Optimized grouping to increase accuracy of prediction of breeding values based on group records in genomic selection breeding programs

Thinh T. Chu*, John W.M. Bastiaansen, Peer Berg, Hans Komen

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Background: Phenotypic records of group means or group sums are a good alternative to individual records for some difficult to measure, but economically important traits such as feed efficiency or egg production. Accuracy of predicted breeding values based on group records increases with increasing relationships between group members. The classical way to form groups with more closely-related animals is based on pedigree information. When genotyping information is available before phenotyping, its use to form groups may further increase the accuracy of prediction from group records. This study analyzed two grouping methods based on genomic information: (1) unsupervised clustering implemented in the STRUCTURE software and (2) supervised clustering that models genomic relationships. Results: Using genomic best linear unbiased prediction (GBLUP) models, estimates of the genetic variance based on group records were consistent with those based on individual records. When genomic information was available to constitute the groups, genomic relationship coefficients between group members were higher than when random grouping of paternal half-sibs and of full-sibs was applied. Grouping methods that are based on genomic information resulted in higher accuracy of genomic estimated breeding values (GEBV) prediction compared to random grouping. The increase was ~ 1.5% for full-sibs and ~ 11.5% for paternal half-sibs. In addition, grouping methods that are based on genomic information led to lower coancestry coefficients between the top animals ranked by GEBV. Of the two proposed methods, supervised clustering was superior in terms of accuracy, computation requirements and applicability. By adding surplus genotyped offspring (more genotyped offspring than required to fill the groups), the advantage of supervised clustering increased by up to 4.5% compared to random grouping of full-sibs, and by 14.7% compared to random grouping of paternal half-sibs. This advantage also increased with increasing family sizes or decreasing genome sizes. Conclusions: The use of genotyping information for grouping animals increases the accuracy of selection when phenotypic group records are used in genomic selection breeding programs.

Original languageEnglish
Article number64
Number of pages12
JournalGenetics Selection Evolution
Volume51
Issue number1
DOIs
Publication statusPublished - 15 Nov 2019

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breeding value
marker-assisted selection
Breeding
Cluster Analysis
genomics
breeding
prediction
Genome Size
Genetic Models
Pedigree
Ovum
genotyping
Software
animal
programme
animals
family size
genetic variance
surpluses
methodology

Cite this

@article{1a44095a27ef427aa829f93bf0134d36,
title = "Optimized grouping to increase accuracy of prediction of breeding values based on group records in genomic selection breeding programs",
abstract = "Background: Phenotypic records of group means or group sums are a good alternative to individual records for some difficult to measure, but economically important traits such as feed efficiency or egg production. Accuracy of predicted breeding values based on group records increases with increasing relationships between group members. The classical way to form groups with more closely-related animals is based on pedigree information. When genotyping information is available before phenotyping, its use to form groups may further increase the accuracy of prediction from group records. This study analyzed two grouping methods based on genomic information: (1) unsupervised clustering implemented in the STRUCTURE software and (2) supervised clustering that models genomic relationships. Results: Using genomic best linear unbiased prediction (GBLUP) models, estimates of the genetic variance based on group records were consistent with those based on individual records. When genomic information was available to constitute the groups, genomic relationship coefficients between group members were higher than when random grouping of paternal half-sibs and of full-sibs was applied. Grouping methods that are based on genomic information resulted in higher accuracy of genomic estimated breeding values (GEBV) prediction compared to random grouping. The increase was ~ 1.5{\%} for full-sibs and ~ 11.5{\%} for paternal half-sibs. In addition, grouping methods that are based on genomic information led to lower coancestry coefficients between the top animals ranked by GEBV. Of the two proposed methods, supervised clustering was superior in terms of accuracy, computation requirements and applicability. By adding surplus genotyped offspring (more genotyped offspring than required to fill the groups), the advantage of supervised clustering increased by up to 4.5{\%} compared to random grouping of full-sibs, and by 14.7{\%} compared to random grouping of paternal half-sibs. This advantage also increased with increasing family sizes or decreasing genome sizes. Conclusions: The use of genotyping information for grouping animals increases the accuracy of selection when phenotypic group records are used in genomic selection breeding programs.",
author = "Chu, {Thinh T.} and Bastiaansen, {John W.M.} and Peer Berg and Hans Komen",
year = "2019",
month = "11",
day = "15",
doi = "10.1186/s12711-019-0509-z",
language = "English",
volume = "51",
journal = "Genetics, Selection, Evolution",
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Optimized grouping to increase accuracy of prediction of breeding values based on group records in genomic selection breeding programs. / Chu, Thinh T.; Bastiaansen, John W.M.; Berg, Peer; Komen, Hans.

