12th National Convention on Statistics (NCS)

EDSA Shangri-La Hotel, Mandaluyong City

October 1-2, 2013

PLANT BREEDING TOOLS: SOFTWARE FOR PLANT BREEDERS

by
Nellwyn Sales, Violeta Bartolome, Alexander Caeda,
Alaine Gulles, Rose Imee Zhella Morantte, Leilani Nora,
Angel Manica Raquel, Christoffer Edd Relente,
Darwin Talay and Guoyou Ye

For additional information, please contact:

Authors name:
Designation:
Affiliation:
Address:
Tel. no.:
E-mail:

Nellwyn Sales
Specialist
International Rice Research Institute
College, Los Baos, Laguna
5362701 loc 2238
n.sales@irri.org

Co-authors name

Violeta Bartolome, Alexander Caeda, Alaine Gulles, Rose Imee

Zhella Morantte, Leilani Nora, Angel Manica Raquel, Christoffer
Edd Relente, Darwin Talay and Guoyou
Senior Associate Scientist - Biometrics, Senior Specialist Software Engineering, Assistant Scientist, Specialist, Assistant
Scientist, Programmer, Programmer, Programmer and Senior
Scientist - Breeding Informatics Specialist
International Rice Research Institute
College, Los Baos, Laguna
5362701 loc 2238
v.bartolome@irri.org, a.caneda@irri.org, a.gulles@irri.org,
r.morantte@irri.org, l.nora@irri.org, a.raquel@irri.org,
c.relente@irri.org, d.talay@irri.org and g.ye@irri.org

Designation:

Affiliation:
Address:
Tel. no.:
E-mail:

PBTools: Software for Plant Breeders

Nellwyn Sales, Violeta Bartolome, Alexander Caeda, Darwin Talay, Alaine Gulles,
Rose Imee Zhella Morantte, Leilani Nora, Angel Manica Raquel,
Christoffer Edd Relente and Guoyou Ye
Abstract
Data from plant breeding trials need to be analyzed properly, with greater speed
to support selection decision making. Genetic information should also be derived from
breeding trials to determine more efficient breeding strategies. Although general
statistical software can be used to analyze breeding trials, many practical breeders are
seeking easy-to-use analytical tools.
PBTools is a free statistical application developed primarily for plant breeders. It
was created using the Eclipse Rich Client Platform (RCP) and R language. It has a userfriendly graphical user interface (GUI). Its current version provides modules for the
following: data management in spreadsheet view, randomization for commonly used
experimental designs, single- and multiple-environment analysis, QTL analysis, selection
index, commonly used mating designs, and generation mean analysis, some of which
are presented in the paper.
Keywords: statistical software, plant breeding
Introduction
Plant breeding research generally involves use of statistical techniques to
determine valid conclusions which aid in selection decision making. Users depend on
statistical software to generate reliable results quickly. However, most software are
developed for general statistical analysis only and are costly. Some are freeware but
have limited functionality or are difficult to use.
R is a language and an environment for statistical computing and graphics. Many
classical and modern statistical methods have been well implemented in R, mainly
through hundreds of add-on packages contributed by leading statisticians. New add-on
packages can be rapidly developed by exploring the functions of existing packages. R
has become increasingly popular. However, some users find its command line interface
challenging. Software with a GUI involving menus, dialog boxes, and spreadsheets is
generally more preferred.
Plant Breeding Tools (PBTools) is a free statistical application created using the
Eclipse Rich Client Platform (RCP), a platform for building and deploying rich client
applications, and R language. It has been developed to assist plant breeders in the
design and analysis of data. It has an easy to navigate GUI that does not require users
to have programming skills to perform data manipulation and analysis.
Its current version provides modules for data management in spreadsheet view,
randomization for commonly used experimental designs, single- and multipleenvironment analysis, QTL analysis, selection index, commonly used mating designs,
and generation mean analysis.

An introduction of the features of PBTools is provided in this paper.

PBTools Environment
Main Window
The PBTools main window (Figure 1) has a menu bar which houses five items:
Project, Data, Analysis, Randomization, and Help. The Project menu contains functions
for creating and managing projects. The Data menu contains functions for reading,
managing and manipulating datasets. The Analysis Menu contains functions to perform
statistical analysis. The Randomization Menu contains functions for generating random
assignment of factor levels for commonly used experimental designs in plant breeding.
Finally, the Help Menu is used to access PBTools users manual and some information
about the software.

Figure 1. PBTools Main Window.

Figure 2 presents the submenu items under the Data, Analysis, and
Randomization menus.

Figure 2. Submenu items for the Data, Analysis, and Randomization menus.
The PBTools main window is divided into two panels: the Project Explorer panel
and the Editor panel. The Project Explorer panel functions as a file manager of the active
project, where names of data files and analysis results files are displayed in tree form,
while the Editor panel serves as viewer for selected data (by means of the Data Viewer
tab) and/or results of analysis (via the Results Viewer tab).
When the name of a data file is selected by double-clicking in the Project
Explorer tree, the file is displayed in a Data Viewer tab in spreadsheet form in the Editor
panel (Figure 3). Data values can be edited in the Data Viewer. Data manipulation can
also be performed here using options available in a toolbar or the submenu items under
the Data menu.

Figure 3. Data Viewer Tab in the Editor Panel of PBTools.

When an analysis is performed or the filename of an output file is selected under
the Output folder in the Project Explorer tree, the results are displayed in a Results
Viewer tab (Figure 4). Depending on the contents of the results folder, the Results
Viewer may have an Output page and/or Graph page.

Figure 4. Results Viewer (Output and Graph Tabs) in the Editor Panel of PBTools.

Handling Data
PBTools uses comma-separated values (csv) format for data files. Data files are
created outside of PBTools and imported into the Data folder of the active project. Data
files (.rda or .txt) may also be imported into PBTools but they will be automatically
converted into .csv format. To represent missing observations, the user can use NA,
period, blank or space.
A selected file is displayed in a Data Viewer tab in the Editor panel. Several Data
Viewers can be seen simultaneously inside the Editor Panel.
Data values can be edited in the Data Viewer. Data manipulation can also be
performed using options available in a toolbar in the Data Viewer (Figure 5) or the
submenu items under the Data menu. These options are: inserting row(s)/column(s)
from the data, deleting row(s)/column(s) from the data, creating a new variable, editing
variable information, sorting, aggregating, reshaping, merging, and appending data sets
and creating data subset.

Figure 5. Toolbar for Data Manipulation in the Data Viewer Tab.

Randomization for Some Experimental Designs

The Randomization menu allows users to generate randomization of treatments
for single- and multi-factor designs. Randomization in PBTools is currently available for
the following designs: randomized complete block (RCB), lattice, alpha-lattice,
augmented Latin square, and augmented RCB design. Depending on the design, the
user needs to provide information on a dialog box (Figure 6).

Figure 6. Sample Dialog Box for Generating Randomization

and Layout.
A field book in csv format is created (Figure 7) and the layout (saved in a text file)
is displayed in the Data Viewer (Figure 8).

Figure 7. Sample Field Book after the Randomization.

Figure 8. Sample Layout after the Randomization.

Analysis
Prior to doing analysis in PBTools, a data set must first be selected and opened
in the Data Viewer. When the needed data set is active, the desired submenu option can
be selected from the Analysis menu.

