Table Of ContentIowa State University Capstones, Theses and
Graduate Theses and Dissertations
Dissertations
2016
Effects of including crossbred relative records on
estimated breeding value prediction accuracies and
selection decisions in swine
Denise Lois Van De Stroet
Iowa State University
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Recommended Citation
Van De Stroet, Denise Lois, "Effects of including crossbred relative records on estimated breeding value prediction accuracies and
selection decisions in swine" (2016).Graduate Theses and Dissertations. 15828.
https://lib.dr.iastate.edu/etd/15828
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Effects of including crossbred relative records on estimated breeding value prediction
accuracies and selection decisions in swine
by
Denise Lois Van De Stroet
A thesis submitted to the graduate faculty
in partial fulfillment of the requirements for the degree of
MASTER OF SCIENCE
Major: Animal Breeding and Genetics
Program of Study Committee:
Kenneth J. Stalder, Major Professor
John W. Mabry
Philip M. Dixon
Iowa State University
Ames, Iowa
2016
Copyright © Denise Lois Van De Stroet, 2016. All rights reserved.
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TABLE OF CONTENTS
Page
LIST OF FIGURES ............................................................................................................... iv
LIST OF TABLES .................................................................................................................. v
ACKNOWLEDGMENTS .................................................................................................... vii
ABSTRACT ............................................................................................................................ ix
CHAPTER 1: GENERAL INTRODUCTION ..................................................................... 1
Introduction ........................................................................................................................... 1
Thesis Organization .............................................................................................................. 3
Expected Outcomes .............................................................................................................. 4
Practical Implications............................................................................................................ 5
Author Contributions ............................................................................................................ 5
CHAPTER 2: LITERATURE REVIEW ............................................................................. 6
Evolution of Selection Indexes ............................................................................................. 6
Indexes for Selecting Maternal Females in the Swine Industry ........................................... 8
Including Crossbred Records in Breeding Value Estimations ............................................ 11
Breeding Value Prediction Accuracy Derivation ............................................................... 15
The Effects of Including Crossbred Records in Calculating Purebred EBVs on
Prediction Accuracy ............................................................................................................ 17
The Effects of Including Crossbred Records in Calculating Crossbred EBVs on
Prediction Accuracy ............................................................................................................ 18
EBV Ranking and Selection Decisions with Crossbred Record Inclusion ......................... 21
Including Crossbred Performance Records in EBV calculations for Purebreds with
Genomic Technology .......................................................................................................... 25
Summary ............................................................................................................................. 26
References ........................................................................................................................... 27
CHAPTER 3: CHANGE IN PUREBRED SELECTION ACCURACY WHEN
INCLUDING CROSSBRED RELATIVE RECORDS IN ESTIMATING
CROSSBRED BREEDING VALUES FOR NUMBER BORN ALIVE AND
LITTERS PER SOW PER YEAR....................................................................................... 34
Abstract ............................................................................................................................... 34
Introduction ......................................................................................................................... 35
Materials and Methods ........................................................................................................ 37
Results and Discussion ....................................................................................................... 40
Conclusions ......................................................................................................................... 50
Acknowledgements ............................................................................................................. 50
References ........................................................................................................................... 51
CHAPTER 4: IMPACT OF INCLUDING RELATIVE CROSSBRED RECORDS
IN SWINE EBV CALCULATIONS ON PUREBRED SELECTION DECISIONS ...... 63
Abstract ............................................................................................................................... 63
Introduction ......................................................................................................................... 64
iii
Materials and Methods ........................................................................................................ 66
Results ................................................................................................................................. 69
Discussion ........................................................................................................................... 71
Conclusions ......................................................................................................................... 74
Acknowledgements ............................................................................................................. 75
References ........................................................................................................................... 75
CHAPTER 5: GENERAL DISCUSSION AND CONCLUSIONS .................................. 83
References ........................................................................................................................... 85
iv
LIST OF FIGURES
Page
Figure 3.1. Sow selection accuracy increases when crossbred records were included in
number born alive (NBA) and litters per sow per year (LSY) crossbred EBV
estimation according to the number of related crossbred records included in the
estimation .................................................................................................................... 60
Figure 3.2. Sire selection accuracy increase when crossbred records were included in
piglet number born alive (NBA) and litters per sow per year (LSY) crossbred EBV
estimations according to the number of relative records included in the estimation .. 62
v
LIST OF TABLES
Page
Table 3.1. Breed by herd type piglet number born alive (NBA) and litters per sow per
year (LSY) record numbers, means, and percentage of records without pedigree
information used in a study to estimate selection accuracy increases from crossbred
record inclusion in EBV estimation ............................................................................ 53
Table 3.2. Variance components, heritabilities, and genetic correlations between
purebreds and crossbreds (r ) used in a study to estimate selection accuracy
pc
