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Scalable sparse testing genomic selection strategy for early yield testing stage

Creator: Atanda, Sikiru Adeniyi
Creator: Olsen, M.
Creator: Crossa, J.
Creator: Burgueño, J.
Creator: Rincent, R.
Creator: Dzidzienyo, D.
Creator: Beyene, Y.
Creator: Gowda, M.
Creator: Dreher, K.
Creator: Prasanna, B.M.
Creator: Tongoona, P.
Creator: Danquah, E.Y.
Creator: Olaoye, G.
Creator: Robbins, K.
Year: 2021
URI: https://hdl.handle.net/10883/21621
Language: English
Publisher: Frontiers
Copyright: CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose
Type: Article
Place of Publication: Switzerland
Volume: 12
DOI: 10.3389/fpls.2021.658978
Keywords: Genomic Selection
Keywords: Preliminary Yield Trials
Keywords: Prediction Accuracy
Keywords: Unstructured Model
Keywords: CDmean
Description: To enable a scalable sparse testing genomic selection (GS) strategy at preliminary yield trials in the CIMMYT maize breeding program, optimal approaches to incorporate genotype by environment interaction (GEI) in genomic prediction models are explored. Two cross-validation schemes were evaluated: CV1, predicting the genetic merit of new bi-parental populations that have been evaluated in some environments and not others, and CV2, predicting the genetic merit of half of a bi-parental population that has been phenotyped in some environments and not others using the coefficient of determination (CDmean) to determine optimized subsets of a full-sib family to be evaluated in each environment. We report similar prediction accuracies in CV1 and CV2, however, CV2 has an intuitive appeal in that all bi-parental populations have representation across environments, allowing efficient use of information across environments. It is also ideal for building robust historical data because all individuals of a full-sib family have phenotypic data, albeit in different environments. Results show that grouping of environments according to similar growing/management conditions improved prediction accuracy and reduced computational requirements, providing a scalable, parsimonious approach to multi-environmental trials and GS in early testing stages. We further demonstrate that complementing the full-sib calibration set with optimized historical data results in improved prediction accuracy for the cross-validation schemes.
Agrovoc: MARKER-ASSISTED SELECTION
Agrovoc: FACTOR ANALYSIS
Agrovoc: MODELS
Related Datasets: https://figshare.com/collections/Scalable_Sparse_Testing_Genomic_Selection_Strategy_for_Early_Yield_Testing_Stage/5478072
ISSN: 1664-462X
Journal: Frontiers in Plant Science
Article number: 658978


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  • Genetic Resources
    Genetic Resources including germplasm collections, wild relatives, genotyping, genomics, and IP
  • Maize
    Maize breeding, phytopathology, entomology, physiology, quality, and biotech

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