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Chromosome evolution and the genetic basis of agronomically important traits in greater yam

The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale...

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Autores principales: Bredeson, Jessen V., Lyons, Jessica B., Oniyinde, Ibukun O., Okereke, Nneka R., Kolade, Olufisayo, Nnabue, Ikenna, Nwadili, Christian O., Hřibová, Eva, Parker, Matthew, Nwogha, Jeremiah, Shu, Shengqiang, Carlson, Joseph, Kariba, Robert, Muthemba, Samuel, Knop, Katarzyna, Barton, Geoffrey J., Sherwood, Anna V., Lopez-Montes, Antonio, Asiedu, Robert, Jamnadass, Ramni, Muchugi, Alice, Goodstein, David, Egesi, Chiedozie N., Featherston, Jonathan, Asfaw, Asrat, Simpson, Gordon G., Doležel, Jaroslav, Hendre, Prasad S., Van Deynze, Allen, Kumar, Pullikanti Lava, Obidiegwu, Jude E., Bhattacharjee, Ranjana, Rokhsar, Daniel S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9010478/
https://www.ncbi.nlm.nih.gov/pubmed/35422045
http://dx.doi.org/10.1038/s41467-022-29114-w
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author Bredeson, Jessen V.
Lyons, Jessica B.
Oniyinde, Ibukun O.
Okereke, Nneka R.
Kolade, Olufisayo
Nnabue, Ikenna
Nwadili, Christian O.
Hřibová, Eva
Parker, Matthew
Nwogha, Jeremiah
Shu, Shengqiang
Carlson, Joseph
Kariba, Robert
Muthemba, Samuel
Knop, Katarzyna
Barton, Geoffrey J.
Sherwood, Anna V.
Lopez-Montes, Antonio
Asiedu, Robert
Jamnadass, Ramni
Muchugi, Alice
Goodstein, David
Egesi, Chiedozie N.
Featherston, Jonathan
Asfaw, Asrat
Simpson, Gordon G.
Doležel, Jaroslav
Hendre, Prasad S.
Van Deynze, Allen
Kumar, Pullikanti Lava
Obidiegwu, Jude E.
Bhattacharjee, Ranjana
Rokhsar, Daniel S.
author_facet Bredeson, Jessen V.
Lyons, Jessica B.
Oniyinde, Ibukun O.
Okereke, Nneka R.
Kolade, Olufisayo
Nnabue, Ikenna
Nwadili, Christian O.
Hřibová, Eva
Parker, Matthew
Nwogha, Jeremiah
Shu, Shengqiang
Carlson, Joseph
Kariba, Robert
Muthemba, Samuel
Knop, Katarzyna
Barton, Geoffrey J.
Sherwood, Anna V.
Lopez-Montes, Antonio
Asiedu, Robert
Jamnadass, Ramni
Muchugi, Alice
Goodstein, David
Egesi, Chiedozie N.
Featherston, Jonathan
Asfaw, Asrat
Simpson, Gordon G.
Doležel, Jaroslav
Hendre, Prasad S.
Van Deynze, Allen
Kumar, Pullikanti Lava
Obidiegwu, Jude E.
Bhattacharjee, Ranjana
Rokhsar, Daniel S.
author_sort Bredeson, Jessen V.
collection PubMed
description The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.
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spelling pubmed-90104782022-04-28 Chromosome evolution and the genetic basis of agronomically important traits in greater yam Bredeson, Jessen V. Lyons, Jessica B. Oniyinde, Ibukun O. Okereke, Nneka R. Kolade, Olufisayo Nnabue, Ikenna Nwadili, Christian O. Hřibová, Eva Parker, Matthew Nwogha, Jeremiah Shu, Shengqiang Carlson, Joseph Kariba, Robert Muthemba, Samuel Knop, Katarzyna Barton, Geoffrey J. Sherwood, Anna V. Lopez-Montes, Antonio Asiedu, Robert Jamnadass, Ramni Muchugi, Alice Goodstein, David Egesi, Chiedozie N. Featherston, Jonathan Asfaw, Asrat Simpson, Gordon G. Doležel, Jaroslav Hendre, Prasad S. Van Deynze, Allen Kumar, Pullikanti Lava Obidiegwu, Jude E. Bhattacharjee, Ranjana Rokhsar, Daniel S. Nat Commun Article The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments. Nature Publishing Group UK 2022-04-14 /pmc/articles/PMC9010478/ /pubmed/35422045 http://dx.doi.org/10.1038/s41467-022-29114-w Text en © This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Bredeson, Jessen V.
Lyons, Jessica B.
Oniyinde, Ibukun O.
Okereke, Nneka R.
Kolade, Olufisayo
Nnabue, Ikenna
Nwadili, Christian O.
Hřibová, Eva
Parker, Matthew
Nwogha, Jeremiah
Shu, Shengqiang
Carlson, Joseph
Kariba, Robert
Muthemba, Samuel
Knop, Katarzyna
Barton, Geoffrey J.
Sherwood, Anna V.
Lopez-Montes, Antonio
Asiedu, Robert
Jamnadass, Ramni
Muchugi, Alice
Goodstein, David
Egesi, Chiedozie N.
Featherston, Jonathan
Asfaw, Asrat
Simpson, Gordon G.
Doležel, Jaroslav
Hendre, Prasad S.
Van Deynze, Allen
Kumar, Pullikanti Lava
Obidiegwu, Jude E.
Bhattacharjee, Ranjana
Rokhsar, Daniel S.
Chromosome evolution and the genetic basis of agronomically important traits in greater yam
title Chromosome evolution and the genetic basis of agronomically important traits in greater yam
title_full Chromosome evolution and the genetic basis of agronomically important traits in greater yam
title_fullStr Chromosome evolution and the genetic basis of agronomically important traits in greater yam
title_full_unstemmed Chromosome evolution and the genetic basis of agronomically important traits in greater yam
title_short Chromosome evolution and the genetic basis of agronomically important traits in greater yam
title_sort chromosome evolution and the genetic basis of agronomically important traits in greater yam
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9010478/
https://www.ncbi.nlm.nih.gov/pubmed/35422045
http://dx.doi.org/10.1038/s41467-022-29114-w
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