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    Genome-wide association analysis for tuber dry matter and oxidative browning in water yam (Dioscorea alata L.)

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    Journal Article (10.37Mb)
    Date
    2020
    Author
    Gatarira, C.
    Agre, P.
    Matsumoto, R.
    Edemodu, A.
    Adetimirin, V.
    Bhattacharjee, R.
    Asiedu, R.
    Asfaw, A.
    Type
    Journal Article
    Review Status
    Peer Review
    Target Audience
    Scientists
    Metadata
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    Abstract/Description
    Yam (Dioscorea spp.) is a nutritional and medicinal staple tuber crop grown in the tropics and sub-tropics. Among the food yam species, water yam (Dioscorea alata L.) is the most widely distributed and cultivated species worldwide. Tuber dry matter content (DMC) and oxidative browning (OxB) are important quality attributes that determine cultivar acceptability in water yam. This study used a single nucleotide polymorphism (SNP) assay from a diversity arrays technology (DArT) platform for a genome-wide association study (GWAS) of the two quality traits in a panel of 100 water yam clones grown in three environments. The marker–trait association analysis identified significant SNPs associated with tuber DMC on chromosomes 6 and 19 and with OxB on chromosome 5. The significant SNPs cumulatively explained 45.87 and 12.74% of the total phenotypic variation for the tuber DMC and OxB, respectively. Gene annotation for the significant SNP loci identified important genes associated in the process of the proteolytic modification of carbohydrates in the dry matter accumulation pathway as well as fatty acid β-oxidation in peroxisome for enzymatic oxidation. Additional putative genes were also identified in the peak SNP sites for both tuber dry matter and enzymatic oxidation with unknown functions. The results of this study provide valuable insight for further dissection of the genetic architecture of tuber dry matter and enzymatic oxidation in water yam. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving food quality traits in water yam.
    https://dx.doi.org/10.3390/plants9080969
    Multi standard citation
    Permanent link to this item
    https://hdl.handle.net/20.500.12478/7024
    IITA Authors ORCID
    Paterne AGREhttps://orcid.org/0000-0003-1231-2530
    Ryo Matsumotohttps://orcid.org/0000-0002-0106-6728
    Ranjana Bhattacharjeehttps://orcid.org/0000-0002-5184-5930
    Robert Asieduhttps://orcid.org/0000-0001-8943-2376
    Asrat Asfawhttps://orcid.org/0000-0002-4859-0631
    Digital Object Identifier (DOI)
    https://dx.doi.org/10.3390/plants9080969
    Research Themes
    Biotech and Plant Breeding
    IITA Subjects
    Agronomy; Food Security; Genetic Improvement; Plant Breeding; Plant Genetic Resources; Plant Production; Yam
    Agrovoc Terms
    Genes; Bibliographic Information; Yams; Dry Matter; Tubers; Quality
    Regions
    Africa; West Africa
    Countries
    Nigeria
    Hubs
    Headquarters and Western Africa Hub
    Journals
    Plants
    Collections
    • Journal and Journal Articles4835
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