Using genomic information to conserve genetic diversity in livestock

Sonia E. Eynard

Research output: Thesisinternal PhD, WUAcademic

Abstract

Concern about the status of livestock breeds and their conservation has increased as selection and small population sizes caused loss of genetic diversity. Meanwhile, dense SNP chips and whole genome sequences (WGS) became available, providing opportunities to accurately quantify the impact of selection on genetic diversity and develop tools to better preserve such genetic diversity for long-term perspectives. This thesis aimed to infer the impact of selection and mitigate its effects on genetic diversity using genomic information. One of the advantages of WGS information, compared to pedigree and SNP chip information, is that it provides information on all variants, including rare ones, and ‘true’ relationships between individuals may be estimated thus being useful for evaluating genetic diversity. Taking into account rare variants had significant effects on estimated relationships. Moreover, optimal contribution (OC) strategy was used to perform selection either in a breeding program, maximising genetic merit while minimising loss of genetic diversity, or to build a gene bank, only maximising the conserved genetic diversity, with the aim to quantify loss of genetic diversity due to selection decisions. More genetic diversity was conserved when genomic information was used for selection decisions instead of pedigree and WGS information revealed a high loss of genetic diversity due to losing rare variants. Ways to reduce the loss of genetic diversity during a genomic selection program were investigated. The choice of individuals to update the reference population was proposed as a promising way to better conserve genetic diversity in a breeding population. In fact, changes in the reference population will lead to changes in prediction equations and thus ultimately to a shift in long-term selection decisions. Differences between reference population design using either random, truncation or OC selection of individuals, on the breeding population were modest but OC achieved conservation of more genetic diversity in the breeding population with only a small reduction in long-term genetic gain. Finally the potential of gene bank material as additional source of genetic diversity in the breeding population was examined, using the Dutch MRY cattle breed as a case study. Including old bulls, containing more genetic diversity than recent bulls, in the population of fathers for the next generation, selected with OC, resulted in both a slightly higher genetic merit and more genetic diversity conserved. The impact of selection on genetic diversity can be monitored by estimating the loss of rare variants over time. For the long-term perspectives of populations it is important to use specialised methods and genomic information to balance between selection response and conservation of genetic diversity.  

LanguageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
Supervisors/Advisors
  • Komen, Hans, Promotor
  • Calus, Mario, Co-promotor
  • Windig, Jack, Co-promotor
  • Restoux, G., Co-promotor, External person
Award date23 Feb 2018
Place of PublicationWageningen
Publisher
Print ISBNs9789463432276
DOIs
Publication statusPublished - 2018

Fingerprint

livestock
genomics
genetic variation
breeding
genetic merit
gene banks
pedigree
genome
bulls
selection response
cattle breeds
fathers
marker-assisted selection
genetic improvement
preserves
population size

Cite this

Eynard, Sonia E.. / Using genomic information to conserve genetic diversity in livestock. Wageningen : Wageningen University, 2018. 200 p.
@phdthesis{8647007531c8492e91ea8bee7f27bbf6,
title = "Using genomic information to conserve genetic diversity in livestock",
abstract = "Concern about the status of livestock breeds and their conservation has increased as selection and small population sizes caused loss of genetic diversity. Meanwhile, dense SNP chips and whole genome sequences (WGS) became available, providing opportunities to accurately quantify the impact of selection on genetic diversity and develop tools to better preserve such genetic diversity for long-term perspectives. This thesis aimed to infer the impact of selection and mitigate its effects on genetic diversity using genomic information. One of the advantages of WGS information, compared to pedigree and SNP chip information, is that it provides information on all variants, including rare ones, and ‘true’ relationships between individuals may be estimated thus being useful for evaluating genetic diversity. Taking into account rare variants had significant effects on estimated relationships. Moreover, optimal contribution (OC) strategy was used to perform selection either in a breeding program, maximising genetic merit while minimising loss of genetic diversity, or to build a gene bank, only maximising the conserved genetic diversity, with the aim to quantify loss of genetic diversity due to selection decisions. More genetic diversity was conserved when genomic information was used for selection decisions instead of pedigree and WGS information revealed a high loss of genetic diversity due to losing rare variants. Ways to reduce the loss of genetic diversity during a genomic selection program were investigated. The choice of individuals to update the reference population was proposed as a promising way to better conserve genetic diversity in a breeding population. In fact, changes in the reference population will lead to changes in prediction equations and thus ultimately to a shift in long-term selection decisions. Differences between reference population design using either random, truncation or OC selection of individuals, on the breeding population were modest but OC achieved conservation of more genetic diversity in the breeding population with only a small reduction in long-term genetic gain. Finally the potential of gene bank material as additional source of genetic diversity in the breeding population was examined, using the Dutch MRY cattle breed as a case study. Including old bulls, containing more genetic diversity than recent bulls, in the population of fathers for the next generation, selected with OC, resulted in both a slightly higher genetic merit and more genetic diversity conserved. The impact of selection on genetic diversity can be monitored by estimating the loss of rare variants over time. For the long-term perspectives of populations it is important to use specialised methods and genomic information to balance between selection response and conservation of genetic diversity.  ",
author = "Eynard, {Sonia E.}",
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year = "2018",
doi = "10.18174/428639",
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Eynard, SE 2018, 'Using genomic information to conserve genetic diversity in livestock', Doctor of Philosophy, Wageningen University, Wageningen. https://doi.org/10.18174/428639

Using genomic information to conserve genetic diversity in livestock. / Eynard, Sonia E.

