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

dc.contributor.authorBredeson, J.V.
dc.contributor.authorLyons, J.B.
dc.contributor.authorOniyinde, I.O.
dc.contributor.authorOkereke, N.R.
dc.contributor.authorKolade, O.
dc.contributor.authorNnabue, I.
dc.contributor.authorNwadili, C.O.
dc.contributor.authorHřibová, E.
dc.contributor.authorParker, M.
dc.contributor.authorNwogha, J.
dc.contributor.authorShu, S.
dc.contributor.authorCarlson, J.
dc.contributor.authorKariba, R.
dc.contributor.authorMuthemba, S.
dc.contributor.authorKnop, K.
dc.contributor.authorBarton, G.J.
dc.contributor.authorSherwood, A.V.
dc.contributor.authorLopez-Montes, A.
dc.contributor.authorAsiedu, R.
dc.contributor.authorJamnadass, R.
dc.contributor.authorMuchugi, A.
dc.contributor.authorGoodstein, D.
dc.contributor.authorEgesi, C.
dc.contributor.authorFeatherston, J.
dc.contributor.authorAsfaw, A.
dc.contributor.authorSimpson, G.G.
dc.contributor.authorDoležel, J.
dc.contributor.authorHendre, P.
dc.contributor.authorVan Deynze, A.
dc.contributor.authorKumar, P.L.
dc.contributor.authorObidiegwu, J.
dc.contributor.authorBhattacharjee, R.
dc.contributor.authorRokhsar, D.S.
dc.date.accessioned2022-05-12T09:11:35Z
dc.date.available2022-05-12T09:11:35Z
dc.date.issued2022
dc.identifier.citationBredeson, J.V., Lyons, J.B., Oniyinde, I.O., Okereke, N.R., Kolade, O., Nnabue, I., ... & Rokhsar, D.S. (2022). Chromosome evolution and the genetic basis of agronomically important traits in greater yam. Nature Communications, 13(1), 1-16.
dc.identifier.issn2041-1723
dc.identifier.urihttps://hdl.handle.net/20.500.12478/7457
dc.description.abstractThe 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.
dc.format.extent1-16
dc.language.isoen
dc.subjectChromosomes
dc.subjectEvolution
dc.subjectYams
dc.subjectQuantitative Trait Loci
dc.subjectBreeding
dc.subjectWest Africa
dc.subjectAgronomic Traits
dc.titleChromosome evolution and the genetic basis of agronomically important traits in greater yam
dc.typeJournal Article
cg.contributor.crpMaize
cg.contributor.crpRoots, Tubers and Bananas
cg.contributor.affiliationUniversity of California
cg.contributor.affiliationInnovative Genomics Institute, USA
cg.contributor.affiliationInternational Institute of Tropical Agriculture
cg.contributor.affiliationNational Root Crops Research Institute, Nigeria
cg.contributor.affiliationInstitute of Experimental Botany of the Czech Academy of Sciences
cg.contributor.affiliationUniversity of Dundee
cg.contributor.affiliationDOE Joint Genome Institute, USA
cg.contributor.affiliationWorld Agroforestry
cg.contributor.affiliationAfrican Orphan Crops Consortium
cg.contributor.affiliationCornell University
cg.contributor.affiliationAgricultural Research Council, South Africa
cg.contributor.affiliationJames Hutton Institute
cg.contributor.affiliationOkinawa Institute of Science and Technology
cg.contributor.affiliationChan-Zuckerberg BioHub, USA
cg.contributor.affiliationUniversity of Copenhagen
cg.contributor.affiliationInternational Trade Center
cg.coverage.regionAfrica
cg.coverage.regionWest Africa
cg.coverage.countryNigeria
cg.coverage.hubHeadquarters and Western Africa Hub
cg.researchthemeBiotech and Plant Breeding
cg.researchthemePlant Production and Health
cg.identifier.bibtexciteidBREDESON:2022
cg.isijournalISI Journal
cg.authorship.typesCGIAR and developing country institute
cg.iitasubjectAgronomy
cg.iitasubjectFood Security
cg.iitasubjectGenetic Improvement
cg.iitasubjectPlant Breeding
cg.iitasubjectPlant Production
cg.iitasubjectYam
cg.journalNature Communications
cg.notesOpen Access Journal; Published online: 14 Apr 2022
cg.accessibilitystatusOpen Access
cg.reviewstatusPeer Review
cg.usagerightslicenseCreative Commons Attribution 4.0 (CC BY 0.0)
cg.targetaudienceScientists
cg.identifier.doihttps://dx.doi.org/10.1038/s41467-022-29114-w
cg.iitaauthor.identifierOlufisayo Kolade: 0000-0003-1920-1972
cg.iitaauthor.identifierAntonio Jose Lopez-Montes: 0000-0001-5801-2475
cg.iitaauthor.identifierRobert Asiedu: 0000-0001-8943-2376
cg.iitaauthor.identifierChiedozie Egesi: 0000-0002-9063-2727
cg.iitaauthor.identifierAsrat Asfaw: 0000-0002-4859-0631
cg.iitaauthor.identifierP. Lava Kumar: 0000-0003-4388-6510
cg.iitaauthor.identifierRanjana Bhattacharjee: 0000-0002-5184-5930
cg.futureupdate.requiredNo
cg.identifier.issue1
cg.identifier.volume13
cg.contributor.acknowledgementsAt 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, Pathology/Virology Unit, and Farm Office at IITA, Ibadan, Nigeria for support in laboratory and field activities. We thank Kwabena Darkwa and Agre Paterne, IITA, Ibadan Nigeria for their support in phenotyping population TDa1401. Boas Pucker provided the single-haploid assembly of D. dumetorum. Christopher Saski and Mary Duke provided WGS data of TDa95/00328 and TDa95-310. We thank Ismail Rabbi for early discussions in proposal development, and he and Gezahegn Girma for providing D. alata DNA of specific breeding lines. This work is based on a project supported by the National Science Foundation BREAD program, Award No. 1543967 to D.S.R., R.B., and J.E.O. We wish to acknowledge subsidy from the Integrated Genotyping Service and Support platform, a collaborative project between the International Livestock Research Institute (ILRI) and the Bill and Melinda Gates Foundation. DNA extractions for PacBio sequencing, and RNA extractions, were carried out at ICRAF with partial support from the African Orphan Crops Consortium. RNA-seq was funded by the Illumina Greater Good Initiative. Nanopore DRS work was supported by The University of Dundee Global Challenges Research Fund to G.G.S. and G.J.B., Biotechnology and Biological Sciences Research Council (BB/M004155/1) to G.G.S. and G.J.B. and H2020 Marie Skłodowska-Curie Actions (799300) to K.K. Sequencing performed at the Vincent J. Coates Genomics Sequencing Laboratory, UC Berkeley, was partially supported by NIH S10 OD018174 Instrumentation Grant. D.S.R. was supported by Chan Zuckerberg BioHub, internal funds at the Okinawa Institute of Science and Technology, and the Marthella Foskett-Brown Chair in Biological Science at UC Berkeley. This research used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.


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