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SECTION 9

GENETIC BASIC FOR BREEDING

IN SELF-POLLINATED CROPS

9.1. Johannsen’s Pure line theory

Conclusions

* Seed weight was effective.

* The original landrace consisted of a
mixture of homozygous plants

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* The within-line phenotypic variation was

environmental in nature and further
selection within a pure line will not result in
further genetic change

* Johannsen’s results clarified the difference

between phenotype and genotype and gave
selection a firm scientific basis.

9.2 The genetic basic of homozygous

(Pure) lines
1. In naturally, self-pollinated species,
populations consist of a heterogeneous
mixture of homozygous (or nearly
homozygous plants (if no out crossing occurs),
each of which will be breed “true” if no cross
pollination or mutation occur.
Cultivated form of such mixtures are called a
land variety or landrace. Landraces are
endemic to an area and are often very buffered
against environmental changes.

2. Outcrossing (cross-pollination) in each

generation will increase the level of
heterozygosity in a given generation, but
this is offset by a decrease in
heterozygosity by one-half for each
generation of selfing.

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3. Basic of decrease in heterozygosity

with selfing, single locus basis:
F1 generation Aa
100%
F2 AA Aa aa
25% 50% 25%
F3 AA Aa aa
25% + 12.5% = 37.5% 25% 37.5%
F4 AA Aa aa
43.75% 12.5% 43.75%
F5 AA Aa aa
46.875% 6.25% 46. 875%
F6 AA Aa aa
48.438% 3.125% 48.438%
F7 AA Aa aa
49.22% 1.56% 49.22%
F8 AA Aa aa
49.61% 0.78% 49.61%
F8+ AA Aa aa
~50% ~0 ~50%

4. Basis of decrease in heterozygosity with

selfing, n loci basis:
•
If assume n = the number of heterozygous,
unlinked gene pairs (i.e. segregating loci), m =
generation of self-fertilization (or backcross to a
homozygote), and equal survival of of genotype,
then:
Proportion of homozygosity in a population = (2m – 1)/2m.
 In other words, all heterozygous loci approach homozygosity
at the same rate regardless of the number of loci (notice n is
not in the formula!).

Proportion of completely homozygous plants in the total

population after m generations = [(2m – 1)/2m]n.

5. Strict self-pollination rapidly reduce any

population to a heterogeneous mixture of
homozygous lines.

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9.3 Source of Genetic Variation in

homozygous Lines
1. Gene mutations
• Homozygous line do not remain homozygous
indefinitely even when strictly selfing pollinated due
to mutation continuously arising.
• Frequency of mutation is different from different
genes and different alleles of a gene, but usually on
the order of 10-5 to 10-7. Most mutations are
recessive and deleterious. But some are useful in
breeding.
• Even low mutation rates can account for a
proportion of variability in crop plants, since
mutations occurs over time (generations) and over
many loci.

2. Hybridization/Recombination
• Cross-pollination among genetically different
individuals of a self-pollinated species (within
and/or between populations) provides
opportunities for recombination in the progeny of
each crosses. Recombinant progenies may be
superior to any existing individuals in a population.
• Hybridization is used extensively in breeding self-
pollinated (or cross-pollinated) crops to generate
new genotypic combination from which to select.

9.4. Hybridizations and Gene Combinations

• The main concerns to a breeder in utilizing

hybridizations in breeding self-pollinated
crops are:
• The type of and extent of variation in the
F2, the first segregation generation.
• The progress of hybrid population towards
complete homozygosity.
• The type of successful combination.

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• Factors affect the number of gene

combinations obtained through hybridization.
• Number of genes differentiating the parents.
• Degree of linkage of genes on the same of
chromosome.
• The number of alleles of gene (at each locus).

• The F2 generation has the maximum number of

different genotypes (gene combination).
• Illustration (Allard, Table 1):
Cross two pure lines to obtain the F1, selfing and
obtaining the F2.
Observe the F2 for segregation of n heterozygous
gene pairs (loci).
How many plants need to observe to see all
genetic variability in the F2 generation.

Table 1

Heterozygous Different Different Total Kinds of F2 Phenotypes,

loci gametes in genotypes in genotypes assuming
F1 F2 possible in F2
Full No
Dominance epistasis,
No
dominance
n 2n 3n 4n 2n 3n
1 2 3 4 2 3
2 4 9 16 4 9
3 8 27 64 8 27
4 16 81 256 16 81
10 1024 59049 1084576
21 2097152 10460353203 4398046511104
50 1015 1023 1030

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a) As n (loci) increases the number of genotypes

possible in the F2 increases exponentially. With
larger n, it is impossible to observe all the F2
genotypes, thus we must take a random sample
of F2 population to properly sample such
variation. A big problem for breeder: evaluating
the large genotypes and phenotypes occurring in
segregation generations. Random sampling of the
variation and efficient screening is of utmost
important.

b) Linkage between loci acts to decrease the

frequency of new gene combinations and favors
parent genotypes.
E.g. If there is a negative linkage between genes
for traits of interest, in order to identify a
favorable recombinant that has broken this
linkage, need to observe a large number of F2
plants to find the desired recombination.

c) The tighter the linkage between genes are, the

lower the frequency of recombination, thus the
rarer the frequency of recombinants in the F2
population.
As the recombination value in column 1 decrease
from 0,5 (no linkage) to 0,01 (tight linkage), the
percent of recombinant F2 individuals decreases.

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4. The genetic composition of any

inbred generation for the F2 or later
generation:

a. Proportion of completely homozygous

plants in the total population after m
segregating generations =
n
(2m  1) / 2m 

b. The proportion of homozygous genotype

is of major interest to the breeder since
these serve as the basic of new varieties
in self-pollinated crops.

The proportion of homozygous genotype is of major

interest to the breeder since these serve as the basic
of new varieties in self-pollinated crops.

 You can obtain more detail about content of

genotype in each generation by binomial
formula:
[1+ (2m – 1)]n.
Where n = the number of heterozygous, unlinked gene pairs
(i.e. segregating loci), and m = #generations of self-
fertilization (after the F1).
 This binomial is expanded to find the value of
all the terms. Recall from algebra that to obtain
the binomial coefficients:

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The coefficients can be obtained using Pascal triangle:

n 1

1 1 1

2 1 2 1

3 1 3 3 1

4 1 4 6 4 1

5 1 5 10 10 5 1

6 1 6 15 20 15 6 1

7 1 7 21 35 35 21 7 1

 Selfing is very powerful in producing

mostly homozygotes in relatively few
generations. Selection for desirable
homozygous genotypes is easier in later
selfing generations of hybrid populations
of self-pollinated crops because there
will be fewer heterozygotes as the
number of selfing generation increases.