1. Planning rice breeding programs for impact
Choosing parents and
managing a pedigree breeding program

2. IRRI: Planning breeding Programs for Impact
Learning objectives
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

3. 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
What is important according to the participants when choosing parents?
IRRI: Planning breeding Programs for Impact

4. IRRI: Planning breeding Programs for Impact
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
IRRI: Planning breeding Programs for Impact

5. IRRI: Planning breeding Programs for Impact
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)
IRRI: Planning breeding Programs for Impact

6. Backcrossing with selection to improve IR64 for drought
% recurrent parent
Plants crossed
Selection
IR64 x donor
F1 x IR64 50
1-5 crossed
None
20 crossed
None
BC1F1 x IR64 75
BC2F1 x IR64
20 crossed
None
87.5 X
20 selfed
None
87.5
BC2F2 X
BC2F3
87.5
2000 selfed
Screened under severe stress
IRRI: Planning breeding Programs for Impact

7. 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
Question to the group
IRRI: Planning breeding Programs for Impact

8. IRRI: Planning breeding Programs for Impact
Describing crosses
Parents are separate by slashes (“/”):
e.g. IR 64/Swarna
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)
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
IRRI: Planning breeding Programs for Impact

9. IRRI: Planning breeding Programs for Impact
Describing lines
Each cross should receive a unique, consecutive number
e.g. The IRRI cross IR /Way Rarem is:
IR74371
(This number can be thought of as referring to the F1.)
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: IR
IRRI: Planning breeding Programs for Impact

10. IRRI: Planning breeding Programs for Impact
Describing lines
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
IRRI: Planning breeding Programs for Impact

11. IRRI: Planning breeding Programs for Impact
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:
Exercise
What proportion of loci that were heterozygous in the F1 are homozygous in the F5 ?
1 – (0.5)n-1
6.25%
IRRI: Planning breeding Programs for Impact

12. 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.

13. 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

14. 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
Group discussion
IRRI: Planning breeding Programs for Impact

15. How many generations should pedigree selection continue?
2 factors to consider:
Phenotypic (visible) uniformity
If the line is not visibly uniform, it needs reselection
Genetic heterogeneity remaining within the line.
Genetic heterogeneity (variability) is the “fuel” of selection
Selecting among genetically homogeneous plants is pointless
IRRI: Planning breeding Programs for Impact

16. 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 F4 F5 F6 F7 F8 25
12.5
6.25
3.13
1.56
0.78
IRRI: Planning breeding Programs for Impact

17. 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)
DTF= Days to flowering
IRRI: Planning breeding Programs for Impact

18. Selection based on family means
Conventional arrangement
Range 1 IR IR IR IR IR IR
Range 2 IR IR IR IR IR IR
Range 3 IR IR IR IR IR IR
IRRI: Planning breeding Programs for Impact

19. Selection based on family means
Blocking by families
Block 1 IR IR IR IR IR IR
Block 2 IR IR IR IR IR IR
(randomize)
Block 3 IR IR IR IR IR IR
(randomize)
Irri’s system; this allows more field variability
IRRI: Planning breeding Programs for Impact

20. Any questions or comments?
IRRI: Planning breeding Programs for Impact

21. 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
IRRI: Planning breeding Programs for Impact

22. IRRI: Planning breeding Programs for Impact
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
IRRI: Planning breeding Programs for Impact