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

Tamiru, Muluneh, Natsume, Satoshi, Takagi, Hiroki, White, Benjamen, Yaegashi, Hiroki, Shimizu, Motoki, Yoshida, Kentaro, Uemura, Aiko, Oikawa, Kaori, Abe, Akira, Urasaki, Naoya, Matsumura, Hideo, Babil, Pachakkil, Yamanaka, Shinsuke, Matsumoto, Ryo, Muranaka, Satoru, Girma, Gezahegn, Lopez-Montes, Antonio, Gedil, Melaku, Bhattacharjee, Ranjana, Abberton, Michael, Kumar, P Lava, Rabbi, Ismail, Tsujimura, Mai, Terachi, Toru, Haerty, Wilfried, Corpas, Manuel, Kamoun, Sophien ORCID:, Kahl, Günter, Takagi, Hiroko, Asiedu, Robert and Terauchi, Ryohei (2017) Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination. BMC Biology, 15. ISSN 1741-7007

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BACKGROUND: 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.

Item Type: Article
Uncontrolled Keywords: metabolism,genetics,genetics,genome, plant,plant breeding,quantitative trait loci,whole genome sequencing,sdg 2 - zero hunger ,/dk/atira/pure/sustainabledevelopmentgoals/zero_hunger
Faculty \ School: Faculty of Science > The Sainsbury Laboratory
UEA Research Groups: Faculty of Science > Research Groups > Plant Sciences
Depositing User: LivePure Connector
Date Deposited: 23 Jul 2018 10:30
Last Modified: 21 Oct 2022 19:33
DOI: 10.1186/s12915-017-0419-x


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