Efficient computation of the additive relationship matrix and its inverse in self-breeding individuals

Rebollo, Inés - Rosas, Juan Eduardo - Aguilar, Ignacio

Resumen:

Inbreeding increases homozygosity and therefore additive relationships within and among related individuals. The main cause of inbreeding is breeding of related individuals in which case the inbreeding coefficient (Fs) = 0.5asd where asd is the additive relationship among the individual's parents. An extreme case of inbreeding is the self-breeding occurring in plant inbred lines such as those generated by multiple generations of self-pollination, or by double haploid production. In the case of selfing generations, Fs = 1 - 0.5n where n is the number of selfing generations. If the parents of an individual are related and then it is self-bred, both sources for inbreeding should be accounted for in the progeny and Fs = 1 - 0.5n + 0.5n (0.5asd). In order to perform Best Linear Unbiased Prediction (BLUP), accurate calculation of the additive relationship coefficients matrix (A) or its inverse (A-1) is needed depending on the solving algorithm, or for single-step genomic BLUP where the submatrix A22 is used. Current methods to calculate A accounting for selfing generations require the expansion of the pedigree, which is computationally inefficient. Furthermore, freely available algorithms for setting up A-1 without generating A and inverting it do not contemplate selfing generations. The objective of this work was to develop efficient methods for calculating A and A-1 matrices accounting for inbreeding in self-bred individuals. Existing algorithms were adapted to account for selfing generations in A that require less memory than existing methods, and algorithms for the direct construction of A-1 accounting for inbreeding and selfing where developed in R. These algorithms are freely available at https://github.com/minesrebollo. In the future, these methods will be tested in large datasets and their performance will be reported.


Detalles Bibliográficos
2020
Agencia Nacional de Investigación e Innovación
self-pollination relationship matrix, computing methods, Single-Step GBLUP.
Ciencias Naturales y Exactas
Matemáticas
Estadística y Probabilidad
Ciencias de la Computación e Información
Ciencias de la Información y Bioinformática
Ciencias Biológicas
Genética y Herencia
Inglés
Agencia Nacional de Investigación e Innovación
REDI
https://hdl.handle.net/20.500.12381/450
https://icqg6.org/wp-content/uploads/2021/04/ines-rebollo-EfficientComputation.mp4
Acceso abierto
Reconocimiento 4.0 Internacional. (CC BY)
_version_ 1814959266153365504
author Rebollo, Inés
author2 Rosas, Juan Eduardo
Aguilar, Ignacio
author2_role author
author
author_facet Rebollo, Inés
Rosas, Juan Eduardo
Aguilar, Ignacio
author_role author
bitstream.checksum.fl_str_mv 2d97768b1a25a7df5a347bb58fd2d77f
0ba2586e0a291a8663150b06bf28da0a
bitstream.checksumAlgorithm.fl_str_mv MD5
MD5
bitstream.url.fl_str_mv https://redi.anii.org.uy/jspui/bitstream/20.500.12381/450/2/license.txt
https://redi.anii.org.uy/jspui/bitstream/20.500.12381/450/1/ines-rebollo-EfficientComputation.mp4
collection REDI
dc.creator.none.fl_str_mv Rebollo, Inés
Rosas, Juan Eduardo
Aguilar, Ignacio
dc.date.accessioned.none.fl_str_mv 2021-09-21T16:59:40Z
dc.date.available.none.fl_str_mv 2021-09-21T16:59:40Z
dc.date.issued.none.fl_str_mv 2020-11-03
dc.description.abstract.none.fl_txt_mv Inbreeding increases homozygosity and therefore additive relationships within and among related individuals. The main cause of inbreeding is breeding of related individuals in which case the inbreeding coefficient (Fs) = 0.5asd where asd is the additive relationship among the individual's parents. An extreme case of inbreeding is the self-breeding occurring in plant inbred lines such as those generated by multiple generations of self-pollination, or by double haploid production. In the case of selfing generations, Fs = 1 - 0.5n where n is the number of selfing generations. If the parents of an individual are related and then it is self-bred, both sources for inbreeding should be accounted for in the progeny and Fs = 1 - 0.5n + 0.5n (0.5asd). In order to perform Best Linear Unbiased Prediction (BLUP), accurate calculation of the additive relationship coefficients matrix (A) or its inverse (A-1) is needed depending on the solving algorithm, or for single-step genomic BLUP where the submatrix A22 is used. Current methods to calculate A accounting for selfing generations require the expansion of the pedigree, which is computationally inefficient. Furthermore, freely available algorithms for setting up A-1 without generating A and inverting it do not contemplate selfing generations. The objective of this work was to develop efficient methods for calculating A and A-1 matrices accounting for inbreeding in self-bred individuals. Existing algorithms were adapted to account for selfing generations in A that require less memory than existing methods, and algorithms for the direct construction of A-1 accounting for inbreeding and selfing where developed in R. These algorithms are freely available at https://github.com/minesrebollo. In the future, these methods will be tested in large datasets and their performance will be reported.