Single-environment analysis
Analyses using mixed models for the following designs are available in PBTools:
Randomized Complete Block (RCB), Augmented RCB, Augmented Latin Square, AlphaLattice and Row-Column. The user should specify in the dialog box some required
information and preferred output or graphs to be generated. If the Environment field is
specified, the analysis will be done per environment level. Otherwise, the data will be
treated as if it came from one environment. The user also has the option to regard
genotype as fixed or random factor while the remaining terms in the model are regarded
as random. As illustration, Figures 9 to 11 show the filled-up tabs for a sample analysis
in RCB.

Figure 9. Model Specifications Tab of Single-Environment

Analysis Dialog Box.

Figure 10. Options Tab of Single-Environment Analysis Dialog Box.

Figure 11. Graph Tab of Single-Environment Analysis Dialog Box.

After providing necessary information and desired options in the dialog box, the
text and graph outputs will be displayed separately in tabs in the Editor panel. Additional
csv files containing the computed residuals and summary statistics (if genotype is fixed)
or predicted means (if genotype is random) are saved inside the results folder. These
generated files can be accessed through the Project Explorer.
Figure 12 shows the sample partial text output of the single-environment
analysis. If genotype is regarded as fixed, the output of the analysis includes the
following: some descriptive statistics of the response variable per environment level;
data summary; estimates of the variance components of the model; test for the
significance of genotypic effect wherein the denominator degrees of freedom in F test is
computed according to a general Satterthwaite approximation; least-square means of
the genotypes; summary statistics of the standard errors of the difference; and, pairwise
mean comparison using Dunnett's procedure if comparing treatments with a control and
HSD if performing all pairwise mean comparisons. If genotype is regarded as random,
the output of the analysis includes the following: some descriptive statistics of the
response variable per environment level; data summary; estimates of the variance
components of the model; test for the significance of genotypic effect using -2
loglikelihood ratio test; test for the significance of the check/control effect, predicted
genotype means derived using the Best Linear Unbiased Prediction (BLUP); leastsquare means of the checks (if checks/controls are specified); and, estimate of
heritability. Genotypic and phenotypic correlation can be performed if two or more
response variables are specified.
DATA FILE: E:/NSALES/pbtools workspace/testing/Data/2013DS_IRvarieties.csv
SINGLE-ENVIRONMENT ANALYSIS
DESIGN: Randomized Complete Block (RCB)
==============================
GENOTYPE AS: Fixed
==============================
-----------------------------RESPONSE VARIABLE: YIELD
-----------------------------DESCRIPTIVE STATISTICS:
1
2

Variable ENV N_NonMissObs

Mean
StdDev
YIELD
1
100 4349.44 781.2752
YIELD
2
100 4338.00 791.9981

-----------------------------ANALYSIS FOR: ENV = 1

-----------------------------DATA SUMMARY:
Number of observations read:
Number of observations used:
Factors
ENTRY
REP

Number of Levels
50
2

100
100
Levels
IR36 IR64
1 2

IR72 ... IRRI168

VARIANCE COMPONENTS TABLE:

Groups
Variance Std.Dev.
1
REP
3029.013 55.03647
2 Residual 239417.453 489.30303
TESTING FOR THE SIGNIFICANCE OF GENOTYPIC EFFECT:
Analysis of Variance Table with Satterthwaite Denominator Df
Df
Sum Sq Mean Sq F value Denom Pr(>F)
ENTRY 49 48306379 985844.5 4.1177
49 0.0000
GENOTYPE LSMEANS AND STANDARD ERRORS:
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44

ENTRY
IR36
IR64
IR72
IRRI102
IRRI103
IRRI104
IRRI105
IRRI106
IRRI108
IRRI109
IRRI112
IRRI113
IRRI115
IRRI116
IRRI117
IRRI118
IRRI119
IRRI120
IRRI122
IRRI123
IRRI124
IRRI125
IRRI127
IRRI128
IRRI133
IRRI134
IRRI135
IRRI136
IRRI139
IRRI140
IRRI141
IRRI143
IRRI145
IRRI146
IRRI147
IRRI148
IRRI149
IRRI150
IRRI151
IRRI152
IRRI154
IRRI155
IRRI156
IRRI157

LSMean StdErrMean
3247.5
348.1689
4461.0
348.1689
3603.5
348.1689
4109.5
348.1689
3826.5
348.1689
4336.5
348.1689
4193.0
348.1689
4091.5
348.1689
4470.5
348.1689
4697.5
348.1689
4443.0
348.1689
4807.5
348.1689
4262.5
348.1689
5218.0
348.1689
4571.5
348.1689
5056.5
348.1689
5530.5
348.1689
5016.5
348.1689
4779.5
348.1689
5193.5
348.1689
3657.0
348.1689
3229.0
348.1689
3313.0
348.1689
2962.5
348.1689
3386.5
348.1689
3765.5
348.1689
4742.0
348.1689
4650.5
348.1689
3468.0
348.1689
4172.5
348.1689
5002.0
348.1689
4403.0
348.1689
3907.0
348.1689
5871.5
348.1689
4368.5
348.1689
4315.0
348.1689
4400.0
348.1689
5076.5
348.1689
4041.0
348.1689
3323.0
348.1689
5120.0
348.1689
3490.0
348.1689
5182.0
348.1689
3134.0
348.1689

10

45
46
47
48
49
50

IRRI161
IRRI162
IRRI163
IRRI164
IRRI165
IRRI168

4840.0
4863.5
4328.5
4943.0
4058.5
5542.5

348.1689
348.1689
348.1689
348.1689
348.1689
348.1689

STANDARD ERROR OF THE DIFFERENCE (SED):

Minimum
Average
Maximum

Estimate
489.3030
489.3030
489.3030

SIGNIFICANT PAIRWISE COMPARISONS (IF ANY):

Compared with control(s)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22

Trmt[i] Trmt[j] Difference

Lower
Upper
IRRI113
IR36
1560.0
29.371879 3090.628
IRRI116
IR36
1970.5 439.871879 3501.128
IRRI118
IR36
1809.0 278.371879 3339.628
IRRI119
IR36
2283.0 752.371879 3813.628
IRRI120
IR36
1769.0 238.371879 3299.628
IRRI122
IR36
1532.0
1.371879 3062.628
IRRI123
IR36
1946.0 415.371879 3476.628
IRRI141
IR36
1754.5 223.871879 3285.128
IRRI146
IR36
2624.0 1093.371879 4154.628
IRRI150
IR36
1829.0 298.371879 3359.628
IRRI154
IR36
1872.5 341.871879 3403.128
IRRI156
IR36
1934.5 403.871879 3465.128
IRRI161
IR36
1592.5
61.871879 3123.128
IRRI162
IR36
1616.0
85.371879 3146.628
IRRI164
IR36
1695.5 164.871879 3226.128
IRRI168
IR36
2295.0 764.371879 3825.628
IRRI116
IR72
1614.5
82.445583 3146.554
IRRI119
IR72
1927.0 394.945583 3459.054
IRRI123
IR72
1590.0
57.945583 3122.054
IRRI146
IR72
2268.0 735.945583 3800.054
IRRI156
IR72
1578.5
46.445583 3110.554
IRRI168
IR72
1939.0 406.945583 3471.054

==============================
GENOTYPE AS: Random
==============================
-----------------------------RESPONSE VARIABLE: YIELD
-----------------------------DESCRIPTIVE STATISTICS:
1
2

