Advanced Plant Breeding PBG 650
Take-Home Final Exam, Fall 2013
Due by Friday, Dec. 13, 2013
Name
KEY
Part I Short Essay
1) Quantitative genetic theory indicates that recurrent selection should be more efficient than
pedigree selection for improving most quantitative traits.
8 pts
1a) Explain why that is so. Use a simple numeric example for the case of a trait controlled by
7 dominant genes to illustrate the principle involved.
With pedigree selection, the chances of obtaining all favorable alleles at 7 loci in a single
individual is low. Furthermore, allele fixation occurs rapidly with successive generations of
inbreeding, so selection during inbreeding is not very effective. For seven loci with p=0.5,
the chance of getting all of the favorable alleles is 1/128. Recurrent selection increases the
frequency of good alleles – it is not necessary for all of the good alleles to occur in one
individual during the selection process. If, for our example, gene frequencies were increased
to p=0.6 for all of the favorable alleles, then the chance of getting an individual with all of
those genes would be increased to 0.028 (about 1/36). Recurrent selection maintains high
levels of genetic variance in a population, which enhances opportunities for long-term gain
through selection. With continual intermating there is increased opportunity to break up
linkages and obtain novel gene combinations.
10 pts
1b) Identify a crop that is amenable to recurrent selection. If recurrent selection is commonly
applied in this crop, indicate what specific selection schemes are utilized and explain the
rationale for using those methods. If recurrent selection is not commonly used, explain
why plant breeders are reluctant to apply recurrent selection to improve this crop. (if you
need or want to do a little research to come up with an answer, please indicate your
sources. Your answer may also be based on your own expert knowledge or examples
from class.)
Answers will vary. Corn in the USA would be a good example. Corn plants can be readily
crossed and selfed, and up to 1000 kernels can be obtained from one cross, so it can be readily
improved through recurrent selection. Recurrent selection is not widely used by private sector
breeding programs in the USA, however. Nearly all of the corn acreage is planted with singlecross hybrids. Inbred lines are developed through pedigree or backcross selection, which are
evaluated as testcrosses. About 90% of the domestic crop is genetically engineered for
resistance to herbicides and/or insect pests. In this context, seed companies prefer to use a
more cautious approach, so that favorable epistatic linkages and established patterns of
heterosis among elite inbred lines are maintained. BLUP and marker assisted selection are
routinely utilized as selection tools. Recurrent selection is often utilized in international maize
breeding programs where open-pollinated varieties and hybrids are both desired.
1
2) Independent culling and index selection are two approaches for multiple trait selection.
Briefly describe these methods and compare their advantages and disadvantages.
10 pts
With independent culling, minimum levels of performance are set independently for each
trait. Genotypes that surpass those standards for all traits under selection are advanced in the
breeding program. An advantage is the ease of implementation and perhaps cost savings as
genotypes can be immediately discarded whenever a trait is evaluated. For example,
genotypes that fail to meet specified agronomic standards do not have to be evaluated for
quality characteristics after harvest. This may be a logical approach for developing pureline
cultivars, because the lines that are being screened may be advanced directly to become
potential new varieties. For cross-pollinating crops, however, varieties may be released as
populations. In this case, the genotypes themselves are transient and the frequency of
favorable alleles is of greatest importance. For index selection, a composite score is assigned
to individuals based on all of the selected traits and the weights that are assigned for each trait.
The methods that are used to assign weights can be relatively simple (a base index) or more
sophisticated (as in the Smith Hazel Index). For the Smith Hazel index, adjustments are made
for the heritabilities of traits and genetic correlations among traits. Good estimates of genetic
variances and genetic correlations are needed for this method to be effective. In theory, a
selection index will always be at least as efficient, and generally more effective, than
independent culling.
Part II Short Answer – Please show your calculations
8 pts
3) All possible single crosses among 5 inbred parents were evaluated for yield, and the averages
for each cross are shown below. Yields of the 5 inbred parents were also determined, and the
average was 7.6. Use Wright’s formula to predict the yield of a synthetic variety developed
by random mating all of the single-crosses.
Single-cross
1x2
1x3
1x4
1x5
2x3
2x4
2x5
3x4
3x5
4x5
Yield
28
35
30
39
26
39
28
56
61
63
 Y -Y 
 40.5-7.6 
μˆ synthetic =Yii' -  ii' i  =40.5- 
 =33.92
n
5




2
28 pts
4) In 2008, 219 half-sib families of meadowfoam from Cycle 5 of the OMF58 population were
evaluated in progeny trials (2 replications, one location). The best 18 families were selected
for seed yield. Remnant seed of selected half-sib families was recombined in an isolated
nursery with insect pollinators to generate Cycle 6. Cycle 5 and Cycle 6 were compared in
five trials conducted over three seasons from 2010-2012.
