Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Genomic prediction in an outcrossing and autotetraploid fruit crop: lessons from blueberry breeding

Luís Felipe V. Ferrão, Rodrigo R. Amadeu, Juliana Benevenuto, Ivone de Bem Oliveira, View ORCID ProfilePatricio R. Munoz
doi: https://doi.org/10.1101/2021.03.05.434007
Luís Felipe V. Ferrão
1Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Rodrigo R. Amadeu
1Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Juliana Benevenuto
1Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ivone de Bem Oliveira
2Hortifrut North America, Inc., Estero, FL 33928, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Patricio R. Munoz
1Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Patricio R. Munoz
  • For correspondence: p.munoz@ufl.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Blueberry (Vaccinium corymbosum and hybrids) is a specialty crop, with expanding production and consumption worldwide. The blueberry breeding program at the University of Florida (UF) has greatly contributed to the expansion of production areas by developing low-chilling cultivars better adapted to subtropical and Mediterranean climates of the globe. The breeding program has historically focused on phenotypic recurrent selection. As an autopolyploid, outcrossing, perennial, long juvenile phase crop, blueberry’s breeding cycles are costly and time-consuming, which results in low genetic gains per unit of time. Motivated by the application of molecular markers for a more accurate selection in early stages of breeding, we performed pioneering genomic prediction studies and optimization for implementation in the blueberry breeding program. We have also addressed some complexities of sequence-based geno- typing and model parametrization for an autopolyploid crop, providing empirical contributions that can be extended to other polyploid species. We herein revisited some of our previous genomic prediction studies and described the current achievements in the crop. In this paper, our contribution for genomic prediction in an autotetraploid crop is three-fold: i) summarize previous results on the relevance of model parametrizations, such as diploid or polyploid methods, and inclusion of dominance effects; ii) assess the importance of sequence depth of coverage and genotype dosage calling steps; iii) demonstrate the real impact of genomic selection on leveraging breeding decisions by using an independent validation set. Altogether, we propose a strategy for the use of genomic selection in blueberry, with potential to be applied to other polyploid species of a similar background.

Competing Interest Statement

The authors have declared no competing interest.

  • Abbreviations

    UF
    (University of Florida)
    GEBV
    (genomic Estimated breeding value)
    GWAS
    (genome-wide association studies (GWAS)
    QTL
    (quantitative trait loci)
    EBLUE
    (empirical best linear unbiased estimates)
    SNP
    (single nucleotide polymorphisms)
    (GxE)
    genotype by environment interaction
    MAS
    (marker-assisted selection)
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
    Back to top
    PreviousNext
    Posted March 07, 2021.
    Download PDF

    Supplementary Material

    Email

    Thank you for your interest in spreading the word about bioRxiv.

    NOTE: Your email address is requested solely to identify you as the sender of this article.

    Enter multiple addresses on separate lines or separate them with commas.
    Genomic prediction in an outcrossing and autotetraploid fruit crop: lessons from blueberry breeding
    (Your Name) has forwarded a page to you from bioRxiv
    (Your Name) thought you would like to see this page from the bioRxiv website.
    CAPTCHA
    This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
    Share
    Genomic prediction in an outcrossing and autotetraploid fruit crop: lessons from blueberry breeding
    Luís Felipe V. Ferrão, Rodrigo R. Amadeu, Juliana Benevenuto, Ivone de Bem Oliveira, Patricio R. Munoz
    bioRxiv 2021.03.05.434007; doi: https://doi.org/10.1101/2021.03.05.434007
    Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
    Citation Tools
    Genomic prediction in an outcrossing and autotetraploid fruit crop: lessons from blueberry breeding
    Luís Felipe V. Ferrão, Rodrigo R. Amadeu, Juliana Benevenuto, Ivone de Bem Oliveira, Patricio R. Munoz
    bioRxiv 2021.03.05.434007; doi: https://doi.org/10.1101/2021.03.05.434007

    Citation Manager Formats

    • BibTeX
    • Bookends
    • EasyBib
    • EndNote (tagged)
    • EndNote 8 (xml)
    • Medlars
    • Mendeley
    • Papers
    • RefWorks Tagged
    • Ref Manager
    • RIS
    • Zotero
    • Tweet Widget
    • Facebook Like
    • Google Plus One

    Subject Area

    • Genomics
    Subject Areas
    All Articles
    • Animal Behavior and Cognition (4658)
    • Biochemistry (10313)
    • Bioengineering (7636)
    • Bioinformatics (26241)
    • Biophysics (13481)
    • Cancer Biology (10650)
    • Cell Biology (15363)
    • Clinical Trials (138)
    • Developmental Biology (8467)
    • Ecology (12776)
    • Epidemiology (2067)
    • Evolutionary Biology (16794)
    • Genetics (11373)
    • Genomics (15431)
    • Immunology (10580)
    • Microbiology (25087)
    • Molecular Biology (10172)
    • Neuroscience (54234)
    • Paleontology (398)
    • Pathology (1660)
    • Pharmacology and Toxicology (2884)
    • Physiology (4326)
    • Plant Biology (9213)
    • Scientific Communication and Education (1582)
    • Synthetic Biology (2545)
    • Systems Biology (6761)
    • Zoology (1459)