dc.description.sponsorship.none.fl_txt_mv Agencia Nacional de Investigación e Innovación
dc.identifier.anii.es.fl_str_mv FSDA_1_2018_1_154120
dc.identifier.uri.none.fl_str_mv https://hdl.handle.net/20.500.12381/450
dc.identifier.url.none.fl_str_mv https://icqg6.org/wp-content/uploads/2021/04/ines-rebollo-EfficientComputation.mp4
dc.language.iso.none.fl_str_mv eng
dc.relation.es.fl_str_mv https://icqg6.org/icqg6-abstracts-book/
dc.rights.es.fl_str_mv Acceso abierto
dc.rights.license.none.fl_str_mv Reconocimiento 4.0 Internacional. (CC BY)
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
dc.source.none.fl_str_mv reponame:REDI
instname:Agencia Nacional de Investigación e Innovación
instacron:Agencia Nacional de Investigación e Innovación
dc.subject.anii.none.fl_str_mv Ciencias Naturales y Exactas
Matemáticas
Estadística y Probabilidad
Ciencias de la Computación e Información
Ciencias de la Información y Bioinformática
Ciencias Biológicas
Genética y Herencia
dc.subject.es.fl_str_mv self-pollination relationship matrix, computing methods, Single-Step GBLUP.
dc.title.none.fl_str_mv Efficient computation of the additive relationship matrix and its inverse in self-breeding individuals
dc.type.es.fl_str_mv Videograbación
dc.type.none.fl_str_mv info:eu-repo/semantics/other
dc.type.version.es.fl_str_mv Publicado
dc.type.version.none.fl_str_mv info:eu-repo/semantics/publishedVersion
description Inbreeding increases homozygosity and therefore additive relationships within and among related individuals. The main cause of inbreeding is breeding of related individuals in which case the inbreeding coefficient (Fs) = 0.5asd where asd is the additive relationship among the individual's parents. An extreme case of inbreeding is the self-breeding occurring in plant inbred lines such as those generated by multiple generations of self-pollination, or by double haploid production. In the case of selfing generations, Fs = 1 - 0.5n where n is the number of selfing generations. If the parents of an individual are related and then it is self-bred, both sources for inbreeding should be accounted for in the progeny and Fs = 1 - 0.5n + 0.5n (0.5asd). In order to perform Best Linear Unbiased Prediction (BLUP), accurate calculation of the additive relationship coefficients matrix (A) or its inverse (A-1) is needed depending on the solving algorithm, or for single-step genomic BLUP where the submatrix A22 is used. Current methods to calculate A accounting for selfing generations require the expansion of the pedigree, which is computationally inefficient. Furthermore, freely available algorithms for setting up A-1 without generating A and inverting it do not contemplate selfing generations. The objective of this work was to develop efficient methods for calculating A and A-1 matrices accounting for inbreeding in self-bred individuals. Existing algorithms were adapted to account for selfing generations in A that require less memory than existing methods, and algorithms for the direct construction of A-1 accounting for inbreeding and selfing where developed in R. These algorithms are freely available at https://github.com/minesrebollo. In the future, these methods will be tested in large datasets and their performance will be reported.
