pedigree breeding method
Method:
• Self the selected F2 plants to get the F3
– Select one or a few plants from the best rows
– Plant selected plants in plant-to-row progeny rows,
keeping progeny rows grouped in families

• Continue similar selections in the F4, F5 and F6 generations.

• In F7 and F8, selections are made between families (members

within of a family is almost identical)
– Initial field trials can be carried out in F 8 to select the 10
best purelines
 Breeding in self pollinated crops- pedigree
breeding method
Method:
• F9 and F10- do replicated trials over seasons

• F11 and F12- multilocational trials

• On-farm trials- to determine performances under

farm conditions.

• F13 to F15- the best 2 or 3 purelines are multiplied

and released as varieties.
 Aspects of pedigree breeding method

• Early generation selection of individuals in

heterozygous and heterogeneous pop. is
referred to as pedigree selection.

• Ultimately, pureline varieties are produced.

• Detailed pedigree records are maintained and

can be traced back to F2 parent plant.
 Breeding in self pollinated crops- pedigree breeding
method
• Pureline varieties produce high yields and are highly adapted to
the environment bred for.
– All plants in a pureline look alike and can produce high yields

– Agronomic practices are easy and mechanization is possible

because of uniformity

– Produce seeds that are fertile and with similar genetic make-
up to parent

– Seeds are easily produced- just self the parent

– Farmers can collect seeds for replanting

 Breeding in self pollinated crops- pedigree
breeding method
Advantages of pedigree breeding
• Each pureline can be traced back to its ancestral F2
plant.
– F2 parent can be reselected to further exploit its within
family variation
– Lots of genetic information can be gathered

• Selection is based on progeny tests.

• Transgressive segregates can be quickly identified in

the F2.
 Breeding in self pollinated crops- pedigree
breeding method
Advantages of pedigree breeding
• Very effective for phenotypic traits with high
heritabilities.

• Only superior plants are brought forward-

reduced cost.

• Used in crops that can be harvested

individually e.g. tobacco, soybean, cowpea.
 Pedigree breeding method
Disadvantages of pedigree breeding
• Requires extensive record keeping to prevent selection of closely related plants
(labour intensive and costly!!!).

• If trait has low heritability, selection in the F2 is unreliable.

– No correlation between a selected F2 plant and yield of it progenies in later generations

• If plants are closely planted in the field, individual plant selection is difficult.

• Extreme uniformity make purelines environmentally inflexible

• May not perform well outside the environment bred for

• Total yield loss occurs if a new disease affects the varieties

 Breeding in self pollinated crops
To reduce the risk associated with purelines, breeders have
developed:

• Bulk varieties with some built-in heterogeneity

• Composite varieties (mixture of different purelines) - look uniform

but are really different genotypes
– Allows environmental flexibility and insurance against pathogen evolution
– In a given environment, adapted pure line outyields the composite variety.

• Multilines (mixtures of isolines)- purelines which differ from each

other by a single gene
– Heterogeneous with respect to only one gene (yields are similar)
– Provide insurance against pathogen evolution
BULK BREEDING
 Bulk population breeding method

• Used for small grain crops that cannot be

harvested singly.

• Early selection is not practiced as selection for

complex traits such as yield is more effective
in later generations.

• Method can be modified to use pureline

selection or mass selection
Can be used to incorporate disease resistance. At each
generation, natural selection only allows resistant progenies
to grow.
Bulk population breeding method
 Bulk population breeding method

Method
• Parental choice- choose genetically diverse true
breeding parents with complementary characteristics.

• Hybridization to create F1 (10- 30 seeds).

– No selection is performed as plants are homogeneous

• Self the F1 to obtain the F2

– F2 plants are grown at normal commercial planting rates
– Seeds are harvested from the entire F2 population and
bulked.
 Bulk population breeding method
Method
• Seeds (10000) are randomly selected from F2 and planted to form the
F3.
– Planted in 1/100th to 1/50th of an acre plot

• This is continued until the F6 generation

– ~500 – 10000 plants in the F6 are planted out.
– Independent culling or index selection is performed
– Each plant is homozygous and with no modifying influences

• At F6 two types of selection can be practiced:

– Pureline selection
– Mass selection- large number of plants are selected, their seeds are
bulked and carried to the next generation.
 Bulk population breeding method

Method
• From F6, bulked seeds can be used in replicated
trials, multi-season trials, multilocational trials.

• Eventual release of bulk variety to farmers at F10

or F11 for commercial production.
 Bulk population breeding method

Advantages
• Used for crop species that are planted at high density
(especially cereals) as individual selections are difficult.

• Late generation selection is advantageous for traits with

complex inheritance and which have low heritabilities.

• Useful for improving the fitness of the population e.g.

winter hardiness, disease resistance

– Natural selection tends to eliminate plants having poor survival values.

 Breeding in self pollinated crops- bulk population breeding method

Advantages
• Flexible enough to produce pureline or bulk
varieties.

• Bulk varieties provide greater environmental

flexibility than purelines.

• Method is convenient, involves much less work

than pedigree breeding and is less costly
 Bulk population breeding method
Disadvantages

• Since selection is not done in F2, transgressive segregates can be missed.