Variable ENV N_NonMissObs

Mean
StdDev
YIELD
1
100 4349.44 781.2752
YIELD
2
100 4338.00 791.9981

-----------------------------ANALYSIS FOR: ENV = 1

------------------------------

11

DATA SUMMARY:
Number of observations read:
Number of observations used:
Factors
ENTRY
REP

Number of Levels
50
2

100
100
Levels
IR36 IR64
1 2

IR72 ... IRRI168

VARIANCE COMPONENTS TABLE:

Groups
Variance Std.Dev.
1 Test:Check 365200.468 604.31818
2
REP
3029.351 55.03954
3
Residual 239417.912 489.30350
TESTING FOR THE SIGNIFICANCE OF GENOTYPIC EFFECT USING -2 LOGLIKELIHOOD RATIO
TEST:
Formula for Model1:
Formula for Model2:

YIELD ~ 1 + Check + (1|REP) + (1|Test:Check)

YIELD ~ 1 + Check + (1|REP)

AIC
BIC
logLik
Chisq Df Pr(>Chisq)
Model2 1566.855 1582.486 -777.4273
Model1 1546.951 1565.187 -766.4756 21.9034 1
0.0000
TESTING FOR THE SIGNIFICANCE OF CHECK EFFECT:
Analysis of Variance Table with Satterthwaite Denominator Df
Df
Sum Sq Mean Sq F value
Denom Pr(>F)
Check 3 912075.5 304025.2 1.2699 45.9965 0.2958
PREDICTED MEANS:
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24

ENTRY
IRRI102
IRRI103
IRRI104
IRRI105
IRRI106
IRRI108
IRRI109
IRRI112
IRRI113
IRRI115
IRRI116
IRRI117
IRRI118
IRRI119
IRRI120
IRRI122
IRRI123
IRRI124
IRRI125
IRRI127
IRRI128
IRRI133
IRRI134
IRRI135

Means
4177.854
3964.718
4348.815
4240.740
4164.297
4449.734
4620.695
4429.023
4703.539
4293.083
5012.700
4525.800
4891.069
5248.053
4860.944
4682.452
4994.248
3837.062
3514.722
3577.985
3314.012
3633.340
3918.777
4654.209

12

25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47

IRRI136
IRRI139
IRRI140
IRRI141
IRRI143
IRRI145
IRRI146
IRRI147
IRRI148
IRRI149
IRRI150
IRRI151
IRRI152
IRRI154
IRRI155
IRRI156
IRRI157
IRRI161
IRRI162
IRRI163
IRRI164
IRRI165
IRRI168

4585.298
3694.720
4225.301
4850.023
4398.898
4025.345
5504.871
4372.915
4332.622
4396.638
4906.132
4126.264
3585.516
4938.893
3711.289
4985.587
3443.174
4728.016
4745.715
4342.789
4805.589
4139.444
5257.091

CHECK/CONTROL LSMEANS:
1
2
3

ENTRY
IR36
IR64
IR72

LSMean StdErrMean
3247.5
697.4388
4461.0
697.4388
3603.5
697.4388

HERITABILITY:
0.75
==============================
GENOTYPIC CORRELATIONS:
Site:

1
YIELD

PLTHGT
YIELD
0.4687
PLTHGT 0.4687

PHENOTYPIC CORRELATIONS:
Site:

1
YIELD

PLTHGT
YIELD
0.4342
PLTHGT 0.4342
==============================

Figure 12. Sample Partial Text Output of the Single-environment Analysis.

Generated graphs can be viewed by clicking the Graph Tab of the displayed
results folder. Sample generated graphs are shown in Figure 13. The distribution of the

13

values of the response variable can be assessed by looking at the boxplot and
histogram while for the distribution of the residuals, diagnostic plots and heatmap are
available.

Figure 13. Sample graph outputs for Single-Environment Analysis.

14

Multi-environment analysis
For experiments done in multiple environments, analysis can be done across
environments. Two options are available for multi-environment analysis: one-stage and
two-stage. One-stage analysis requires raw data while two-stage analysis requires
summary data generated from single environment analysis as input. In this paper, only
one-stage analysis is presented.
One-stage analysis is available for RCB, Alpha-Lattice and Row-Column
designs. Sample filled-up tabs for RCB are shown in Figures 14 to 16.

Figure 14. Model Specifications Tab of Multi-Environment Analysis

(One-Stage) Dialog Box.

15

Figure 15. Options Tab of Multi-Environment Analysis (One-Stage)

Dialog Box.

Figure 16. Graph Tab of Multi-Environment Analysis (One-Stage) Dialog Box.

16

After processing the analysis, a text output is displayed in the Editor panel.
Figure 17 shows the sample partial result of the analysis. If genotype is regarded as
fixed, the output of the analysis includes the following: data summary; some descriptive
statistics of the response variable; estimates of the variance components of the model;
test for the significance of genotypic effect wherein the denominator degrees of freedom
in F test is computed according to a general Satterthwaite approximation; test for the
significance of environment and genotypic environment effects using -2 loglikelihood
ratio test; genotypic environment means; least-square means of the genotypes;
summary statistics of the standard errors of the difference; pairwise mean comparison
using Dunnett's procedure if comparing treatments with a control and HSD if performing
all pairwise mean comparisons; stability analysis using Finlay-Wilkinson model and
Shuklas model; and, additive main effects and multiplicative interaction (AMMI) analysis.
If genotype is regarded as random, the output of the analysis includes the following: data
summary; some descriptive statistics of the response variable; estimates of the variance
components of the model; test for the significance of genotypic, environment and
genotypic environment effects using -2 loglikelihood ratio test; genotypic
environment means; predicted genotype means derived using the Best Linear Unbiased
Prediction (BLUP); and, estimate of heritability.
DATA FILE: E:/NSALES/pbtools workspace/testing/Data/RCB_ME.csv
MULTI-ENVIRONMENT ANALYSIS (ONE-STAGE)
DESIGN: Randomized Complete Block (RCB)
==============================
GENOTYPE AS: Fixed
==============================
-----------------------------RESPONSE VARIABLE: Yield
-----------------------------DATA SUMMARY:
Number of observations read:
Number of observations used:
Factors
Env
Genotype
Block

Number of Levels
11
15
3

495
495
Levels
E1 E10 E11 ... E9
GEN1 GEN10 GEN11 ... GEN9
1 2 3

DESCRIPTIVE STATISTICS:
1

Variable N_NonMissObs
Mean
StdDev
Yield
495 1718.596 1117.791

VARIANCE COMPONENTS TABLE:

Groups
Variance Std.Dev.
1 Genotype:Env 664747.696 815.32061
2
Block:Env
6497.161 80.60497
3
Env 530979.863 728.68365
4
Residual 94709.288 307.74874

17

TESTING FOR THE SIGNIFICANCE OF GENOTYPIC EFFECT:

Analysis of Variance Table with Satterthwaite Denominator Df
Df Sum Sq Mean Sq F value
Denom Pr(>F)
Genotype 14 1386210
99015 1.0455 139.9947 0.4127
TESTING FOR THE SIGNIFICANCE OF ENVIRONMENT EFFECT USING -2 LOGLIKELIHOOD RATIO
TEST:
Formula for Model1:
Formula for Model2:

Yield ~ 1 + Genotype + (1|Env) + (1|Block:Env) + (1|Genotype:Env)

Yield ~ 1 + Genotype + (1|Block:Env) + (1|Genotype:Env)

