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    Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices

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    Journal Article (847.5Kb)
    Date
    2021
    Author
    Wolfe, M.
    Chan, A.W.
    Kulakow, P.
    Rabbi, I.Y.
    Jannink, J.
    Type
    Journal Article
    Review Status
    Peer Review
    Target Audience
    Scientists
    Metadata
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    Abstract/Description
    Diverse crops are both outbred and clonally propagated. Breeders typically use truncation selection of parents and invest significant time, land, and money evaluating the progeny of crosses to find exceptional genotypes. We developed and tested genomic mate selection criteria suitable for organisms of arbitrary homozygosity level where the full-sibling progeny are of direct interest as future parents and/or cultivars. We extended cross variance and covariance variance prediction to include dominance effects and predicted the multivariate selection index genetic variance of crosses based on haplotypes of proposed parents, marker effects, and recombination frequencies. We combined the predicted mean and variance into usefulness criteria for parent and variety development. We present an empirical study of cassava (Manihot esculenta), a staple tropical root crop. We assessed the potential to predict the multivariate genetic distribution (means, variances, and trait covariances) of 462 cassava families in terms of additive and total value using cross-validation. Most variance (89%) and covariance (70%) prediction accuracy estimates were greater than zero. The usefulness of crosses was accurately predicted with good correspondence between the predicted and the actual mean performance of family members breeders selected for advancement as new parents and candidate varieties. We also used a directional dominance model to quantify significant inbreeding depression for most traits. We predicted 47,083 possible crosses of 306 parents and contrasted them to those previously tested to show how mate selection can reveal the new potential within the germplasm. We enable breeders to consider the potential of crosses to produce future parents (progeny with top breeding values) and varieties (progeny with top own performance).
    https://dx.doi.org/10.1093/genetics/iyab122
    Multi standard citation
    Permanent link to this item
    https://hdl.handle.net/20.500.12478/7350
    IITA Authors ORCID
    Peter Kulakowhttps://orcid.org/0000-0002-7574-2645
    Ismail Rabbihttps://orcid.org/0000-0001-9966-2941
    Digital Object Identifier (DOI)
    https://dx.doi.org/10.1093/genetics/iyab122
    Research Themes
    Biotech and Plant Breeding
    IITA Subjects
    Agronomy; Cassava; Food Security; Plant Breeding; Plant Production
    Agrovoc Terms
    Genomics; Marker-Assisted Selection; Cassava; Forecasting; Genetic Covariance
    Regions
    Africa; West Africa
    Countries
    Nigeria
    Hubs
    Headquarters and Western Africa Hub
    Journals
    Genetics
    Collections
    • Journal and Journal Articles4835
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