• Large populations required in the F6 for selection to be effective (costly!!!).

• Heterosis slows down the attainment of homozygosity, hence requires

more generations to fix genes.

• Method requires at least 25 generations for natural selection to be

effective- poor method to improve fitness.

• Pedigree records cannot be kept, so little genetic information can be

obtained from the records.
Modified Bulk population breeding method
 Breeding in self pollinated crops
Pedigree selection Mass selection

Individual plant selection Selection of a large number of

individuals whose seeds are
bulked

Seeds from each plant are Bulk seeds are taken to the
carried forward as plant-to-row next generation en masse
progenies

Selection begins in early Selection begins later at F6, at

segregating generation (F2) which time they are highly
homozygous and true breeding.
 Breeding in self pollinated crops
• Both pedigree breeding and bulk breeding have one major
disadvantage:

– Both methods are performing selection and attainment of

homozygosity (fixing genes to genotypes) at the same time

• Pedigree method- inefficient especially for characters

with low heritability.

• Bulk breeding- incapable of selecting rare transgressive

segregates in F2; inefficient at obtaining homozygosity

• Solution- method of single seed descent

SINGLE SEED DESCENT
 Breeding in self pollinated crops- single seed
descent
• Proposed by Glouden (1939):
– Processes of obtaining homozygosity and selection are
separated onto two phases.
• Phase-1:
– Homozygosity is attained in the shortest possible time
while still maintaining the genetic base of the F2
generation.
• Phase-2:
– Selection is practiced among homozygous plants.
 Single seed descent

Method
• Phase 1:
– Grow large F2 population and retain one seed from each plant to
produce the next generation

– Advance generations to F5 using single seed descent. Achieved by:

• Off season planting at high density in greenhouses

• Forcing crop to mature and fruit early by withholding nutrients

• Use of growth retardants so that plants grow smaller and planted at high
density

• Plants are harvested at first fruit and the next generation planted
immediately- increase the number of cycles per season/year
Single seed descent

10 plants

No heterosis

Selection between rows

 Single seed descent

Method
• Phase 2:
– Selection starts at F6 generation when homozygosity is achieved and additive
genetic effects are high
• No modifying factors
• Variation in F2 is represented in F6 generation through single seed descent
• F6 grown in plant to row progenies
• Inferior lines are culled using independent culling or index selection

– F7 lines are planted in multi-row plots

• Preliminary yield trials are performed

• Promising lines are subjected to replicated trials, multi-season trials and multilocational
trials

– Promising varieties are subjected to on-farm trials.

 Single seed descent
Advantages

• Generations can be advanced quickly

– Homozygosity is achieved faster than pedigree or bulk breeding
– Off season planting at high density can further reduce time to homozygosity
– Replanting can be done as soon as first fruits ripen

• Cost can be reduced by forcing plants to fruit by withholding nutrients or using growth
retardants

• Maximum genetic gain per unit of time as selection is performed when it is most effective

• Broad base pop. is maintained, transgressives are not lost

• Reduced labour cost- less area planted, less harvesting cost, fewer harvests

• Method is amenable to modification: e.g. can be used to produce hybrids.

 Single seed descent

Disadvantages
• Within family variation is not exploited as each F2 is
represented by 1 plant
– Cannot obtain varieties as good as in pedigree breeding

• Attrition losses: sometimes the single seed saved is

not viable

• For highly heritable traits, pedigree method is more

efficient.
HAPLOID BREEDING
HAPLOID BREEDING
 Haploid breeding
• All the methods mentioned thus far require repeated selection
and selfing until homozygosity results

• Haploids provide a way to achieve homozygosity in the shortest

possible time
– saves on time and cost
– Selection is effective as haploids do not suffer from modifying influences
– Genetic gain is high

• Haploid breeding depends on

– Production of haploid plants
– Production of doubled haploids
– Selection among doubled haploid lines
 Haploid breeding

• Haploid lines can be produced by:

– Chromosome elimination (e.g. in barley)
– Semigamy (e.g. in cotton)
– Natural genetic factors (some forage crops slip into the haploid
state)
– Mutagenesis
– Androgenesis (anther culture)

• Doubled haploids can be produced by:

– Spontaneous doubling (10% of corn haploids produce double
haploids when fertilized)
– Chemical mutagen (colchicine, etc.)
 Haploid breeding

• Selection among double haploid lines aims at

determining the transgressive variants in the pop.

• Depends on:
– The number of doubled haploids produced
– Where selection is performed
• In vitro selection is very effective and requires little space
• Selection for characters such as yield and quality cannot be
done in vitro
– If RFLP markers are known for economic traits, marker
assisted selection can be performed early (rice)
 Haploid breeding
Advantages
• Homozygosity is achieved very quickly.

• Only method in self-incompatible and dioecious crops that can

result in purelines

• 100% homozygosity achieved in doubled haploids

– Other methods never reach absolute homozygosity
– Not affected by modifying factors

• Homozygosity is achieved without selection

– Selection reduces the chance of picking the best transgressives
as some cannot compete well in segregating populations
 Haploid breeding

Advantages
• For a given gene, A, doubled diploids are 50% AA and 50% aa. There
is no Aa.
– In diploids, only ¼ of the progenies are AA and aa. The remaining 50% is Aa.
– Hence prob. of obtaining a desired doubled haploid with ‘n’ number of
genes is (1/2)n whereas it is (1/4)n in normal diploids.