AIC
BIC
logLik
Chisq Df Pr(>Chisq)
Model2 7513.743 7589.425 -3738.871
Model1 7457.593 7537.480 -3709.797 58.1496 1
0.0000
TESTING FOR THE SIGNIFICANCE
LOGLIKELIHOOD RATIO TEST:
Formula for Model1:
Formula for Model2:

OF

GENOTYPE

ENVIRONMENT

EFFECT

USING

-2

Yield ~ 1 + Genotype + (1|Env) + (1|Block:Env) + (1|Genotype:Env)

Yield ~ 1 + Genotype + (1|Env) + (1|Block:Env)

AIC
BIC
logLik
Chisq Df Pr(>Chisq)
Model2 7942.529 8018.211 -3953.264
Model1 7457.593 7537.480 -3709.797 486.9356 1
0.0000
GENOTYPE X ENVIRONMENT MEANS: (some rows are deleted)
1
2
3
4
5
6
7
8
9
10
.
.
.
165

Genotype Env Yield_means

GEN1 E1
2958.1639
GEN1 E5
352.6978
GEN1 E4
1294.7984
GEN1 E11
2072.8784
GEN1 E7
514.8013
GEN1 E3
1373.9847
GEN1 E6
1800.7020
GEN1 E10
1026.3886
GEN1 E2
782.0394
GEN1 E9
4034.1663

GEN9

E9

1517.3235

GENOTYPE LSMEANS AND STANDARD ERRORS:

1
2
3
4
5
6
7
8
9
10

Genotype
GEN1
GEN10
GEN11
GEN12
GEN13
GEN14
GEN15
GEN2
GEN3
GEN4

LSMean StdErrMean
1500.965
334.2864
1804.918
334.2864
1902.555
334.2864
2023.497
334.2864
1953.552
334.2864
2163.924
334.2864
1829.575
334.2864
1826.130
334.2864
1615.296
334.2864
1557.518
334.2864

18

11
12
13
14
15

GEN5
GEN6
GEN7
GEN8
GEN9

1246.419
1606.112
1523.806
1871.903
1352.776

334.2864
334.2864
334.2864
334.2864
334.2864

STANDARD ERROR OF THE DIFFERENCE (SED):

Minimum
Average
Maximum

Estimate
355.8134
355.8134
355.8134

SIGNIFICANT PAIRWISE COMPARISONS (IF ANY):

Compared with control(s)
(No significant pairwise comparisons.)

STABILITY ANALYSIS USING FINLAY-WILKINSON MODEL:

GEN1
GEN10
GEN11
GEN12
GEN13
GEN14
GEN15
GEN2
GEN3
GEN4
GEN5
GEN6
GEN7
GEN8
GEN9

Slope
1.2781068
0.6527849
1.6932433
1.6800025
1.0057795
1.5848878
1.0948669
1.1363548
0.8969413
0.3024868
0.7151867
0.6888218
0.6136909
0.9025519
0.7542942

SE
0.2844126
0.2813760
0.2287290
0.2291829
0.3020917
0.5707898
0.3462029
0.2719630
0.4169984
0.2899820
0.1240071
0.2543126
0.2464923
0.3482402
0.2547682

t.value
4.493847
2.319973
7.402837
7.330400
3.329384
2.776658
3.162501
4.178344
2.150947
1.043123
5.767305
2.708563
2.489696
2.591751
2.960708

Prob
MSReg
MSDev
1.502182e-03 9332417.6 462123.09
4.548779e-02 2434445.5 452307.80
4.091093e-05 16379423.5 298883.70
4.418676e-05 16124257.8 300071.21
8.807711e-03 5779170.2 521359.88
2.151802e-02 14350165.8 1861282.35
1.150386e-02 6848296.6 684733.14
2.381936e-03 7377136.1 422551.36
5.994425e-02 4596083.4 993410.28
3.240997e-01
522724.4 480398.97
2.703442e-04 2922125.1
87852.27
2.405402e-02 2710651.2 369484.01
3.443918e-02 2151588.5 347109.54
2.912969e-02 4653763.4 692815.70
1.594118e-02 3250434.9 370809.14

STABILITY ANALYSIS USING SHUKLA'S MODEL:

GEN1
GEN10
GEN11
GEN12
GEN13
GEN14
GEN15
GEN2
GEN3
GEN4
GEN5
GEN6
GEN7
GEN8
GEN9

lower
est.
upper
264.805740 703.6167 1869.584
16.424694 738.2801 33185.250
151.126221 937.3589 5813.959
135.445669 943.9686 6578.851
177.323849 786.7224 3490.405
182.708778 1427.7333 11156.674
211.352595 953.4036 4300.767
163.700619 778.2112 3699.514
125.120648 944.0875 7123.534
5.338358 687.2203 88467.608
3.165181 218.8051 15125.728
46.682322 511.4079 5602.508
28.716855 497.1291 8606.003
160.228588 787.3109 3868.589
124.674720 621.5542 3098.701

19

AMMI ANALYSIS:
Percentage of Total Variation Accounted for by the Principal Components:
PC1
PC2
PC3
PC4
PC5
PC6
PC7
PC8
PC9
PC10
PC11

percent acum
38.2 38.2
23.9 62.1
19.2 81.3
8.7 90.0
5.4 95.4
2.4 97.8
1.2 99.0
0.6 99.6
0.4 100.0
0.0 100.0
0.0 100.0

Df
Sum.Sq
Mean.Sq F.value
Pr.F
23 101890340.4 4430014.80
46.77 0.0000
21 63620736.9 3029558.90
31.99 0.0000
19 51267271.5 2698277.45
28.49 0.0000
17 23217503.0 1365735.47
14.42 0.0000
15 14268487.9 951232.52
10.04 0.0000
13
6282476.7 483267.44
5.10 0.0000
11
3123773.8 283979.43
3.00 0.0008
9
1635022.9 181669.21
1.92 0.0487
7
1129431.9 161347.42
1.70 0.1084
5
100764.4
20152.87
0.21 0.9582
3
0.0
0.00
0.00 1.0000

==============================
GENOTYPE AS: Random
==============================
-----------------------------RESPONSE VARIABLE: Yield
-----------------------------DATA SUMMARY:
Number of observations read:
Number of observations used:
Factors
Env
Genotype
Block

Number of Levels
11
15
3

495
495
Levels
E1 E10 E11 ... E9
GEN1 GEN10 GEN11 ... GEN9
1 2 3

DESCRIPTIVE STATISTICS:
1

Variable N_NonMissObs
Mean
StdDev
Yield
495 1718.596 1117.791

VARIANCE COMPONENTS TABLE:

Groups
Variance Std.Dev.
1 Genotype:Env 664747.522 815.32050
2
Block:Env
6497.219 80.60533
3
Genotype
2876.978 53.63747
4
Env 530984.967 728.68715
5
Residual 94709.311 307.74878
TESTING FOR THE SIGNIFICANCE OF GENOTYPIC EFFECT USING -2 LOGLIKELIHOOD RATIO
TEST:
Formula for Model1: Yield ~ 1 + (1|Genotype) + (1|Env) + (1|Block:Env) + (1|Genotype:Env)
Formula for Model2: Yield ~ 1 + (1|Env) + (1|Block:Env) + (1|Genotype:Env)

AIC
BIC
logLik Chisq Df Pr(>Chisq)
Model2 7627.446 7648.469 -3808.723
Model1 7629.433 7654.661 -3808.717 0.0127 1
0.9102

