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    Chromosome evolution and the genetic basis of agronomically important traits in greater yam

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    Journal Article (560.7Kb)
    Date
    2022
    Author
    Bredeson, J.V.
    Lyons, J.B.
    Oniyinde, I.O.
    Okereke, N.R.
    Kolade, O.
    Nnabue, I.
    Nwadili, C.O.
    Hřibová, E.
    Parker, M.
    Nwogha, J.
    Shu, S.
    Carlson, J.
    Kariba, R.
    Muthemba, S.
    Knop, K.
    Barton, G.J.
    Sherwood, A.V.
    Lopez-Montes, A.
    Asiedu, R.
    Jamnadass, R.
    Muchugi, A.
    Goodstein, D.
    Egesi, C.
    Featherston, J.
    Asfaw, A.
    Simpson, G.G.
    Doležel, J.
    Hendre, P.
    Van Deynze, A.
    Kumar, P.L.
    Obidiegwu, J.
    Bhattacharjee, R.
    Rokhsar, D.S.
    Type
    Journal Article
    Review Status
    Peer Review
    Target Audience
    Scientists
    Metadata
    Show full item record
    Abstract/Description
    The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.
    Acknowledgements
    At the University of California, Davis, Genome and Biomedical Sciences facility, we thank Oanh Nguyen for troubleshooting and advice for DNA isolation and PacBio sequencing, Emily Kumimoto for mate-pair libraries, and Lutz Froenicke for management. For facilitating DArTseq genotyping, we thank: Andrzej Kilian (Diversity Arrays Technology); and Clay Sneller, Jackline Chepkoech, Mercy Chepngetich, and IGSS/SEQART staff at BecA-ILRI Hub. We thank the staff of Bioscience Center, Yam Breeding Unit, ...
    https://dx.doi.org/10.1038/s41467-022-29114-w
    Multi standard citation
    Permanent link to this item
    https://hdl.handle.net/20.500.12478/7457
    IITA Authors ORCID
    Olufisayo Koladehttps://orcid.org/0000-0003-1920-1972
    Antonio Jose Lopez-Monteshttps://orcid.org/0000-0001-5801-2475
    Robert Asieduhttps://orcid.org/0000-0001-8943-2376
    Chiedozie Egesihttps://orcid.org/0000-0002-9063-2727
    Asrat Asfawhttps://orcid.org/0000-0002-4859-0631
    P. Lava Kumarhttps://orcid.org/0000-0003-4388-6510
    Ranjana Bhattacharjeehttps://orcid.org/0000-0002-5184-5930
    Digital Object Identifier (DOI)
    https://dx.doi.org/10.1038/s41467-022-29114-w
    Research Themes
    Biotech and Plant Breeding; Plant Production and Health
    IITA Subjects
    Agronomy; Food Security; Genetic Improvement; Plant Breeding; Plant Production; Yam
    Agrovoc Terms
    Chromosomes; Evolution; Yams; Quantitative Trait Loci; Breeding; West Africa; Agronomic Traits
    Regions
    Africa; West Africa
    Countries
    Nigeria
    Hubs
    Headquarters and Western Africa Hub
    Journals
    Nature Communications
    Collections
    • Journal and Journal Articles4835
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