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Incorporating selfing to purge deleterious alleles in a cassava genomic selection program

View ORCID ProfileMohamed Somo, View ORCID ProfileJean-Luc Jannink
doi: https://doi.org/10.1101/2020.04.04.025841
Mohamed Somo
1Dept. of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
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Jean-Luc Jannink
1Dept. of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
2USDA-ARS, R.W. Holley Center for Agriculture and Health, Ithaca, NY, USA
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  • ORCID record for Jean-Luc Jannink
  • For correspondence: jeanluc.jannink@usda.gov
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Abstract

Cassava has been found to carry high levels of recessive deleterious mutations and it is known to suffer from inbreeding depression. Breeders therefore consider specific approaches to decrease cassava’s genetic load. Using self fertilization to unmask deleterious recessive alleles and therefore accelerate their purging is one possibility. Before implementation of this approach we sought to understand better its consequences through simulation. Founder populations with high directional dominance were simulated using a natural selection forward simulator. The founder population was then subjected to five generations of genomic selection in schemes that did or did not include a generation of phenotypic selection on selfed progeny. We found that genomic selection was less effective under the directional dominance model than under the additive models that have commonly been used in simulations. While selection did increase favorable allele frequencies, increased inbreeding during selection caused decreased gain in genotypic values under the directional dominance. While purging selection on selfed individuals was effective in the first breeding cycle, it was not effective in later cycles, an effect we attributed to the fact that the generation of selfing decreased the relatedness of the genomic prediction training population from selection candidates. That decreased relatedness caused genomic prediction accuracy to be lower in schemes incorporating selfing. We found that selection on individuals partially inbred by one generation of selfing did increase mean genetic value of the partially inbred population, but that this gain was accompanied by a relatively small increase in favorable allele frequencies such that improvement in the outbred population was lower than might have been intuited.

Footnotes

  • https://github.com/jeanlucj/PurgingBySelfingSimulations

  • Abbreviations

    BSL
    Breeding Scheme Language
    CET
    clonal evaluation trial
    GEBV
    genomic estimated breeding value
    GS
    genomic selection
    PYT
    preliminary yield trial
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.
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    Posted April 05, 2020.
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    Incorporating selfing to purge deleterious alleles in a cassava genomic selection program
    Mohamed Somo, Jean-Luc Jannink
    bioRxiv 2020.04.04.025841; doi: https://doi.org/10.1101/2020.04.04.025841
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    Incorporating selfing to purge deleterious alleles in a cassava genomic selection program
    Mohamed Somo, Jean-Luc Jannink
    bioRxiv 2020.04.04.025841; doi: https://doi.org/10.1101/2020.04.04.025841

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