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 Deynze, Pullikanti Lava Kumar, Jude E. Obidiegwu (), Ranjana Bhattacharjee () and Daniel S. Rokhsar ()
Additional contact information
Jessen V. Bredeson: Department of Molecular & Cell Biology, University of California
Jessica B. Lyons: Department of Molecular & Cell Biology, University of California
Ibukun O. Oniyinde: International Institute of Tropical Agriculture
Nneka R. Okereke: National Root Crops Research Institute (NRCRI)
Olufisayo Kolade: International Institute of Tropical Agriculture
Ikenna Nnabue: National Root Crops Research Institute (NRCRI)
Christian O. Nwadili: National Root Crops Research Institute (NRCRI)
Eva Hřibová: Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research
Matthew Parker: University of Dundee
Jeremiah Nwogha: National Root Crops Research Institute (NRCRI)
Shengqiang Shu: DOE Joint Genome Institute
Joseph Carlson: DOE Joint Genome Institute
Robert Kariba: World Agroforestry (CIFOR-ICRAF)
Samuel Muthemba: World Agroforestry (CIFOR-ICRAF)
Katarzyna Knop: University of Dundee
Geoffrey J. Barton: University of Dundee
Anna V. Sherwood: University of Dundee
Antonio Lopez-Montes: International Institute of Tropical Agriculture
Robert Asiedu: International Institute of Tropical Agriculture
Ramni Jamnadass: World Agroforestry (CIFOR-ICRAF)
Alice Muchugi: World Agroforestry (CIFOR-ICRAF)
David Goodstein: DOE Joint Genome Institute
Chiedozie N. Egesi: International Institute of Tropical Agriculture
Jonathan Featherston: Agricultural Research Council, Biotechnology Platform
Asrat Asfaw: International Institute of Tropical Agriculture
Gordon G. Simpson: University of Dundee
Jaroslav Doležel: Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research
Prasad S. Hendre: World Agroforestry (CIFOR-ICRAF)
Allen Deynze: University of California, Davis
Pullikanti Lava Kumar: International Institute of Tropical Agriculture
Jude E. Obidiegwu: National Root Crops Research Institute (NRCRI)
Ranjana Bhattacharjee: International Institute of Tropical Agriculture
Daniel S. Rokhsar: Department of Molecular & Cell Biology, University of California

Nature Communications, 2022, vol. 13, issue 1, 1-16

Abstract: 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 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.

Date: 2022
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DOI: 10.1038/s41467-022-29114-w

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