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Title: Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination
Authors: Tamiru, Muluneh
Natsume, Satoshi
Takagi, Hiroki
White, Benjamen
Yaegashi, Hiroki
Shimizu, Motoki
Yoshida, Kentaro  kyouindb  KAKEN_id  orcid (unconfirmed)
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
Kahl, Günter
Takagi, Hiroko
Asiedu, Robert
Terauchi, Ryohei  kyouindb  KAKEN_id  orcid (unconfirmed)
Author's alias: 夏目, 俊
高木, 宏樹
八重樫, 弘樹
清水, 元樹
吉田, 健太郎
植村, 亜衣子
及川, 香梨
阿部, 陽
浦崎, 直也
松村, 英生
山中, 愼介
松本, 亮
村中, 聡
辻村, 真衣
寺地, 徹
高木, 洋子
寺内, 良平
Keywords: Yam
Whole-genome sequence
Sex determination
Issue Date: 19-Sep-2017
Publisher: Springer Nature
Journal title: BMC Biology
Volume: 15
Thesis number: 86
Abstract: 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.
Rights: © The Author(s). 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.
DOI(Published Version): 10.1186/s12915-017-0419-x
PubMed ID: 28927400
Appears in Collections:Journal Articles

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