increases from crossbred record inclusion in EBV estimation ................................... 55
Table 3.3. Selection accuracies and their increases (mean ± SD) for piglet number born
alive (NBA) and litters per sow per year (LSY) crossbred EBV in a study to
estimate selection accuracy increases from crossbred record inclusion in EBV
estimation .................................................................................................................... 56
Table 3.4. Selection accuracy increases from crossbred record inclusion in number born
alive and litters per sow per year crossbred EBV estimation according to herd type
from a study which estimated selection accuracy increases from crossbred record
inclusion in EBV estimation ....................................................................................... 57
Table 3.5. Selection accuracy increases for number born alive (NBA) and litters per sow
per year (LSY) crossbred EBV according to the number of additional farms from
which crossbred records originated in a study which estimated selection accuracy
increases from crossbred record inclusion in EBV estimation ................................... 58
Table 4.1. Heritability estimates (on diagonal) for number born alive (NBA) and litters
per sow per year (LSY) and genetic correlations used for breeding value estimation
by breed from a study to estimate selection decision changes from crossbred record
inclusion in EBV estimation ....................................................................................... 78
Table 4.2. Mean EBVs, Spearman rank correlations, selection decisions, percent change
in selection decisions, and the crossbred EBV increase for selected individuals
between EBVs estimated using purebred information only (PLS) and combined
crossbred and purebred information (CCPS) from a study to estimate selection
decision changes from crossbred record inclusion in EBV estimation ....................... 79
Table 4.3. Sow contemporary group Spearman rank correlations and percent change in
selection decisions between crossbred EBVs calculated using purebred
information only and combined purebred and crossbred information by herd
categorization from a study to estimate selection decision changes from crossbred
record inclusion in EBV estimation ............................................................................ 81
vi
Table 4.4 Sow contemporary group Spearman rank correlations and percent change in
selection decisions between crossbred EBVs calculated using purebred
information only and combined purebred and crossbred information by breed from
a study to estimate selection decision changes from crossbred record inclusion in
EBV estimation ........................................................................................................... 82
vii
ACKNOWLEDGMENTS
First and foremost, I would like to thank my incredible family for all of their love and
support over the past two years. It is crazy to think that in my two years of graduate school,
my already-large family has doubled in size. Caleb, you have supported me tremendously
throughout graduate school. It is you who inspire me to work hard, each and every day, to
accomplish the task that I have set out to do. Dad and Grandpa, thank you for motivating me
to learn as much as I can about pig production. You have taught me more about agriculture
than I could ever hope to learn elsewhere. Mom, words cannot sum up all that I owe you. Your
spiritual and emotional wisdom have made me into the woman I am today. Joy, Josh, and
Mindy, how could I ever forget the fun that we had working, showing pigs, hunting, and fishing
together? You fill my life with spunk and energy, no matter how many miles lie between us.
To the Van De Stroets, thank you for providing me with a home away from home. You have
so graciously accepted me as one of your own and have allowed me to enjoy a taste of farm
life throughout graduate school.
Drs. Stalder and Mabry, thank you for your support and patience with me over the past
two years. You have taught me greatly about the applied aspects of swine breeding and genetics
and encourage me to grow in my knowledge of modern pig production. I am extremely grateful
for all of the time, effort, and insight that you have given towards the completion of this project
and my professional goals. My other committee member, Dr. Philip Dixon, has also ensured
that my thesis is completed satisfactorily by offering comments and suggestions. Without your
help, this work would not have been possible.
I am extremely grateful for help and encouragement from Dr. Julia Calderón Díaz. She
taught me much of what I know about statistical analysis and scientific writing. Without her
viii
effort and support, this thesis would not have been possible. My lab and office mates, both past
and present, have supported me immensely throughout graduate school. Thank you to Dr.
Emily Waide, Joseph Stock, Brady McNeil, Austin Putz, Jared Mumm, Amber Danielson,
Tasha Gruhot, Muhammed Walugembe, and Shoki Hirano for your comradery and thought-
provoking discussions.
Lastly, I would like to say thank you to my friends and church family from both Iowa
and Pennsylvania for their love, encouragement, support, and occasional food boxes. You are
a critical part of my life; without you, I would not be who I am today. If I mentioned each of
you and the ways that you have supported this project, the length of this thesis would not
suffice. I hope that I can find a way to repay you. Above all, I would like to say thank you to
my Lord and Savior, Jesus Christ, who led me to come to Iowa State when I was not sure that
I wanted to and who has guided me throughout this project.
ix
ABSTRACT
The overall objectives of this study were to 1) evaluate the impact of including
crossbred relative records on estimated breeding value selection accuracy for crossbred
performance and to 2) estimate the subsequent extent of animal re-ranking and differences in
selection decisions. Number born alive (NBA) and litters per sow per year (LSY) records were
obtained from a large swine breeding company which maintains a database consisting of
nucleus, multiplier, commercial, and rotational cross herds. The dataset included 187,674
litters from 46,749 Landrace (LR); 117,782 litters from 31,665 Large White (LW); and
295,163 litters from 76,925 LR × LW (F ) females, respectively. Variance components for
1
each breed were calculated in REMLF90 using bivariate models with one purebred trait and
the respective F trait. Number born alive and LSY crossbred breeding values and accuracies
1
were estimated for purebred sows separately with purebred information only (EBV ) and
PLS
with combined crossbred and purebred information (EBV ) in BLUPF90. Purebred sow
CCPS
contemporary groups with >10 sows each were obtained according to herd weaning schedule
from the most recent six months of data from each herd. Sows were ranked within
contemporary groups for EBV and EBV . Spearman rank correlations between EBV
PLS CCPS
rankings and selection decision differences were calculated for each contemporary group,
boars used for artificial insemination, and a multiplier herd (HP) with seven commercial herds
which contained F progeny with > 98% pedigree information. Selection accuracy increases,
1
contemporary group Spearman rank correlations, and percentages of change in selection
decisions were evaluated separately for NBA and LSY EBV using mixed model equations.
Including crossbred relative records in crossbred EBV calculations improved selection
accuracy for boars and sows from all herd types. Sow re-ranking and differences in selection
Description:accuracies and selection decisions in swine by. Denise Lois Van De Stroet. A thesis submitted to the graduate faculty in partial fulfillment of the requirements for the degree of. MASTER OF SCIENCE. Major: Animal Breeding and Genetics. Program of Study Committee: Kenneth J. Stalder, Major Professor