Results from the 2008 Trial:
Mean of all families from Cycle 5: 2215 kg/ha
Mean of 18 selected families: 2695 kg/ha
Estimate of the variance among half-sib families for seed yield σ2F =40448
Estimate of the phenotypic variance among half-sib family means σ2P =72003
Results from multiyear trials (2010-2012):
Mean of MF58 Cycle 5: 1661 kg/ha
Mean of MF58 Cycle 6: 1941 kg/ha
4a) What is the selection differential (S) for the 2008 trial?
S=XS -X 0 =2695-2215=480
4b) Estimate the narrow sense heritability from the 2008 trial results (for family means).
σ 2F 40448
h = 2=
=0.5617
σ P 72003
2
4c) Use your results from a and b above to calculate the expected response to selection.
Expected Response
R = h2S = 0.5617*480 = 269.6 kg/ha
4d) Calculate the standardized selection differential from the information provided.
i= S/P = 480/ 72003=1.79
4e) Suppose that you had no knowledge of the actual selection differential (S) for this
experiment. Use the proportion selected, a table of standardized selection differentials
and the estimates of genetic variances to predict response to selection.
Selection intensity = 18/219 = 0.082192 ≈ 8%
Standardized selection differential from table = 1.86
R=
i 14 σ 2A
σ
2
P(HS)
=
1.86*40448
72003
=280.37 kg/ha
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4f) (cont’d) Calculate the observed response to selection in kg/ha. What is the percent gain from
selection?
Observed R = 1941-1661 = 280 kg/ha
% gain = (280/1661)*100 = 16.86%
4g) Calculate the realized heritability based on the actual selection response. How does this
estimate compare with the one from the half-sib analysis (question 4b)?
h2 =
R XC6 -XC5 1941-1661 280
=
=
=
=0.583
S XS -X0 2695-2215 480
They are very similar but we actually did slightly better than expected. This supports earlier
findings indicating that GXE bias in estimating genetic variances from a single location in
one year is not a major concern for meadowfoam in the Willamette Valley. Large GXE
variance would have inflated our heritability estimate from the 2008 experiment, in which
case the observed response would have been less than predicted.
36 pts
Part III
Reading and Interpretation
Choose one of the following two articles to review for this section:
Option 1
Przystalski, M., A. Osman, E.M. Thiemt, B. Rolland, L. Ericson, H. Østergård, L. Levy, M.
Wolfe, A. Büchse, H.-P. Piepho, and P. Krajewski. 2008. Comparing the performance of
cereal varieties in organic and non-organic cropping systems in different European countries.
Euphytica 163: 417-433.
Option 2
Windhausen, V.S., S. Wagener, C. Magorokosho, D. Makumbi, B. Vivek, H.-P. Piepho, A.E.
Melchinger, and G.N. Atlin. 2012. Strategies to subdivide a target population of
environments: results from the CIMMYT-led maize hybrid testing programs in Africa. Crop
Science 52: 2143-2152.
Both of these papers report results of applied investigations of GXE and use a mixed model
approach. Environments are analogous to multiple traits that can be combined in a selection
index. The objective in both studies is to determine optimal strategies for selection across
environments. The underlying theory for both papers is presented in the article below. You do
not need to read this article to complete this exam, but it may be useful for future reference.
Peipho, H.P., and J. Mohring. 2005. Best Linear unbiased prediction of cultivar effects for
subdivided target regions. Crop Sci. 45: 1151–1159.
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Questions for Option 1 (Przystalski et al., 2008, organic vs non-organic cropping systems)
1. Which production system is of primary interest in this study, and why is it important to
quantify the genetic correlation between organic and non-organic trials?
The main purpose of the study is to determine the best methods for improving performance
in organic production systems. Genetic correlations are needed to determine whether or not
results from non-organic trials can help in selecting genotypes suitable for organic systems,
and for determining the optimum allocation of organic and non-organic testing sites for the
purposes of identifying genotypes suitable for organic systems.
2. This study analyzed data from ongoing trials in 7 European countries. Consequently,
there were some inconsistencies in trial design among the countries. Review the methods
section and indicate any issues that you think might have impacted the outcome or
interpretation of the analyses.