• Doubled haploids are either homozygous dominant (AA) or recessive

(aa) = to a test cross
– Useful in linkage studies

• Early generation selection is possible even when characters are not

highly heritable
– Additive genetic effects is twice that of normal diploids in early stages
 Haploid breeding

Advantages
• Mutagenesis and selection is more effective in the
haploid stage as all recessive mutations are homozygous
recessive in doubled haploids and are never masked by
dominance and epistasis.

• Somatic hybridization (protoplast fusion) of haploid

plants is an ideal method of producing interspecific
hybrids

• Paternally inherited cytoplasmic organelles may lead to

new variation
 Haploid breeding
Disadvantages
• Expensive process- requires tissue culture labs,
equipment, and skills.

• If cultures are kept too long, the chances of

somaclonal variation increases and these may
produce undesirable genotypes.

• If the number of haploids and double haploids

produced are limited, the ability to select superior
clones is undermined.
BACKCROSS BREEDING
 Backcross breeding
• Suggested by Harlan and Pope (1922) and extensively studied
by Briggs (1930- 1958)

• Method can be used in both self pollinated and cross

pollinated crops.

• Backcross breeding is a type of recurrent hybridization by

which a superior characteristic is added to an already
desirable variety
– Results in incremental improvement in the commercial variety
– The recurrent parent is the commercial variety
– Variety with the desired trait is the donor parent
– Last generation is selfed to make incorporated gene homozygous.
 Backcross breeding
Requirements:

• A suitable commercial variety.

• A donor plant with a major gene character of interest

• Method to identify the trait of interest

• Sufficient number of backcrosses to reconstitute the

recurrent parent
Backcross breeding
 Breeding in self pollinated crops- backcross breeding
• The number of genes in the donor plant is reduced by
half following each generation of backcrossing.

• After ‘n’ backcrosses the precise content of donor

parent genes in the progenies is (1/2)n

• For a backcross generation, m, the proportion of

homozygosity is given by:
(2m – 1)/ 2m

After 6 generations, degree of homozygosity is (26 – 1)/ 26 =

98.4%
Backcross breeding

Purple- commercial parent

(recurrent parent)

Velvet- donor parent

 Backcross breeding
Number of backcrosses depend on:
• Similarity of donor parent to the recurrent parent
– If similar, fewer backcrosses required (4-5 backcrosses)

– If dissimilar, more backcrosses required (~10 backcrosses) to

reconstitute the recurrent parent

• Pop. size and selection of recurrent parent

– With large pop., fewer backcrosses are needed to reconstitute
recurrent parent

– Chance of finding a progeny most similar to recurrent parent is

higher
 Backcross breeding
Number of backcrosses depend on:
• Extent of linkage between desirable and
undesirable genes:
– The prob. (p) of eliminating an undesirable linked gene
is given by:
P = 1 – (1 – p)m+1; p = linkage value; m = no. of
backcrosses .

Smaller p, more backcrosses are required.

Can be hastened by using marker assisted selection.

 Backcross breeding

Marker assisted selection hastens backcross breeding

 Backcross breeding
Advantages
• Incremental breeding

• High degree of genetic control over the population, unlike

selective breeding.

• Faster method than pedigree method to obtain homozygosity

– Requires 4-5 generations less!!!

• Requires smaller pop. sizes compared to pedigree method

– 50% of plants are desirable in each backcross generation
– 25% are desirable (AA = 1/4) in F2 generation.
 Backcross breeding
Advantages:
• Effective means of removing undesirable linkages or linkage drag

• The heritability of the trait is not important

– Already starting with a superior parent.
– In the end, the superior parent is reconstituted with the additional desirable
gene.

• No evaluation program is required

• Breeding can be carried out in any environment where the gene of

interest can be expressed

• Isolines of the recurrent parent can be created

– Isolines differ by only 1 gene (e.g. a resistance gene)
– Isolines can be mated to create multilines (greater environ. flexibility)
 Backcross breeding
Disadvantages:

• The superiority of the variety developed depends on the recurrent

parent
– If the recurrent parent is not the best variety, the new variety will also not
be the best variety

• Cannot exploit transgressive segregants

• Not effective for polygenic traits (controlled by more than 3 genes)

• If the desirable trait in the donor parent is recessive, an additional

selfing has to be performed after each backcross
– Lengthens the time of breeding
 Backcross breeding
• Suppose resistance is recessive (rr)

• If recurrent parent is RR (susceptible) and donor is rr

– F1 is Rr (susceptible)

– Selfing the F1 (Rr x Rr) will give 1RR: 2Rr: 1rr

– Only F1 genotype ‘rr’ will be resistant.

– Now cross resistant F1 (rr) with recurrent parent.

– Repeat the process for several generations

– At the last backcross, self the progenies and select the one with genotype, ‘rr’.
Backcross breeding

self

self