20

TESTING FOR THE SIGNIFICANCE OF ENVIRONMENT EFFECT USING -2 LOGLIKELIHOOD RATIO

TEST:
Formula for Model1: Yield ~ 1 + (1|Genotype) + (1|Env) + (1|Block:Env) + (1|Genotype:Env)
Formula for Model2: Yield ~ 1 + (1|Genotype) + (1|Block:Env) + (1|Genotype:Env)

AIC
BIC
logLik
Chisq Df Pr(>Chisq)
Model2 7686.930 7707.953 -3838.465
Model1 7629.433 7654.661 -3808.717 59.4969 1
0.0000
TESTING FOR THE SIGNIFICANCE
LOGLIKELIHOOD RATIO TEST:

OF

GENOTYPE

ENVIRONMENT

EFFECT

USING

-2

Formula for Model1: Yield ~ 1 + (1|Genotype) + (1|Env) + (1|Block:Env) + (1|Genotype:Env)

Formula for Model2: Yield ~ 1 + (1|Genotype) + (1|Env) + (1|Block:Env)

AIC
BIC
logLik
Chisq Df Pr(>Chisq)
Model2 8114.369 8135.392 -4052.184
Model1 7629.433 7654.661 -3808.717 486.9356 1
0.0000
GENOTYPE X ENVIRONMENT MEANS: (some rows are deleted)
1
2
3
4
5
6
7
.
.
.
165

Genotype Env Yield_means

GEN1 E1
2967.6279
GEN1 E5
362.1033
GEN1 E4
1304.2393
GEN1 E11
2082.3420
GEN1 E7
524.2095
GEN1 E3
1383.4127
GEN1 E6
1810.1753

GEN9

E9

1533.2220

PREDICTED GENOTYPE MEANS:

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

Genotype
GEN1
GEN10
GEN11
GEN12
GEN13
GEN14
GEN15
GEN2
GEN3
GEN4
GEN5
GEN6
GEN7
GEN8
GEN9

Mean
1709.135
1722.349
1726.594
1731.851
1728.811
1737.956
1723.421
1723.271
1714.106
1711.594
1698.069
1713.706
1710.128
1725.261
1702.693

HERITABILITY:
0.05

Figure 17. Sample Partial Text Output of Multi-environment (One-stage) Analysis.

21

Sample generated graphs are shown in Figure 18. Boxplot and histogram are
available for the evaluation of the distribution of the values of the response variable while
diagnostic plots for the distribution of the residuals. If AMMI analysis is requested, biplots
are generated to aid in the assessment of the interaction between genotype and
environment.

Figure 18. Sample graph outputs of Multi-environment (One-stage) Analysis.

22

Quantitative Trait Locus (QTL) Analysis

To link certain complex traits to specific regions of the chromosomes, quantitative
trait locus (QTL) analysis can be used. In the current version of PBTools, QTL analysis
is done per environment level only. The following files are needed as input: a csv file
containing phenotypic data which can be either the predicted means or raw data, a tabdelimited txt file containing genotypic data and a tab-delimited txt file containing the
genetic map. Both the genotypic data and genetic map files should be in the Flapjack
format. The dialog box for QTL analysis with raw data as input are shown in Figures 19
to 21.

Figure 19. Data Input Tab of QTL Analysis Dialog Box.

Figure 20. Model Specifications Tab of QTL Analysis

Dialog Box.

23

Figure 21. Options Tab of QTL Analysis Dialog Box.

A text file is generated after the analysis. Figure 22 shows the sample partial text
output which contains the following: results of the single-environment analysis; LOD
scores of all the markers; and statistics on the selected/significant markers.
DATA FILE: E:/NSALES/pbtools workspace/SampleProject/Data/QTL_pheno.csv
SINGLE-ENVIRONMENT ANALYSIS
DESIGN: Randomized Complete Block (RCB)
-----------------------------RESPONSE VARIABLE: HEIGHT
-----------------------------DESCRIPTIVE STATISTICS:
1
2

Variable ENV N_NonMissObs

Mean
StdDev
HEIGHT
1
606 88.69455 31.62887
HEIGHT
2
606 86.69455 31.62887

-----------------------------ANALYSIS FOR: ENV = 1

-----------------------------DATA SUMMARY:
Number of observations read:
Number of observations used:
Factors
GENOTYPE
REP

Number of Levels
202
3

606
606
Levels
G_001 G_002
1 2 3

G_003 ... P2

24

VARIANCE COMPONENTS TABLE:

Groups Variance Std.Dev.
1
REP 611.3356 24.72520
2 Residual 302.7346 17.39927
TESTING FOR THE SIGNIFICANCE OF GENOTYPIC EFFECT:
Analysis of Variance Table with Satterthwaite Denominator Df
Df
Sum Sq Mean Sq F value
Denom Pr(>F)
GENOTYPE 201 235948.7 1173.874 3.8776 401.9975 0.0000
GENOTYPE LSMEANS AND STANDARD ERRORS: (some rows are deleted)
1
2
3
4
5
6
7
8
9
10
.
.
.
202

GENOTYPE
G_001
G_002
G_003
G_004
G_005
G_006
G_007
G_008
G_009
G_010

P2

LSMean StdErrMean
106.09469
17.45067
69.11523
17.45067
131.68455
17.45067
116.59435
17.45067
110.58281
17.45067
65.38761
17.45067
77.01282
17.45067
99.30493
17.45067
90.64883
17.45067
61.68259
17.45067

77.78512

17.45067

STANDARD ERROR OF THE DIFFERENCE (SED):

Minimum
Average
Maximum

Estimate
14.2064
14.2064
14.2064

==============================
QTL ANALYSIS
METHOD: CIM
-----------------------------RESPONSE VARIABLE: HEIGHT
----------------------------------------------------------ANALYSIS FOR: ENV = 1
-----------------------------QTL RESULT (ALL): (some rows are deleted)
marker Chr Pos
LOD
1
M_0001
1
0 0.998238082
2
M_0002
1
1 1.029862513
3
M_0006
1
5 1.097213383
4
1_loc10
1 10 0.683066798
5
M_0018
1 17 0.127036203
6
1_loc20
1 20 0.107014795
7
M_0022
1 21 0.098035804

25

8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
.
.
.
284

1_loc30
M_0032
1_loc40
M_0042
1_loc50
M_0053
M_0056
M_0058
1_loc60
M_0062
M_0063
M_0066
M_0069
1_loc70
M_0076
M_0081
M_0083
M_0085

M_1087

1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1

30
31
40
41
50
52
55
57
60
61
62
65
68
70
75
80
82
84

0.126238502
0.124952527
0.675666296
7.910819471
9.507940316
8.808176807
7.075115150
6.531686512
0.023835142
0.010078575
0.497989434
0.511330577
1.022791170
0.849382305
0.286639058
0.157442187
1.915089343
2.384399583

7 150

0.154691409

QTL RESULT (SELECTED):

marker Chr Pos
LOD
m.eff
Rsq
1 1_loc50
1 50 9.507940 8.388484 0.03366559
2 2_loc10
2 10 7.066201 -6.655585 0.05975959
3
M_0340
3 42 6.479474 -4.977133 0.07389893
4
M_0543
4 74 3.921155 4.776014 0.09046470
5 6_loc120
6 120 3.699853 3.778455 0.14220448
6
M_0989
7 52 10.649286 7.272148 0.17627526

Figure 22. Sample Partial Text Output of QTL Analysis

Sample generated graphs are shown in Figure 23. These include heatmap of
LOD scores and recombination fractions, plot of pairwise genotypic differences, marker
map, visualization of genotypes, plot of missing genotypes and QTL maps.

