Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination
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, pri...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2017
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/89726 |
| _version_ | 1855534843713028096 |
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| author | Tamiru, M. Natsume, S. Takagi, H. White, B. Yaegashi, H. Shimizu, M. Yoshida, K. Uemura, A. Oikawa, K. Abe, A. Urasaki, N. Matsumura, H Babil, P. Yamanaka, S. Matsumoto, R. Muranaka, S. Girma, G. López Montes, Antonio José Gedil, Melaku A Bhattacharjee, Ranjana Abberton, Michael T. Kumar, P. Lava Rabbi, Ismail Y. Tsujimura, M. Terachi, T. Haerty, W. Corpas, M. Kamoun, S. Kahl, G. Asiedu, Robert Terauchi, R. |
| author_browse | Abberton, Michael T. Abe, A. Asiedu, Robert Babil, P. Bhattacharjee, Ranjana Corpas, M. Gedil, Melaku A Girma, G. Haerty, W. Kahl, G. Kamoun, S. Kumar, P. Lava López Montes, Antonio José Matsumoto, R. Matsumura, H Muranaka, S. Natsume, S. Oikawa, K. Rabbi, Ismail Y. Shimizu, M. Takagi, H. Tamiru, M. Terachi, T. Terauchi, R. Tsujimura, M. Uemura, A. Urasaki, N. White, B. Yaegashi, H. Yamanaka, S. Yoshida, K. |
| author_facet | Tamiru, M. Natsume, S. Takagi, H. White, B. Yaegashi, H. Shimizu, M. Yoshida, K. Uemura, A. Oikawa, K. Abe, A. Urasaki, N. Matsumura, H Babil, P. Yamanaka, S. Matsumoto, R. Muranaka, S. Girma, G. López Montes, Antonio José Gedil, Melaku A Bhattacharjee, Ranjana Abberton, Michael T. Kumar, P. Lava Rabbi, Ismail Y. Tsujimura, M. Terachi, T. Haerty, W. Corpas, M. Kamoun, S. Kahl, G. Asiedu, Robert Terauchi, R. |
| author_sort | Tamiru, M. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace89726 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace897262025-11-11T10:40:55Z Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination Tamiru, M. Natsume, S. Takagi, H. White, B. Yaegashi, H. Shimizu, M. Yoshida, K. Uemura, A. Oikawa, K. Abe, A. Urasaki, N. Matsumura, H Babil, P. Yamanaka, S. Matsumoto, R. Muranaka, S. Girma, G. López Montes, Antonio José Gedil, Melaku A Bhattacharjee, Ranjana Abberton, Michael T. Kumar, P. Lava Rabbi, Ismail Y. Tsujimura, M. Terachi, T. Haerty, W. Corpas, M. Kamoun, S. Kahl, G. Asiedu, Robert Terauchi, R. yams dioscorea sex determination food security genome molecular marker guinea yam whole-genome sequence dioecy 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. 2017-12 2017-12-13T13:21:32Z 2017-12-13T13:21:32Z Journal Article https://hdl.handle.net/10568/89726 en Open Access application/pdf Springer Tamiru, 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. |
| spellingShingle | yams dioscorea sex determination food security genome molecular marker guinea yam whole-genome sequence dioecy Tamiru, M. Natsume, S. Takagi, H. White, B. Yaegashi, H. Shimizu, M. Yoshida, K. Uemura, A. Oikawa, K. Abe, A. Urasaki, N. Matsumura, H Babil, P. Yamanaka, S. Matsumoto, R. Muranaka, S. Girma, G. López Montes, Antonio José Gedil, Melaku A Bhattacharjee, Ranjana Abberton, Michael T. Kumar, P. Lava Rabbi, Ismail Y. Tsujimura, M. Terachi, T. Haerty, W. Corpas, M. Kamoun, S. Kahl, G. Asiedu, Robert Terauchi, R. Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination |
| title | Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination |
| title_full | Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination |
| title_fullStr | Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination |
| title_full_unstemmed | Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination |
| title_short | Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination |
| title_sort | genome sequencing of the staple food crop white guinea yam enables the development of a molecular marker for sex determination |
| topic | yams dioscorea sex determination food security genome molecular marker guinea yam whole-genome sequence dioecy |
| url | https://hdl.handle.net/10568/89726 |
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