Wageningen : Wageningen University, 2018. 200 p.

Research output: Thesisinternal PhD, WUAcademic

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T1 - Using genomic information to conserve genetic diversity in livestock

AU - Eynard, Sonia E.

N1 - WU thesis 6870 Ph.D. thesis AgroParisTech, 2018 Includes bibliographical references. - With summaries in English and French

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N2 - Concern about the status of livestock breeds and their conservation has increased as selection and small population sizes caused loss of genetic diversity. Meanwhile, dense SNP chips and whole genome sequences (WGS) became available, providing opportunities to accurately quantify the impact of selection on genetic diversity and develop tools to better preserve such genetic diversity for long-term perspectives. This thesis aimed to infer the impact of selection and mitigate its effects on genetic diversity using genomic information. One of the advantages of WGS information, compared to pedigree and SNP chip information, is that it provides information on all variants, including rare ones, and ‘true’ relationships between individuals may be estimated thus being useful for evaluating genetic diversity. Taking into account rare variants had significant effects on estimated relationships. Moreover, optimal contribution (OC) strategy was used to perform selection either in a breeding program, maximising genetic merit while minimising loss of genetic diversity, or to build a gene bank, only maximising the conserved genetic diversity, with the aim to quantify loss of genetic diversity due to selection decisions. More genetic diversity was conserved when genomic information was used for selection decisions instead of pedigree and WGS information revealed a high loss of genetic diversity due to losing rare variants. Ways to reduce the loss of genetic diversity during a genomic selection program were investigated. The choice of individuals to update the reference population was proposed as a promising way to better conserve genetic diversity in a breeding population. In fact, changes in the reference population will lead to changes in prediction equations and thus ultimately to a shift in long-term selection decisions. Differences between reference population design using either random, truncation or OC selection of individuals, on the breeding population were modest but OC achieved conservation of more genetic diversity in the breeding population with only a small reduction in long-term genetic gain. Finally the potential of gene bank material as additional source of genetic diversity in the breeding population was examined, using the Dutch MRY cattle breed as a case study. Including old bulls, containing more genetic diversity than recent bulls, in the population of fathers for the next generation, selected with OC, resulted in both a slightly higher genetic merit and more genetic diversity conserved. The impact of selection on genetic diversity can be monitored by estimating the loss of rare variants over time. For the long-term perspectives of populations it is important to use specialised methods and genomic information to balance between selection response and conservation of genetic diversity.  

AB - Concern about the status of livestock breeds and their conservation has increased as selection and small population sizes caused loss of genetic diversity. Meanwhile, dense SNP chips and whole genome sequences (WGS) became available, providing opportunities to accurately quantify the impact of selection on genetic diversity and develop tools to better preserve such genetic diversity for long-term perspectives. This thesis aimed to infer the impact of selection and mitigate its effects on genetic diversity using genomic information. One of the advantages of WGS information, compared to pedigree and SNP chip information, is that it provides information on all variants, including rare ones, and ‘true’ relationships between individuals may be estimated thus being useful for evaluating genetic diversity. Taking into account rare variants had significant effects on estimated relationships. Moreover, optimal contribution (OC) strategy was used to perform selection either in a breeding program, maximising genetic merit while minimising loss of genetic diversity, or to build a gene bank, only maximising the conserved genetic diversity, with the aim to quantify loss of genetic diversity due to selection decisions. More genetic diversity was conserved when genomic information was used for selection decisions instead of pedigree and WGS information revealed a high loss of genetic diversity due to losing rare variants. Ways to reduce the loss of genetic diversity during a genomic selection program were investigated. The choice of individuals to update the reference population was proposed as a promising way to better conserve genetic diversity in a breeding population. In fact, changes in the reference population will lead to changes in prediction equations and thus ultimately to a shift in long-term selection decisions. Differences between reference population design using either random, truncation or OC selection of individuals, on the breeding population were modest but OC achieved conservation of more genetic diversity in the breeding population with only a small reduction in long-term genetic gain. Finally the potential of gene bank material as additional source of genetic diversity in the breeding population was examined, using the Dutch MRY cattle breed as a case study. Including old bulls, containing more genetic diversity than recent bulls, in the population of fathers for the next generation, selected with OC, resulted in both a slightly higher genetic merit and more genetic diversity conserved. The impact of selection on genetic diversity can be monitored by estimating the loss of rare variants over time. For the long-term perspectives of populations it is important to use specialised methods and genomic information to balance between selection response and conservation of genetic diversity.  

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DO - 10.18174/428639

M3 - internal PhD, WU

SN - 9789463432276

PB - Wageningen University

CY - Wageningen

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