In: Genetics Selection Evolution, Vol. 51, No. 1, 64, 15.11.2019.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Optimized grouping to increase accuracy of prediction of breeding values based on group records in genomic selection breeding programs

AU - Chu, Thinh T.

AU - Bastiaansen, John W.M.

AU - Berg, Peer

AU - Komen, Hans

PY - 2019/11/15

Y1 - 2019/11/15

N2 - Background: Phenotypic records of group means or group sums are a good alternative to individual records for some difficult to measure, but economically important traits such as feed efficiency or egg production. Accuracy of predicted breeding values based on group records increases with increasing relationships between group members. The classical way to form groups with more closely-related animals is based on pedigree information. When genotyping information is available before phenotyping, its use to form groups may further increase the accuracy of prediction from group records. This study analyzed two grouping methods based on genomic information: (1) unsupervised clustering implemented in the STRUCTURE software and (2) supervised clustering that models genomic relationships. Results: Using genomic best linear unbiased prediction (GBLUP) models, estimates of the genetic variance based on group records were consistent with those based on individual records. When genomic information was available to constitute the groups, genomic relationship coefficients between group members were higher than when random grouping of paternal half-sibs and of full-sibs was applied. Grouping methods that are based on genomic information resulted in higher accuracy of genomic estimated breeding values (GEBV) prediction compared to random grouping. The increase was ~ 1.5% for full-sibs and ~ 11.5% for paternal half-sibs. In addition, grouping methods that are based on genomic information led to lower coancestry coefficients between the top animals ranked by GEBV. Of the two proposed methods, supervised clustering was superior in terms of accuracy, computation requirements and applicability. By adding surplus genotyped offspring (more genotyped offspring than required to fill the groups), the advantage of supervised clustering increased by up to 4.5% compared to random grouping of full-sibs, and by 14.7% compared to random grouping of paternal half-sibs. This advantage also increased with increasing family sizes or decreasing genome sizes. Conclusions: The use of genotyping information for grouping animals increases the accuracy of selection when phenotypic group records are used in genomic selection breeding programs.

AB - Background: Phenotypic records of group means or group sums are a good alternative to individual records for some difficult to measure, but economically important traits such as feed efficiency or egg production. Accuracy of predicted breeding values based on group records increases with increasing relationships between group members. The classical way to form groups with more closely-related animals is based on pedigree information. When genotyping information is available before phenotyping, its use to form groups may further increase the accuracy of prediction from group records. This study analyzed two grouping methods based on genomic information: (1) unsupervised clustering implemented in the STRUCTURE software and (2) supervised clustering that models genomic relationships. Results: Using genomic best linear unbiased prediction (GBLUP) models, estimates of the genetic variance based on group records were consistent with those based on individual records. When genomic information was available to constitute the groups, genomic relationship coefficients between group members were higher than when random grouping of paternal half-sibs and of full-sibs was applied. Grouping methods that are based on genomic information resulted in higher accuracy of genomic estimated breeding values (GEBV) prediction compared to random grouping. The increase was ~ 1.5% for full-sibs and ~ 11.5% for paternal half-sibs. In addition, grouping methods that are based on genomic information led to lower coancestry coefficients between the top animals ranked by GEBV. Of the two proposed methods, supervised clustering was superior in terms of accuracy, computation requirements and applicability. By adding surplus genotyped offspring (more genotyped offspring than required to fill the groups), the advantage of supervised clustering increased by up to 4.5% compared to random grouping of full-sibs, and by 14.7% compared to random grouping of paternal half-sibs. This advantage also increased with increasing family sizes or decreasing genome sizes. Conclusions: The use of genotyping information for grouping animals increases the accuracy of selection when phenotypic group records are used in genomic selection breeding programs.

U2 - 10.1186/s12711-019-0509-z

DO - 10.1186/s12711-019-0509-z

M3 - Article

VL - 51

JO - Genetics, Selection, Evolution

JF - Genetics, Selection, Evolution

SN - 0999-193X

IS - 1

M1 - 64

ER -