Planning rice breeding programs
for impact
Choosing parents and
managing a pedigree breeding program
Learning objectives
1.
2.
3.
4.
5.
6.
7.
8.
Strategies for choosing parents
Types of crosses
F2 population size
Describing lines and crosses
Pedigree versus bulk selection
Traits for early-generation selection
How many generations?
Field design for pedigree nurseries
IRRI: Planning breeding Programs for Impact
Question:
What is important when
choosing parents?
• At least 1 adapted parent should be used
• Improved donors should be used to avoid linkage
drag
• “Pre-breeding” of improved donors is important
• MAS allows major gene to be moved with less
linkage drag
• At least 1 high-quality parent should be used
• Backcross to high-quality parent may be necessary
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Types of crosses
• 2-way, 3-way (“topcrosses”), and double crosses can
be used if lines are of similar performance or quality,
but break up adapted linkage blocks and epistatic
combinations
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Types of crosses
Backcross populations
When use them?
if the objective is to improve one adapted parent
with genes from a donor
(BC1 and BC2 populations have proven very useful
in developing lines with improved drought stress
tolerance in IR64 background at IRRI)
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Backcrossing with selection
to improve IR64 for drought
Cross
IR64 x donor
% recurrent parent
Plants
crossed
Selection
F1 x IR64
50
1-5 crossed
None
BC1F1 x IR64
75
20 crossed
None
BC2F1 x IR64
87.5
20 crossed
None
87.5
20 selfed
None
87.5
2000 selfed
X
BC2F2
X
BC2F3
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Screened
under severe
stress
Question:
How many crosses
should one make?
• Most programs make too many crosses, examine
populations that are too small
• Choosing parents carefully is more important than
making many crosses.
• Some programs make very few crosses with diverse
parents
E.g. Witcombe and collaborators in India and Nepal:
– Crossed Kalinga III/IR64
– Farmers selected both upland- and lowland-adapted
cultivars from the cross
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Describing crosses
1. Parents are separate by slashes (“/”):
e.g. IR 64/Swarna
2. In complex pedigrees, additional slashes are used to
describe more recent crosses.
e.g. IR64/Swarna//PSBRC 80 (PSBRC 80 was crossed to
plants derived from IR64/Swarna)
3. Backcrosses are denoted by a number indicating
number of doses of recurrent parent, followed by an
asterisk or ‘x’.
e.g. if Kalinga III is crossed to IR64 and then the F1 is
backcrossed to IR 64, the cross is described as:
Kalinga III/2*IR 64
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Describing lines
1. Each cross should receive a unique, consecutive
number
e.g. The IRRI cross IR55419-04/Way Rarem is:
IR74371
(This number can be thought of as referring to the F1.)
2. Individual plants selected from segregating generations
(F2 onward for a single cross) are given a unique plant
number. Lines derived from these plants are identified
by the plant number:
e.g. The line derived from the 24th F2 plant
selected from IR74371 is: IR74371-24.
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Describing lines
3. If a generation is harvested in bulk, without single plant
selection, the resulting population is denoted “B”.
e.g. If the F2 of IR74371 is harvested in bulk, without selection, it is
denoted IR74371-B
IR74371-B-7 denotes the 7th F3 plant selected from a bulk F2
Exercise
Describe the selection history of
line IR74371-B-5-6-B-B-43
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Homozygosity of a line
For a line in F generation n, the proportion of loci that
are homozygous, relative to the number of
heterozygous loci in the F1, is:
1 – (0.5)n-1
Exercise
 What proportion of loci that were heterozygous in
the F1 are homozygous in the F5 ?
6.25%
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Homogeneity of a line
• Homogeneity means sameness or uniformity
• Lines derived from homozygous plants are homogeneous
• Lines derived from heterozygous plants are segregating
and non-uniform
• The degree of genetic uniformity of a line is determined by
the level of homozygosity of the plant from which it was
derived
e.g. A single plant selected from an F3 bulk has a homozygosity
level of 1-(.5)2 = 0.75, relative to the F1. A line derived from this
plant by selfing is fixed at 75% of the loci that were heterozygous in
the F1.
