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

View ORCID ProfileJessen V. Bredeson, View ORCID ProfileJessica B. Lyons, View ORCID ProfileIbukun O. Oniyinde, View ORCID ProfileNneka R. Okereke, View ORCID ProfileOlufisayo Kolade, View ORCID ProfileIkenna Nnabue, View ORCID ProfileChristian O. Nwadili, View ORCID ProfileEva Hřibová, View ORCID ProfileMatthew Parker, View ORCID ProfileJeremiah Nwogha, View ORCID ProfileShengqiang Shu, View ORCID ProfileJoseph Carlson, View ORCID ProfileRobert Kariba, View ORCID ProfileSamuel Muthemba, View ORCID ProfileKatarzyna Knop, View ORCID ProfileGeoffrey J. Barton, Anna V. Sherwood, View ORCID ProfileAntonio Lopez-Montes, View ORCID ProfileRobert Asiedu, View ORCID ProfileRamni Jamnadass, View ORCID ProfileAlice Muchugi, View ORCID ProfileDavid Goodstein, View ORCID ProfileChiedozie N. Egesi, View ORCID ProfileJonathan Featherston, View ORCID ProfileAsrat Asfaw, View ORCID ProfileGordon G. Simpson, View ORCID ProfileJaroslav Doležel, Prasad S. Hendre, View ORCID ProfileAllen Van Deynze, View ORCID ProfilePullikanti Lava Kumar, View ORCID ProfileJude E. Obidiegwu, View ORCID ProfileRanjana Bhattacharjee, View ORCID ProfileDaniel S. Rokhsar
doi: https://doi.org/10.1101/2021.04.14.439117
Jessen V. Bredeson
1Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720 USA
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Jessica B. Lyons
1Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720 USA
2Innovative Genomics Institute
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Ibukun O. Oniyinde
3International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan,Nigeria
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Nneka R. Okereke
4National Root Crops Research Institute (NRCRI), Umudike, Nigeria
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Olufisayo Kolade
3International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan,Nigeria
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Ikenna Nnabue
4National Root Crops Research Institute (NRCRI), Umudike, Nigeria
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Christian O. Nwadili
4National Root Crops Research Institute (NRCRI), Umudike, Nigeria
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Eva Hřibová
5Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
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Matthew Parker
6School of Life Sciences, University of Dundee, Dundee, United Kingdom
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Jeremiah Nwogha
4National Root Crops Research Institute (NRCRI), Umudike, Nigeria
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Shengqiang Shu
7DOE Joint Genome Institute
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Joseph Carlson
7DOE Joint Genome Institute
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Robert Kariba
8World Agroforestry (CIFOR-ICRAF)
9African Orphan Crops Consortium
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Samuel Muthemba
8World Agroforestry (CIFOR-ICRAF)
9African Orphan Crops Consortium
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Katarzyna Knop
6School of Life Sciences, University of Dundee, Dundee, United Kingdom
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Geoffrey J. Barton
6School of Life Sciences, University of Dundee, Dundee, United Kingdom
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Anna V. Sherwood
6School of Life Sciences, University of Dundee, Dundee, United Kingdom
10Department of Biology, University of Copenhagen, Copenhagen, Denmark
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Antonio Lopez-Montes
3International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan,Nigeria
11International Trade Center, Accra, Ghanad
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Robert Asiedu
3International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan,Nigeria
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Ramni Jamnadass
8World Agroforestry (CIFOR-ICRAF)
9African Orphan Crops Consortium
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Alice Muchugi
8World Agroforestry (CIFOR-ICRAF)
9African Orphan Crops Consortium
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David Goodstein
7DOE Joint Genome Institute
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Chiedozie N. Egesi
4National Root Crops Research Institute (NRCRI), Umudike, Nigeria
3International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan,Nigeria
12Cornell University
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Jonathan Featherston
13Agricultural Research Council, Biotechnology Platform
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Asrat Asfaw
3International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan,Nigeria
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Gordon G. Simpson
14James Hutton Institute
6School of Life Sciences, University of Dundee, Dundee, United Kingdom
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Jaroslav Doležel
5Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
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Prasad S. Hendre
8World Agroforestry (CIFOR-ICRAF)
9African Orphan Crops Consortium
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Allen Van Deynze
15University of California, Davis
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Pullikanti Lava Kumar
3International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan,Nigeria
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Jude E. Obidiegwu
4National Root Crops Research Institute (NRCRI), Umudike, Nigeria
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  • ORCID record for Jude E. Obidiegwu
  • For correspondence: ejikeobi@yahoo.com r.bhattacharjee@cgiar.org dsrokhsar@gmail.com
Ranjana Bhattacharjee
3International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan,Nigeria
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  • For correspondence: ejikeobi@yahoo.com r.bhattacharjee@cgiar.org dsrokhsar@gmail.com
Daniel S. Rokhsar
1Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720 USA
7DOE Joint Genome Institute
2Innovative Genomics Institute
16Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
17Chan-Zuckerberg BioHub, 499 Illinois St., San Francisco, CA 94158 USA
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  • For correspondence: ejikeobi@yahoo.com r.bhattacharjee@cgiar.org dsrokhsar@gmail.com
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Abstract