- Length of time that the sites had been under organic production
- Organic and non-organic plots were not always located on the same site
- Differences in fertilizer treatments
- Different criteria and objectives for choosing varieties in the trial
- Lack of common checks across testing sites
3. For index selection, what factors will determine the relative weights that are given to the
phenotypic values in organic and non-organic trials?
- Want to maximize the correlation between the index and the genotypic values of the
genotypes under organic conditions.
- Genetic variances, covariances, and numbers of trials under both systems will influence
the weights
4. Were there any notable differences between means and genetic variances in the organic
and non-organic systems? If so, give a few examples.
- Yield in the organic systems was always lower (for all countries)
- There was less lodging in organic systems, and disease infection was generally lower
- Genetic variance for yield, lodging, and protein was generally smaller in organic systems
- Genetic variance for hectoliter weight, soil coverage, brown rust and septoria was greater
in organic systems
5. In general, would you say that genetic correlations between the organic and non-organic
sites were in the low, medium, or high range?
They all look pretty high to me, and frequently correlations were estimated as >1.
-
-
The authors estimated selection response from index selection (RI), direct selection (R1),
and indirect selection (R2). Briefly discuss their findings and the conclusions that can be
drawn from the study.
Direct selection under organic systems is always outperformed by index selection, but in
most cases not by very much
Index selection was always better than indirect selection in non-organic environments
Conclude that non-organic trials can aid in selection for organic environments, but that
some amount of testing in organic environments is needed for optimal results.
5
Questions for Option 2 (Windhausen et al., 2012, Target maize hybrid environments)
1. What is meant by the TPE, broad adaptation and narrow adaptation for the purposes of
this study? Why do breeders tend to favor selection for broad adaptation?
- TPE stands for target population of environments and refers to the range of environments
for which a particular breeding program aims to develop varieties. In this case, the goal is
to develop high-yielding and stable maize hybrids for East and Southern Africa.
- Broad adaptation implies that a hybrid can be grown in diverse environments across a
wide geographic area.
- Specific adaptation would refer to selection for particular environments that are relatively
homogeneous as shown by the absence of GXE within that area.
- Selection for broad adaptation is generally more cost effective because the hybrids can be
grown on a wider scale for a given level of investment.
2. CIMMYT currently divides its breeding objectives in Africa based on two major
subregions (East and Southern Africa). What conditions would need to be met to justify
the existing and/or further subdivision of the TPE? Why is there a potential to increase
genetic variance by subdividing the TPE?
- Genotype x subregion interactions must be repeatable so that subdivision of the TPE
results in greater gains from selection.
- Genotypic correlations between subregions should be low.
- GXE variance can contribute to genetic variance within a homogenous subregion.
3. What germplasm was included in the study and what traits were analyzed?
- 448 elite maize hybrids from national programs, private seed companies, and CIMMYT,
who conducted research in 17 countries in eastern and southern Africa. The hybrids were
divided into two groups based on maturity. This study analyzed yield data from those
trials.
4.
-
What criteria were considered as possible means for subdividing the region?
Climate
Altitude
Yield level
Geographic region
Country
5. The authors used a nested model rather than the typical factorial model that is generally
used for trials conducted in multiple years and locations. Which factors were nested and
how was that justified?
- Years were nested within subregions, because a common year effect is not likely across
such a large geographic area
- Environments (year-location-trial combinations) were nested within years because this
was necessary to obtain solutions for the mixed model analysis
6. List the four approaches that were used to predict genotype means
- Direct selection based on local means from targeted subregion
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-
Indirect selection from the complementary subregion
Indirect selection using a global mean, ignoring subregion
Index selection with local means, with the subregion effect treated as fixed
7. Why is it appropriate to use broad sense heritability estimates to predict gain from
selection in this case?
- Because individual plants for each hybrid are genetically identical and can be maintained
as hybrids
8. Which subdivision was found to explain the greatest proportion of GXE? How was this
reflected in the genotypic correlation between groups for this subdivision?
- The yield level subdivision
- It was moderate, but lower than for other subdivisions (0.81 for early hybrids and 0.69 for
late maturing hybrids)
9. Summarize the recommendations that were made as the result of this study, and indicate
what evidence was used to support those conclusions.
- Estimate hybrid means by stratifying the TPE by yield level. Utilize information from
both subregions (low and high yielding trials) in a selection index, appropriately
weighted. Selection response from this strategy was at least 10% more effective than
direct selection within each yield level alone. Results should be reported separately for
low and high yielding subregions, but all information should be used to estimate the
means. The results did not support the current practice of dividing the TPE between East
and Southern Africa.
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