Cargando…
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...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
---|---|
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 |
_version_ | 1784687485864902656 |
---|---|
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. |
format | Online Article Text |
id | pubmed-9010478 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT bredesonjessenv chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT lyonsjessicab chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT oniyindeibukuno chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT okerekennekar chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT koladeolufisayo chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT nnabueikenna chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT nwadilichristiano chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT hribovaeva chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT parkermatthew chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT nwoghajeremiah chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT shushengqiang chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT carlsonjoseph chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT karibarobert chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT muthembasamuel chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT knopkatarzyna chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT bartongeoffreyj chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT sherwoodannav chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT lopezmontesantonio chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT asiedurobert chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT jamnadassramni chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT muchugialice chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT goodsteindavid chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT egesichiedozien chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT featherstonjonathan chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT asfawasrat chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT simpsongordong chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT dolezeljaroslav chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT hendreprasads chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT vandeynzeallen chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT kumarpullikantilava chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT obidiegwujudee chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT bhattacharjeeranjana chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam AT rokhsardaniels chromosomeevolutionandthegeneticbasisofagronomicallyimportanttraitsingreateryam |