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 greater yam combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient lineage-specific genome duplication, followed by extensive genome-wide reorganization. Using our new genomic tools we find quantitative trait loci for susceptibility 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.

Competing Interest Statement

Author Daniel Rokhsar is a member of the Scientific Advisory Board of, and a minor shareholder in, Dovetail Genomics LLC, which provides as a service the high-throughput chromatin conformation capture (Hi-C) technology used in this study.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted April 15, 2021.
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Chromosome evolution and the genetic basis of agronomically important traits in greater yam
Jessen V. Bredeson, Jessica B. Lyons, Ibukun O. Oniyinde, Nneka R. Okereke, Olufisayo Kolade, Ikenna Nnabue, Christian O. Nwadili, Eva Hřibová, Matthew Parker, Jeremiah Nwogha, Shengqiang Shu, Joseph Carlson, Robert Kariba, Samuel Muthemba, Katarzyna Knop, Geoffrey J. Barton, Anna V. Sherwood, Antonio Lopez-Montes, Robert Asiedu, Ramni Jamnadass, Alice Muchugi, David Goodstein, Chiedozie N. Egesi, Jonathan Featherston, Asrat Asfaw, Gordon G. Simpson, Jaroslav Doležel, Prasad S. Hendre, Allen Van Deynze, Pullikanti Lava Kumar, Jude E. Obidiegwu, Ranjana Bhattacharjee, Daniel S. Rokhsar
bioRxiv 2021.04.14.439117; doi: https://doi.org/10.1101/2021.04.14.439117
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Chromosome evolution and the genetic basis of agronomically important traits in greater yam
Jessen V. Bredeson, Jessica B. Lyons, Ibukun O. Oniyinde, Nneka R. Okereke, Olufisayo Kolade, Ikenna Nnabue, Christian O. Nwadili, Eva Hřibová, Matthew Parker, Jeremiah Nwogha, Shengqiang Shu, Joseph Carlson, Robert Kariba, Samuel Muthemba, Katarzyna Knop, Geoffrey J. Barton, Anna V. Sherwood, Antonio Lopez-Montes, Robert Asiedu, Ramni Jamnadass, Alice Muchugi, David Goodstein, Chiedozie N. Egesi, Jonathan Featherston, Asrat Asfaw, Gordon G. Simpson, Jaroslav Doležel, Prasad S. Hendre, Allen Van Deynze, Pullikanti Lava Kumar, Jude E. Obidiegwu, Ranjana Bhattacharjee, Daniel S. Rokhsar
bioRxiv 2021.04.14.439117; doi: https://doi.org/10.1101/2021.04.14.439117

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