eu_rights_str_mv openAccess
format other
id REDI_e950f75a23178d433d2d3ed8ddd0ceaa
identifier_str_mv FSDA_1_2018_1_154120
instacron_str Agencia Nacional de Investigación e Innovación
institution Agencia Nacional de Investigación e Innovación
instname_str Agencia Nacional de Investigación e Innovación
language eng
network_acronym_str REDI
network_name_str REDI
oai_identifier_str oai:redi.anii.org.uy:20.500.12381/450
publishDate 2020
reponame_str REDI
repository.mail.fl_str_mv jmaldini@anii.org.uy
repository.name.fl_str_mv REDI - Agencia Nacional de Investigación e Innovación
repository_id_str 9421
rights_invalid_str_mv Reconocimiento 4.0 Internacional. (CC BY)
Acceso abierto
spelling Reconocimiento 4.0 Internacional. (CC BY)Acceso abiertoinfo:eu-repo/semantics/openAccess2021-09-21T16:59:40Z2021-09-21T16:59:40Z2020-11-03https://hdl.handle.net/20.500.12381/450FSDA_1_2018_1_154120https://icqg6.org/wp-content/uploads/2021/04/ines-rebollo-EfficientComputation.mp4Inbreeding increases homozygosity and therefore additive relationships within and among related individuals. The main cause of inbreeding is breeding of related individuals in which case the inbreeding coefficient (Fs) = 0.5asd where asd is the additive relationship among the individual's parents. An extreme case of inbreeding is the self-breeding occurring in plant inbred lines such as those generated by multiple generations of self-pollination, or by double haploid production. In the case of selfing generations, Fs = 1 - 0.5n where n is the number of selfing generations. If the parents of an individual are related and then it is self-bred, both sources for inbreeding should be accounted for in the progeny and Fs = 1 - 0.5n + 0.5n (0.5asd). In order to perform Best Linear Unbiased Prediction (BLUP), accurate calculation of the additive relationship coefficients matrix (A) or its inverse (A-1) is needed depending on the solving algorithm, or for single-step genomic BLUP where the submatrix A22 is used. Current methods to calculate A accounting for selfing generations require the expansion of the pedigree, which is computationally inefficient. Furthermore, freely available algorithms for setting up A-1 without generating A and inverting it do not contemplate selfing generations. The objective of this work was to develop efficient methods for calculating A and A-1 matrices accounting for inbreeding in self-bred individuals. Existing algorithms were adapted to account for selfing generations in A that require less memory than existing methods, and algorithms for the direct construction of A-1 accounting for inbreeding and selfing where developed in R. These algorithms are freely available at https://github.com/minesrebollo. In the future, these methods will be tested in large datasets and their performance will be reported.Agencia Nacional de Investigación e Innovaciónenghttps://icqg6.org/icqg6-abstracts-book/self-pollination relationship matrix, computing methods, Single-Step GBLUP.Ciencias Naturales y ExactasMatemáticasEstadística y ProbabilidadCiencias de la Computación e InformaciónCiencias de la Información y BioinformáticaCiencias BiológicasGenética y HerenciaEfficient computation of the additive relationship matrix and its inverse in self-breeding individualsVideograbaciónPublicadoinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/otherINIA//Ciencias Naturales y Exactas/Matemáticas/Estadística y Probabilidad//Ciencias Naturales y Exactas/Ciencias de la Computación e Información/Ciencias de la Información y Bioinformática//Ciencias Naturales y Exactas/Ciencias Biológicas/Genética y Herenciareponame:REDIinstname:Agencia Nacional de Investigación e Innovacióninstacron:Agencia Nacional de Investigación e InnovaciónRebollo, InésRosas, Juan EduardoAguilar, IgnacioLICENSElicense.txtlicense.txttext/plain; charset=utf-84746https://redi.anii.org.uy/jspui/bitstream/20.500.12381/450/2/license.txt2d97768b1a25a7df5a347bb58fd2d77fMD52ORIGINALines-rebollo-EfficientComputation.mp4ines-rebollo-EfficientComputation.mp4Archivo mp4 Presentación en videoapplication/octet-stream13295677https://redi.anii.org.uy/jspui/bitstream/20.500.12381/450/1/ines-rebollo-EfficientComputation.mp40ba2586e0a291a8663150b06bf28da0aMD5120.500.12381/4502021-09-21 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- Agencia Nacional de Investigación e Innovaciónfalse
spellingShingle Efficient computation of the additive relationship matrix and its inverse in self-breeding individuals
Rebollo, Inés
self-pollination relationship matrix, computing methods, Single-Step GBLUP.
Ciencias Naturales y Exactas
Matemáticas
Estadística y Probabilidad
Ciencias de la Computación e Información
Ciencias de la Información y Bioinformática
Ciencias Biológicas
Genética y Herencia
status_str publishedVersion
title Efficient computation of the additive relationship matrix and its inverse in self-breeding individuals
title_full Efficient computation of the additive relationship matrix and its inverse in self-breeding individuals
title_fullStr Efficient computation of the additive relationship matrix and its inverse in self-breeding individuals
title_full_unstemmed Efficient computation of the additive relationship matrix and its inverse in self-breeding individuals
title_short Efficient computation of the additive relationship matrix and its inverse in self-breeding individuals
title_sort Efficient computation of the additive relationship matrix and its inverse in self-breeding individuals
topic self-pollination relationship matrix, computing methods, Single-Step GBLUP.
Ciencias Naturales y Exactas
Matemáticas
Estadística y Probabilidad
Ciencias de la Computación e Información
Ciencias de la Información y Bioinformática
Ciencias Biológicas
Genética y Herencia
url https://hdl.handle.net/20.500.12381/450
https://icqg6.org/wp-content/uploads/2021/04/ines-rebollo-EfficientComputation.mp4