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 |
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Acceso abierto | |
Reconocimiento 4.0 Internacional. (CC BY) |
Sumario: | 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. |
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