Homogeneity of a line
Lines in the same inbreeding generations can have
very different levels of homogeneity!
Example: consider 2 lines in the F6. One derived from a single F3
plant, the other from an F5 plant.
•In the F3 plant, 75% of loci are homozygous
•In the F5 plant, 93.75% of loci are homozygous
 An F3 –derived F6 line is therefore more homogeneous than an F5
derived F6 line, although the plants in each are equally homozygous.
For the example above:
The F3 –derived line in the F6 is denoted as: F3,6
The F5 –derived line in the F6 is denoted as: F 5,6
What is your opinion on:
Pedigree versus bulk selection
• Advancing in bulk to F3 is almost always more
efficient than pure pedigree selection
• Even using bulk method, mild selection for plant type,
grain shape can be applied
• About 2000 plants should be carried per generation
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How many generations should
pedigree selection continue?
2 factors to consider:
1. Phenotypic (visible) uniformity
If the line is not visibly uniform, it needs reselection
2. Genetic heterogeneity remaining within the line.
Genetic heterogeneity (variability) is the “fuel” of selection
Selecting among genetically homogeneous plants is pointless
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Exercise
Construct a table for lines established from the F3
through the F8 generation, indicating the proportion of
segregating loci expected within the line.
Generation
Proportion of
segregating loci
F3
25
F4
12.5
F5
6.25
F6
3.13
F7
1.56
F8
0.78
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Controlling field variability
in pedigree nurseries
• Field variability can have a big impact on even highly
heritable traits like height, DTF etc.
• Use repeated checks, but not too many
• Select among nearby lines (gridding)
• Treat groups of advanced sister lines as replicates of
a family; select on the basis of family means rather
than individual line performance (or select the best
lines from the best families)
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Selection based on
family means
Conventional arrangement
Range 1
Range 2
Range 3
IR70000-1-1-1
IR70002-3-1-1
IR70007-6-4-1
IR70000-1-1-2
IR70002-3-1-2
IR70007-6-4-2
IR70000-1-1-3
IR70002-3-1-3
IR70007-6-4-3
IR70000-2-14-1
IR70005-5-7-1
IR70010-3-8-1
IR70000-2-14-2
IR70005-5-7-2
IR70010-3-8-2
IR70000-2-14-3
IR70005-5-7-3
IR70010-3-8-3
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Selection based on
family means
Blocking by families
Block 1
Block 2
Block 3
IR70000-1-1-1
IR70000-1-1-2
IR70000-1-1-3
IR70000-2-14-1
IR70000-2-14-2
IR70000-2-14-3
IR70002-3-2-1
IR70002-3-2-2
IR70002-3-2-3
IR70005-5-7-1
IR70005-5-7-2
IR70005-5-7-3
IR70007-6-4-1
IR70007-6-4-2
IR70007-6-4-3
IR70010-3-8-1
IR70010-3-8-2
IR70010-3-8-3
(randomize)
(randomize)
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Any questions or comments?
IRRI: Planning breeding Programs for Impact
Summary 1
• Most successful crosses have at least 1 high-quality,
adapted parent that is preferred by farmers in the
TPE
• BC1- or BC2-derived populations may be efficient for
generating high-quality, high-yield lines because they
leave adapted gene blocks in the elite recurrent
parents intact
• At least 2000 plants should be screened in the F2
• A standard pedigree description system should be
used
• Bulk inbreeding in the F2 and F3 generations is used
by some breeders to inexpensively produce uniform
lines
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Summary 2
• Pedigree selection should focus only on highly
heritable, easily-scored traits (unless family selection
is used.)
• There is little genetic variability among F6 sister lines
derived from the same F5 plant
• Regularly occurring checks should be included in
pedigree nurseries, but their frequency should not
exceed 10% of the total number of plots
• Selection among families of closely-related lines can
be used in advanced pedigree generations.
Individual lines in a family can be treated as
replicates, and planted in different blocks to
overcome the effect of field variability
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