TY  - JOUR
A1  - Tamiru, Muluneh
A1  - Natsume, Satoshi
A1  - Takagi, Hiroki
A1  - White, Benjamen
A1  - Yaegashi, Hiroki
A1  - Shimizu, Motoki
A1  - Yoshida, Kentaro
A1  - Uemura, Aiko
A1  - Oikawa, Kaori
A1  - Abe, Akira
A1  - Urasaki, Naoya
A1  - Matsumura, Hideo
A1  - Babil, Pachakkil
A1  - Yamanaka, Shinsuke
A1  - Matsumoto, Ryo
A1  - Muranaka, Satoru
A1  - Girma, Gezahegn
A1  - Lopez-Montes, Antonio
A1  - Gedil, Melaku
A1  - Bhattacharjee, Ranjana
A1  - Abberton, Michael
A1  - Kumar, P. Lava
A1  - Rabbi, Ismail
A1  - Tsujimura, Mai
A1  - Terachi, Toru
A1  - Haerty, Wilfried
A1  - Corpas, Manuel
A1  - Kamoun, Sophien
A1  - Kahl, Günter
A1  - Takagi, Hiroko
A1  - Asiedu, Robert
A1  - Terauchi, Ryohei
T1  - Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination
T2  - BMC biology
N2  - 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.
KW  - Yam
KW  - Dioscorea
KW  - Whole-genome sequence
KW  - Dioecy
KW  - Sex determination
Y1  - 2017
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/46688
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-466881
SN  - 1741-7007
N1  - Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), 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 (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
VL  - 15
IS  - 1, Art. 86
SP  - 1
EP  - 20
PB  - Springer
CY  - Berlin ; Heidelberg
ER  -