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