26

27

Figure 23. Sample graph outputs of QTL analysis.

Selection Index Analysis

To be able to select favorable genotypes based on several traits, a linear function
of these traits referred to as selection index can be used. Four phenotypic selection
indices and two molecular selection indices are available in PBTools. If any of the
phenotypic selection indices is selected, a csv file containing the weights is needed while
for the molecular selection indices, weights, marker and QTL files should be specified.
The dialog box for selection index analysis appears in Figure 24.

Figure 24. Dialog box for Selection Index Analysis.

28

Figure 25 shows the sample output of the analysis. The output includes genetic
and phenotypic correlation matrices, molecular covariance matrix, statistics on the
values of the selection index and breeding values, characteristics of the selected
individuals, and values of the selection index for all individuals.
DATA FILE: E:/Program Files/PBTools/Projects/SampleProject/Data/SI_ traits.csv
Lande and Thompson Selection Index
DESIGN: Lattice
Genetic and Phenotypic Correlation Matrices
GENETIC CORRELATION MATRIX
MFL1
FFL1
EHT1
PHT1
GY1
MFL.2
FFL2
EHT2
PHT2
GY2

MFL1
1.00
0.88
0.19
-0.33
-0.62
0.96
0.88
0.23
-0.25
-0.36

FFL1 EHT1 PHT1

GY1 MFL.2 FFL2 EHT2
0.88 0.19 -0.33 -0.62 0.96 0.88 0.23
1.00 0.18 -0.20 -0.77 0.83 0.68 0.15
0.18 1.00 0.75 -0.03 0.18 0.04 1.09
-0.20 0.75 1.00 0.32 -0.23 -0.28 0.75
-0.77 -0.03 0.32 1.00 -0.59 -0.70 0.09
0.83 0.18 -0.23 -0.59 1.00 0.91 0.31
0.68 0.04 -0.28 -0.70 0.91 1.00 0.27
0.15 1.09 0.75 0.09 0.31 0.27 1.00
-0.28 0.96 1.09 0.40 -0.23 -0.23 0.77
-0.41 0.13 0.28 0.98 -0.52 -0.61 -0.08

PHT2
-0.25
-0.28
0.96
1.09
0.40
-0.23
-0.23
0.77
1.00
0.20

GY2
-0.36
-0.41
0.13
0.28
0.98
-0.52
-0.61
-0.08
0.20
1.00

PHENOTYPIC CORRELATION MATRIX

MFL1
FFL1
EHT1
PHT1
GY1
MFL.2
FFL2
EHT2
PHT2
GY2

MFL1
1.00
0.71
0.01
-0.37
-0.47
0.63
0.56
0.10
-0.17
-0.29

FFL1
0.71
1.00
0.04
-0.26
-0.48
0.54
0.51
0.03
-0.20
-0.31

EHT1
0.01
0.04
1.00
0.80
0.07
0.13
0.06
0.71
0.51
0.06

PHT1
-0.37
-0.26
0.80
1.00
0.32
-0.14
-0.15
0.49
0.53
0.17

GY1
-0.47
-0.48
0.07
0.32
1.00
-0.35
-0.39
0.04
0.15
0.44

MFL.2
0.63
0.54
0.13
-0.14
-0.35
1.00
0.72
0.05
-0.31
-0.40

FFL2
0.56
0.51
0.06
-0.15
-0.39
0.72
1.00
0.05
-0.21
-0.45

EHT2
0.10
0.03
0.71
0.49
0.04
0.05
0.05
1.00
0.81
0.15

PHT2
-0.17
-0.20
0.51
0.53
0.15
-0.31
-0.21
0.81
1.00
0.34

GY2
-0.29
-0.31
0.06
0.17
0.44
-0.40
-0.45
0.15
0.34
1.00

MOLECULAR COVARIANCE MATRIX

MFL1 FFL1 EHT1 PHT1
MFL1
1.00 0.33 0.69 0.63
FFL1
0.33 1.00 0.46 0.37
EHT1
0.69 0.46 1.00 0.48
PHT1
0.63 0.37 0.48 1.00
GY1
0.11 0.02 0.23 -0.21
MFL.2 0.43 0.24 0.51 0.47
FFL2 -0.23 0.22 -0.41 0.25
EHT2
0.48 0.16 0.58 0.48
PHT2
0.79 0.23 0.41 0.50
GY2
0.37 -0.12 0.13 -0.10

GY1 MFL.2 FFL2 EHT2 PHT2

GY2
0.11 0.43 -0.23 0.48 0.79 0.37
0.02 0.24 0.22 0.16 0.23 -0.12
0.23 0.51 -0.41 0.58 0.41 0.13
-0.21 0.47 0.25 0.48 0.50 -0.10
1.00 -0.04 -0.34 -0.01 0.27 -0.18
-0.04 1.00 0.15 0.73 0.31 0.04
-0.34 0.15 1.00 -0.14 -0.04 -0.16
-0.01 0.73 -0.14 1.00 0.32 0.01
0.27 0.31 -0.04 0.32 1.00 -0.02
-0.18 0.04 -0.16 0.01 -0.02 1.00

29

COVARIANCE BETWEEN SELECTION INDEX AND BREEDING VALUE:

VARIANCE OF THE SELECTION INDEX:

1.50582

VARIANCE OF THE BREEDING VALUE:

6.145354

3.205508

CORRELATION BETWEEN SELECTION INDEX AND BREEDING VALUE:

VALUES OF THE
INDIVIDUALS

TRAITS,

Entry 240
Entry 2
Entry 21
Entry 132
Entry 167
Entry 179
Entry 220
Entry 174
Entry 165
Entry 161
Entry 87
Mean of
Selected Individuals
Mean of
all Individuals
Selection Differential
Expected Genetic Gain
for 5%

SELECTION

MFL1
102.01
104.88
101.23
104.69
106.75
104.39
105.34
103.13
104.61
103.12
101.53

INDEX,

0.9999

MEANS,

GAINS

FFL1
EHT1
PHT1
102.12 80.53 140.12
104.42 100.22 148.82
100.75 93.45 163.42
104.71 75.75 126.00
105.49 81.67 132.64
101.50 76.00 126.03
104.37 78.75 137.92
102.54 96.84 146.33
103.66 90.75 150.25
99.05 85.75 148.50
100.88 103.66 156.84

GY1
0.00
28.72
34.45
44.00
0.83
23.78
97.16
47.44
79.00
82.50
68.33

FOR

THE

MFL.2
100.70
99.60
100.23
97.88
106.21
100.74
99.84
96.59
99.32
101.46
102.34

5%

FFL2
100.74
100.36
98.34
100.35
108.25
99.34
98.31
99.25
103.80
103.00
99.20

103.79 102.68

87.58 143.35

102.01 102.12
1.78
0.56

80.53 140.12 75.99 100.70 100.74

7.04
3.23 -29.97 -0.26
0.26

1.57

1.64

1.52

SELECTED

46.02 100.44 100.99

1.19

-1.13

1.95

1.37

EHT2
PHT2
GY2 LT index
Entry 240
78.47 133.44
0.00
2.88
Entry 2
106.75 161.75 140.00
2.59
Entry 21
89.69 156.81
1.50
2.34
Entry 132
76.09 127.28 33.39
2.24
Entry 167
75.00 113.64
0.00
2.14
Entry 179
74.31 124.14
9.24
2.14
Entry 220
87.00 143.50 129.50
1.94
Entry 174
94.93 149.59 18.61
1.83
Entry 165
96.25 160.25 41.00
1.80
Entry 161
76.50 125.69 12.75
1.74
Entry 87
91.95 140.56 35.00
1.70
Mean of Selected Individuals 86.08 139.69 38.27
NA
Mean of all Individuals
78.47 133.44 51.70
NA
Selection Differential
7.61
6.26 -13.43
NA
Expected Genetic Gain for 5%
1.73
1.08 -1.02
NA

