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    Genomic prediction and QTL discovery in a cassava training population constructed from multiple breeding stages

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    Journal Article (1.300Mb)
    Date
    2020
    Author
    Somo, M.
    Kulembeka, H.
    Mtunda, K.
    Mrema, E.
    Salum, K.
    Wolfe, M.
    Rabbi, I.Y.
    Egesi, C.
    Kawuki, R.
    Ozimati, A.
    Lozano, R.
    Jannink, J.
    Type
    Journal Article
    Review Status
    Peer Review
    Target Audience
    Scientists
    Metadata
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    Abstract/Description
    Assembly of a training population (TP) is an important component of effective genomic selection‐based breeding programs. In this study, we examined the power of diverse germplasm assembled from two cassava (Manihot esculenta Crantz) breeding programs in Tanzania at different breeding stages to predict traits and discover quantitative trait loci (QTL). This is the first genomic selection and genome‐wide association study (GWAS) on Tanzanian cassava data. We detected QTL associated with cassava mosaic disease (CMD) resistance on chromosomes 12 and 16; QTL conferring resistance to cassava brown streak disease (CBSD) on chromosomes 9 and 11; and QTL on chromosomes 2, 3, 8, and 10 associated with resistance to CBSD for root necrosis. We detected a QTL on chromosome 4 and two QTL on chromosome 12 conferring dual resistance to CMD and CBSD. The use of clones in the same stage to construct TPs provided higher trait prediction accuracy than TPs with a mixture of clones from multiple breeding stages. Moreover, clones in the early breeding stage provided more reliable trait prediction accuracy and are better candidates for constructing a TP. Although larger TP sizes have been associated with improved accuracy, in this study, adding clones from Kibaha to those from Ukiriguru and vice versa did not improve the prediction accuracy of either population. Including the Ugandan TP in either population did not improve trait prediction accuracy. This study applied genomic prediction to understand the implications of constructing TP from clones at different breeding stages pooled from different locations on trait accuracy.
    https://dx.doi.org/10.1002/csc2.20003
    Multi standard citation
    Permanent link to this item
    https://hdl.handle.net/20.500.12478/6847
    IITA Authors ORCID
    Ismail Rabbihttps://orcid.org/0000-0001-9966-2941
    Chiedozie Egesihttps://orcid.org/0000-0002-9063-2727
    Non-IITA Authors ORCID
    Jean-Luc Janninkhttps://orcid.org/0000-0003-4849-628X
    Digital Object Identifier (DOI)
    https://dx.doi.org/10.1002/csc2.20003
    Research Themes
    Biotech and Plant Breeding
    IITA Subjects
    Agronomy; Cassava; Disease Control; Food Security; Genetic Improvement; Plant Breeding; Plant Diseases; Plant Genetic Resources; Plant Production
    Agrovoc Terms
    Cassava; Breeding; African Cassava Mosaic Virus; Food Security; Germplasm; Genomics
    Regions
    Africa; East Africa
    Countries
    Tanzania; Uganda
    Hubs
    Eastern Africa Hub
    Journals
    Crop Science
    Collections
    • Journal and Journal Articles4839
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