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

Gordon G Simpson, Antonio Lopez-Montes, Robert Asiedu, Ramni Jamnadass, Alice Muchugi, David Goodstein, Chiedozie N Egesi, Jonathan Featherston, Asrat Asfaw, Anna V Sherwood, Jaroslav Doležel, Prasad S Hendre, Allen Van Deynze, Pullikanti Lava Kumar, Jude E Obidiegwu, Ranjana Bhattacharjee, Daniel S Rokhsar, Jessen V Bredeson, Geoffrey J Barton, Katarzyna Knop, Samuel Muthemba, Robert Kariba, Joseph Carlson, Shengqiang Shu, Jeremiah Nwogha, Matthew Parker, Eva Hřibová, Christian O Nwadili, Ikenna Nnabue, Olufisayo Kolade, Nneka R Okereke, Ibukun O Oniyinde, Jessica B Lyons

Journal: Nature communications 2022;13(1):2001

PMID: 35422045

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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 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.

Address: Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA.; Innovative Genomics Institute, Berkeley, CA, USA.; International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria.; National Root Crops Research Institute (NRCRI), Umudike, Nigeria.; Institute 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.; School of Life Sciences, University of Dundee, Dundee, UK.; DOE Joint Genome Institute, Berkeley, CA, USA.; World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya.; African Orphan Crops Consortium, Nairobi, Kenya.; Department of Biology, University of Copenhagen, Copenhagen, Denmark.; International Trade Center, Accra, Ghana.; Cornell University, Ithaca, NY, 14850, USA.; Agricultural Research Council, Biotechnology Platform, Pretoria, South Africa.; James Hutton Institute, Dundee, UK.; University of California, Davis, Davis, CA, 95616, USA.; National Root Crops Research Institute (NRCRI), Umudike, Nigeria. [email protected].; International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria. [email protected].; Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA. [email protected].; Innovative Genomics Institute, Berkeley, CA, USA. [email protected].; DOE Joint Genome Institute, Berkeley, CA, USA. [email protected].; Okinawa Institute of Science and Technology, Onna, Okinawa, Japan. [email protected].; Chan-Zuckerberg BioHub, 499 Illinois St., San Francisco, CA, 94158, USA. [email protected].

DOI: 10.1038/s41467-022-29114-w

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MeSH Terms: Chromosomes, Dioscorea, Humans, Plant Breeding, Plant Tubers, Quantitative Trait Loci