30

VALUES OF THE TRAITS AND THE SELECTION INDEX FOR ALL INDIVIDUALS
Entry
Entry
Entry
.
.
.
(some

1
2
3

MFL1
FFL1
EHT1
PHT1
102.21 100.25 71.45 123.75
104.88 104.42 100.22 148.82
98.97 100.44 80.17 154.36

GY1
42.45
28.72
77.78

MFL.2
FFL2
EHT2
PHT2
GY2
99.29 98.95 68.51 117.47 16.87
99.60 100.36 106.75 161.75 140.00
97.93 96.82 66.75 133.75 116.00

rows are deleted)

Figure 25. Sample Partial Text Output of Selection Index Analysis.

Mating Designs
Several mating designs were developed to estimate genetic variance
components. Experiments which used the following mating designs can be analyzed in
PBTools: North Carolina I to III, Triple Test Cross and Diallel I to IV. For each mating
design, the experiment can be laid out in any of these four experimental designs:
Completely Randomized, RCB, Alpha-Lattice, and Row-Column design. In this paper,
only analyses for North Carolina II and Diallel II are presented.
For North Carolina II, analysis can be done per environment level or across
environments. To illustrate analysis per environment level, a sample completed dialog
box is shown in Figure 26.

Figure 26. Dialog Box for North Carolina Experiment II.

31

The results of the analysis as shown in Figure 27 includes data summary,

ANOVA table (assuming fixed model), estimates of the variance components and
estimates of the genetic variance components.
DATA FILE: E:/NSALES/pbtools workspace/SampleProject/Data/NCII_ME.csv
DESIGN: NORTH CAROLINA EXPERIMENT II IN RCB (INBRED)
----------------------------RESPONSE VARIABLE: Y
--------------------------------------------------------ANALYSIS FOR: Env = A
----------------------------DATA SUMMARY:
Factors
Env
Female
Male
Block

No of Levels
1
8
8
3

Levels
A
1 2 3 ... 8
10 11 12 ... 9
1 2 3

Number of observations read: 192

Number of observations used: 192
ANOVA TABLE FOR THE EXPERIMENT:
Df
Sum Sq Mean Sq F value Pr(>F)
Block
2
22.3531 11.1766
1.14 0.3220
Male
7 1112.6490 158.9498
16.26 0.0000
Female
7 735.2669 105.0381
10.75 0.0000
Male:Female 49 823.1469 16.7989
1.72 0.0086
Residuals
126 1231.4730
9.7736
------REMARK: Raw dataset is balanced.
LINEAR MIXED MODEL FIT BY RESTRICTED MAXIMUM LIKELIHOOD:
Formula:

Y ~ 1 + (1|Block) + (1|Male) + (1|Female) + (1|Male:Female)

AIC
BIC
logLik deviance REMLdev
1057.665 1077.21 -522.8323 1047.758 1045.665
Fixed Effects:
Estimate Std. Error t value
(Intercept) 55.6076
1.1379 48.8702
Random Effects:
Groups
Variance Std. Deviation
Male:Female
2.3418
1.5303
Female
3.6767
1.9175
Male
5.9229
2.4337
Block
0.0219
0.1481
Residual
9.7736
3.1263

32

ESTIMATES OF GENETIC VARIANCE COMPONENTS:

VA
VD
Narrow sense heritability(plot-mean based)
Broad sense heritability(plot-mean based)
Dominance Ratio

Estimate
9.599670
2.341800
0.442075
0.549917
0.698492

Figure 27. Sample Text Output of North Carolina II Per Environment Analysis
For multiple-environment analysis, the sample output as shown in Figure 28
includes data summary, ANOVA table (assuming fixed model), estimates of the variance
components and estimates of the genetic variance components.

DATA FILE: E:/NSALES/pbtools workspace/SampleProject/Data/NCII_ME.csv

MULTIPLE ENVIRONMENT ANALYSIS
DESIGN: NORTH CAROLINA EXPERIMENT II IN RCB (INBRED)
----------------------------RESPONSE VARIABLE: Y
----------------------------DATA SUMMARY:
Factors
Env
Female
Male
Block

No of Levels
2
8
8
3

Levels
A B
1 2 3 ... 8
10 11 12 ... 9
1 2 3

Number of observations read: 384

Number of observations used: 384
ANOVA TABLE:
Df
Sum Sq Mean Sq F value Pr(>F)
Env
1
8.7665
8.7665
0.38 0.5724
Env:Block
4
93.0194 23.2549
2.21 0.0682
Male
7 840.6569 120.0938
11.43 0.0000
Female
7 821.7501 117.3929
11.17 0.0000
Male:Female
49 1233.6320 25.1762
2.40 0.0000
Env:Male
7 493.0000 70.4286
6.70 0.0000
Env:Female
7 215.9051 30.8436
2.93 0.0057
Env:Male:Female 49 974.2153 19.8819
1.89 0.0009
Residuals
252 2648.7840 10.5110
------REMARK: Raw dataset is balanced.

33

LINEAR MIXED MODEL FIT BY RESTRICTED MAXIMUM LIKELIHOOD:

Formula: Y ~ 1 + (1|Env) + (1|Env:Block) + (1|Male) + (1|Female) +
(1|Male:Female) + (1|Env:Male) + (1|Env:Female) + (1|Env:Male:Female)
AIC
BIC
logLik deviance REMLdev
2147.079 2186.586 -1063.54 2128.376 2127.079
Fixed Effects:
Estimate Std. Error t value
(Intercept) 55.7587
0.7634 73.042
Random Effects:
Groups
Variance Std. Deviation
Env:Male:Female
3.1506
1.7750
Male:Female
0.8681
0.9317
Env:Female
0.3985
0.6313
Env:Male
1.8441
1.3580
Female
1.7219
1.3122
Male
1.0554
1.0273
Env:Block
0.1792
0.4233
Env
0.0000
0.0000
Residual
10.5157
3.2428
ESTIMATES OF GENETIC VARIANCE COMPONENTS:
VA
VAxE
VD
VDxE
h2-narrow sense
H2-broad sense
Dominance Ratio

Estimate
2.777330
2.242660
0.868100
3.150620
0.142031
0.186425
0.790653

Figure 28. Sample Text Output of North Carolina II Mulit-environment Analysis

In cases where information on effects due to reciprocal, maternal, general
combining ability (GCA) and the specific combining ability (SCA) of parents in crosses
are of interest, diallel design can be used. In analyzing such designs, PBTools makes
use of the Griffing Method. The sample dialog box for Diallel II analysis is shown in
Figure 29.

34

Figure 29. Dialog Box for Diallel Analysis (Griffing Method 2).

