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    Genetic mapping using genotypingbysequencing in the clonally propagated cassava

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    Date
    2014
    Author
    Rabbi, Ismail Y
    Hamblin, M.
    Gedil, M.
    Kulakow, P.A.
    Ferguson, M.
    Ikpan, A.
    Ly, D.
    Jannink, Jean-Luc
    Type
    Journal Article
    Metadata
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    Abstract/Description
    Cassava (Manihot esculenta L.) is one of the most important food crops in the tropics, but yields are far below their potential. The gene pool of cassava contains natural genetic diversity relevant to many important breeding goals, but breeding progress has been slow, partly because of insuf-ficient genomic resources. As a first step toward implementing genomewide genetic studies that will facilitate rapid genetic gain through breed-ing, we genotyped-by-sequencing a set of 182 full-sibs population of cassava that segregated in several traits: resistance to the cassava mosaic disease (CMD) and yield under CMD pressure; increased carotenoid content in storage roots; color of stem exterior and anthocyanin pigmen-tation in the petioles, inner root skin, and api-cal leaves. Employing a rare-cutting restriction enzyme, PstI, in a genotyping-by-sequencing (GBS) library preparation, we obtained 2478 segregating single nucleotide polymorphisms (SNPs), of which 1257 passed standard filter-ing for missing genotypes and deviation from expected genotypic frequencies. We mapped 772 SNPs across 19 linkage groups and anchored 313 unique scaffolds from the version 4.1 of the cassava genome assembly. Most of the stud-ied morphological traits as well as resistance to CMD and root carotenoid content showed quali-tative inheritance. As expected, quantitative trait loci analysis for these traits revealed single loci surrounded by small confidence intervals. Yield under CMD was associated with the CMD resis-tance locus. We show that GBS is a powerful genotyping tool that provides a sufficient number of markers for unraveling the genetic architecture of Mendelian traits in cassava in addition to the development of a robust genetic map that can help anchor unassembled genomic scaffolds.
    https://dx.doi.org/10.2135/cropsci2013.07.0482
    Multi standard citation
    Permanent link to this item
    https://hdl.handle.net/20.500.12478/1012
    Digital Object Identifier (DOI)
    https://dx.doi.org/10.2135/cropsci2013.07.0482
    IITA Subjects
    Cassava
    Agrovoc Terms
    Genetic; Cassava; Dna
    Regions
    Africa; West Africa
    Countries
    Nigeria
    Journals
    Crop Science
    Collections
    • Journal and Journal Articles4835
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