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Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination

dc.contributor.authorTamiru, M.
dc.contributor.authorNatsume, S.
dc.contributor.authorTakagi, H.
dc.contributor.authorWhite, B.
dc.contributor.authorYaegashi, H.
dc.contributor.authorShimizu, M.
dc.contributor.authorYoshida, K.
dc.contributor.authorUemura, A.
dc.contributor.authorOikawa, K.
dc.contributor.authorAbe, A.
dc.contributor.authorUrasaki, N.
dc.contributor.authorMatsumura, H
dc.contributor.authorBabil, P.
dc.contributor.authorYamanaka, S.
dc.contributor.authorMatsumoto, R.
dc.contributor.authorMuranaka, S.
dc.contributor.authorGirma, G.
dc.contributor.authorLópez Montes, A.
dc.contributor.authorGedil, M.
dc.contributor.authorBhattacharjee, R.
dc.contributor.authorAbberton, M.T.
dc.contributor.authorKumar, P.L.
dc.contributor.authorRabbi, Ismail Y
dc.contributor.authorTsujimura, M.
dc.contributor.authorTerachi, T.
dc.contributor.authorHaerty, W.
dc.contributor.authorCorpas, M.
dc.contributor.authorKamoun, S.
dc.contributor.authorKahl, G.
dc.contributor.authorTakagi, H.
dc.contributor.authorAsiedu, Robert
dc.contributor.authorTerauchi, R
dc.date.accessioned2019-12-04T11:10:59Z
dc.date.available2019-12-04T11:10:59Z
dc.date.issued2017
dc.identifier.citationTamiru, M., Natsume, S., Takagi, H., White, B., Yaegashi, H., Shimizu, M., ... & Terauchi, R. (2017). Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination. BMC Biology, 15(86), 1-20.
dc.identifier.issn1741-7007
dc.identifier.urihttps://hdl.handle.net/20.500.12478/2320
dc.descriptionOpen Access Journal; Published online: 19 Sept 2017
dc.description.abstractBackground Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected “orphan” crop that would benefit from crop improvement efforts. However, the lack of genetic and genomic tools has impeded the improvement of this staple crop. Results To accelerate marker-assisted breeding of yam, we performed genome analysis of white Guinea yam (Dioscorea rotundata) and assembled a 594-Mb genome, 76.4% of which was distributed among 21 linkage groups. In total, we predicted 26,198 genes. Phylogenetic analyses with 2381 conserved genes revealed that Dioscorea is a unique lineage of monocotyledons distinct from the Poales (rice), Arecales (palm), and Zingiberales (banana). The entire Dioscorea genus is characterized by the occurrence of separate male and female plants (dioecy), a feature that has limited efficient yam breeding. To infer the genetics of sex determination, we performed whole-genome resequencing of bulked segregants (quantitative trait locus sequencing [QTL-seq]) in F1 progeny segregating for male and female plants and identified a genomic region associated with female heterogametic (male = ZZ, female = ZW) sex determination. We further delineated the W locus and used it to develop a molecular marker for sex identification of Guinea yam plants at the seedling stage. Conclusions Guinea yam belongs to a unique and highly differentiated clade of monocotyledons. The genome analyses and sex-linked marker development performed in this study should greatly accelerate marker-assisted breeding of Guinea yam. In addition, our QTL-seq approach can be utilized in genetic studies of other outcrossing crops and organisms with highly heterozygous genomes. Genomic analysis of orphan crops such as yam promotes efforts to improve food security and the sustainability of tropical agriculture.
dc.description.sponsorshipJapan International Research Center for Agricultural Sciences
dc.format.extent1-20
dc.language.isoen
dc.subjectYams
dc.subjectDioscorea
dc.subjectSex Determination
dc.subjectFood Security
dc.subjectGenome
dc.subjectMolecular Marker
dc.subjectGuinea Yam
dc.subjectWhole-Genome Sequence
dc.subjectDioecy
dc.titleGenome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination
dc.typeJournal Article
dc.description.versionPeer Review
cg.contributor.crpGrain Legumes
cg.contributor.crpMaize
cg.contributor.crpRoots, Tubers and Bananas
cg.contributor.affiliationIwate Biotechnology Research Center, Japan
cg.contributor.affiliationEarlham Institute
cg.contributor.affiliationKobe University
cg.contributor.affiliationOkinawa Agricultural Research Center
cg.contributor.affiliationShinshu University
cg.contributor.affiliationTokyo University of Agriculture
cg.contributor.affiliationJapan International Research Center for Agricultural Sciences
cg.contributor.affiliationInternational Institute of Tropical Agriculture
cg.contributor.affiliationKyoto Sangyo University
cg.contributor.affiliationSainsbury Laboratory, UK
cg.contributor.affiliationUniversity of Frankfurt
cg.coverage.regionAfrica
cg.coverage.regionAsia
cg.coverage.regionEast Asia
cg.coverage.regionWest Africa
cg.coverage.countryJapan
cg.coverage.countryNigeria
cg.isijournalISI Journal
cg.authorship.typesCGIAR and advanced research institute
cg.iitasubjectGenetic Improvement
cg.iitasubjectPlant Genetic Resources
cg.iitasubjectYam
cg.journalBMC Biology
cg.howpublishedFormally Published
cg.accessibilitystatusOpen Access
local.dspaceid92018
cg.targetaudienceScientists
cg.identifier.doihttp://dx.doi.org/10.1186/s12915-017-0419-x


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