Partial results are shown in Figure 30. This consists of data summary, test for the
significance of the crosses, test for the significance of GCA and SCA effects, GCA, SCA
and residual variance estimates, estimates of genetic variance components and
estimates of the GCA and SCA effects.

35

DATA FILE: E:/NSALES/pbtools workspace/SampleProject/Data/Diallel_M2.csv

DIALLEL ANALYSIS: GRIFFING METHOD II IN RCB (CROSS)
----------------------------RESPONSE VARIABLE: Plant_height
--------------------------------------------------------ANALYSIS FOR: Env = Normal
----------------------------DATA SUMMARY:
Factors
P1
P2
Block
Env

No of Levels
7
7
3
1

Levels
1 2 3
1 2 3
1 2 3
Normal

4
4

5
5

6
6

7
7

Number of observations read: 84

Number of observations used: 84
TESTING FOR THE SIGNIFICANCE OF CROSS EFFECT: (Crosses = P1:P2)
Formula for Model 1: Plant_height ~ Crosses + (1|Block)
Formula for Model 2: Plant_height ~ (1|Block)
AIC
BIC
logLik
Chisq Df Pr(>Chisq)
Model2 758.9207 766.2131 -376.4603
Model1 466.3195 539.2440 -203.1597 346.6012 1
0.0000
MATRIX OF MEANS:
1
2
3
4
5
6
7
1 142.9000 148.3333 163.9000 152.9000 142.3667 160.6667 191.3333
2
129.6667 142.9000 143.9000 131.5667 143.5333 186.6667
3
131.5667 163.5667 136.9000 166.4333 189.7667
4
159.3333 149.8000 164.8000 200.2333
5
122.4333 138.9000 175.7667
6
146.1333 195.5667
7
157.5333
ANALYSIS OF VARIANCE:
SV
Df Sum Sq Mean Sq F value Pr(>F)
GCA
6 7784.37 1297.39
6.05 0.0008
SCA
21 4500.58 214.31
14.56 0.0000
Error 54 794.66
14.72
ESTIMATES OF VARIANCE COMPONENTS:
Estimate Std. Error
GCA
120.3424
217.0737
SCA
199.5973
66.1426
Error 14.7160
2.8321

36

ESTIMATES OF GENETIC VARIANCE COMPONENTS:

Estimate
VA
481.369471
VD
798.389175
h2-narrow sense
0.371865
H2-broad sense
0.988632
Dominance Ratio
1.821307
GENERAL COMBINING ABILITY EFFECTS (diagonal), SPECIFIC COMBINING
ABILITY EFFECTS (above diagonal):
1
1
2
3
4
5
6
7

2
-0.6608

3.1454
-10.5571

3
4
5
6
7
10.8935 -7.5806
1.1861
3.7083 13.0157
-0.2102 -6.6843
0.2824 -3.5287 18.2454
-2.7386
5.1639 -2.2028 11.5528 13.5269
4.7354
3.2231
2.4454 16.5194
-14.5646 -4.1546 11.3528
1.2132 15.3750
22.5725

TABLE OF STANDARD ERRORS AND LSDs:

Gi
Sii
Sij
Gi-Gj
Sii-Sjj
Sij-Sik
Sij-Skl

Std. Error
LSD
1.1839
2.9299
3.4430
1.8084 3.6256
4.0437 8.1070
5.1149 10.2547
4.7845 9.5924

Figure 30. Sample Text Output of Diallel II Per Environment Analysis.

For multiple-environment analysis, the sample output as shown in Figure 31

includes data summary, test for the significance of the crosses environment effect, test
for the significance of GCA and SCA effects, estimates of the GCA and SCA effects,
GCA, SCA and residual variance estimates and estimates of genetic variance
components.

37

DATA FILE: E:/NSALES/pbtools workspace/SampleProject/Data/Diallel_M2.csv

MULTIPLE ENVIRONMENT ANALYSIS
DIALLEL ANALYSIS: GRIFFING METHOD II IN RCB (CROSS)
----------------------------RESPONSE VARIABLE: Plant_height
----------------------------DATA SUMMARY:
Factors
P1
P2
Env
Block

No of Levels
7
7
2
3

Levels
1 2 3 4 5 6
1 2 3 4 5 6
Normal Saline
1 2 3

7
7

Number of observations read: 168

Number of missing observations: 0
ANOVA TABLE:
Df
Sum Sq Mean Sq F value
Env
1 17111.43 17111.43
28.18
Block(Env)
4 2429.29
607.32
14.44
Crosses
27 80041.58 2964.50
31.42
Crosses x Env 27 2547.46
94.35
2.24
Error
108 4543.85
42.07
------REMARK: Raw dataset is balanced.

Pr(>F)
0.0061
0.0000
0.0000
0.0019

ANOVA TABLE:
Df
Sum Sq Mean Sq F value
GCA
6 54367.67 9061.28
51.14
SCA
21 25673.91 1222.57
17.30
GCAxE
6 1063.14 177.19
4.21
SCAxE 21 1484.32
70.68
1.68
Error 108 4543.85
42.07
------REMARK: Raw dataset is balanced.

Pr(>F)
0.0001
0.0000
0.0008
0.0450

MATRIX OF MEANS:
1
2
1 131.0000 133.8333
2
116.8333
3
4
5
6
7
------REMARK: Raw dataset

3
153.5500
130.5500
122.0000

4
140.7333
133.8500
154.5000
137.3333

5
128.9000
122.7167
131.2167
138.5667
111.8833

6
154.4333
129.0500
153.2167
155.7833
132.5667
143.0167

7
182.2833
175.9000
177.7833
195.2333
166.3333
188.6167
155.1000

is balanced.

38

GENERAL COMBINING ABILITY EFFECTS, SPECIFIC COMBINING ABILITY EFFECTS (above

diagonal)
1
2
3
4
5
6
1
1.4884 11.7329 -6.4745 -1.7227
6.5181
2
-0.5819 -2.6727
2.7792 -8.1801
3
8.5051
1.8069
6.5144
4
3.7662
3.6903
5
-2.9412
6
7
GCA -1.6418 -12.3270 -2.8548
2.5360 -14.0492
3.2434

7
12.5181
16.8199
9.2310
21.2903
8.9755
13.9662
25.0934

TABLE OF STANDARD ERRORS AND LSDs:

Gi
Sii
Sij
Gi-Gj
Sii-Sjj
Sij-Sik
Sij-Skl

Std. Error
0.8172
2.3767
2.0225
1.2483
2.7913
3.5307
3.3027

LSD

2.4743
5.5328
6.9985
6.5465

ESTIMATES OF VARIANCE COMPONENTS:

Estimate
GCA
143.1889
SCA
191.9809
GCAxE
3.9448
SCAxE
9.5364
Error 42.0727
ESTIMATES OF GENETIC VARIANCE COMPONENTS:
Estimate
VA
572.755727
VAxE
15.779056
VD
767.923608
VDxE
38.145415
h2-narrow sense
0.398667
H2-broad sense
0.933181
Dominance Ratio
1.637530

Figure 31. Sample Text Output of Diallel II Multi-environment Analysis.

Future Direction
In succeeding versions, analysis for other experimental designs will be made
available for single-environment analysis. Also, other input data options will be
introduced. This includes allowing subsampling data for mating designs and accepting
input files of different formats for QTL analysis. Finally, a module for multi-environment
QTL analysis will also be added.

39