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    Candidate gene sequencing and validation of SNP markers linked to carotenoid content in cassava (Manihot esculenta Crantz)

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    Authors
    Udoh, L.I.
    Gedil, M.
    Parkes, E.Y.
    Kulakow, Peter A.
    Adesoye, A.I.
    Nwuba, C.
    Rabbi, Ismail Y
    Date
    2017
    Language
    en
    Type
    Journal Article
    Review status
    Peer Review
    Accessibility
    Limited Access
    Metadata
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    Citation
    Udo, L.I., Gedil, M., Parkes, E.Y., Kulakow, P., Adesoye, A., Nwuba, C. & Rabbi, I.Y. (2017). Candidate gene sequencing and validation of SNP markers linked to carotenoid content in cassava (Manihot esculenta Crantz). Molecular Breeding, 37(123), 1-12.
    Permanent link to cite or share this item: http://hdl.handle.net/10568/83509
    DOI: http://dx.doi.org/10.1007/s11032-017-0718-5
    Abstract/Description
    Cassava is a widely grown staple in Sub-Saharan Africa and consumed as a cheap source of calories, but the crop is deficient in micronutrients including pro-vitamin A carotenoids. This challenge is currently being addressed through biofortification breeding that relies on phenotypic selection. Genebased markers linked to pro-vitamin A content variation are expected to increase the rate of genetic gain for this critical trait. We sequenced four candidate carotenoid genes from 167 cassava accessions representing the diversity of elite breeder lines from IITA. Total carotenoid content was determined using spectrophotometer and total β-carotene was quantified by highperformance liquid chromatography. Storage root yellowness due to carotenoid pigmentation was assessed. We carried out candidate gene association analysis that accounts for population structure and kinship using genome-wide single nucleotide polymorphisms (SNPs) generated through genotyping-by-sequencing. Significant SNPs were used to design competitive allele-specific PCR assays and validated on the larger population for potential use in markerassisted selection breeding. Candidate gene sequencing of the genes β-carotene hydroxylase (crtRB), phytoene synthase (PSY2), lycopene epsilon cyclase (lcyE), and lycopene beta cyclase (lcyB) yielded a total of 37 SNPs. Total carotenoid content, total β-carotene, and color parameters were significantly associated with markers in the PSY2 gene. The SNPs from lcyE were significantly associated with color while those of lcyB and crtRB were not significantly associated with carotenoids or color parameters. These validated and breeder-friendly markers have potential to enhance the efficiency of selection for high β-carotene cassava, thus accelerating genetic gain.
    Notes
    Published online: 11 Sept. 2017
    CGIAR Affiliations
    Roots, Tubers and Bananas
    AGROVOC Keywords
    CASSAVA; VITAMIN A; CAROTINOIDS; SUBSAHARAN AFRICA; NIGERIA; MARKER-ASSISTED SELECTION; CANDIDATE GENE ASSOCIATION; BIOFORTIFICATION
    Subjects
    CASSAVA
    Countries
    NIGERIA
    Regions
    AFRICA; WEST AFRICA
    Investors/sponsors
    HarvestPlus; CGIAR Research Program on Roots, Tubers, and Bananas
    Collections
    • RTB Journal Articles [665]
    • IITA Journal Articles [1862]

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