Chromosome evolution and the genetic basis of agronomically important traits in greater yam
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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.
| Originalsprog | Engelsk |
|---|---|
| Artikelnummer | 2001 |
| Tidsskrift | Nature Communications |
| Vol/bind | 13 |
| Antal sider | 16 |
| ISSN | 2041-1723 |
| DOI | |
| Status | Udgivet - 2022 |
Bibliografisk note
Funding Information:
At the University of California, Davis, Genome and Biomedical Sciences facility, we thank Oanh Nguyen for troubleshooting and advice for DNA isolation and PacBio sequencing, Emily Kumimoto for mate-pair libraries, and Lutz Froenicke for management. For facilitating DArTseq genotyping, we thank: Andrzej Kilian (Diversity Arrays Technology); and Clay Sneller, Jackline Chepkoech, Mercy Chepngetich, and IGSS/SEQART staff at BecA-ILRI Hub. We thank the staff of Bioscience Center, Yam Breeding Unit, Pathology/Virology Unit, and Farm Office at IITA, Ibadan, Nigeria for support in laboratory and field activities. We thank Kwabena Darkwa and Agre Paterne, IITA, Ibadan Nigeria for their support in phenotyping population TDa1401. Boas Pucker provided the single-haploid assembly of D. dumetorum. Christopher Saski and Mary Duke provided WGS data of TDa95/00328 and TDa95-310. We thank Ismail Rabbi for early discussions in proposal development, and he and Gezahegn Girma for providing D. alata DNA of specific breeding lines. This work is based on a project supported by the National Science Foundation BREAD program, Award No. 1543967 to D.S.R., R.B., and J.E.O. We wish to acknowledge subsidy from the Integrated Genotyping Service and Support platform, a collaborative project between the International Livestock Research Institute (ILRI) and the Bill and Melinda Gates Foundation. DNA extractions for PacBio sequencing, and RNA extractions, were carried out at ICRAF with partial support from the African Orphan Crops Consortium. RNA-seq was funded by the Illumina Greater Good Initiative. Nanopore DRS work was supported by The University of Dundee Global Challenges Research Fund to G.G.S. and G.J.B., Biotechnology and Biological Sciences Research Council (BB/M004155/1) to G.G.S. and G.J.B. and H2020 Marie Skłodowska-Curie Actions (799300) to K.K. Sequencing performed at the Vincent J. Coates Genomics Sequencing Laboratory, UC Berkeley, was partially supported by NIH S10 OD018174 Instrumentation Grant. D.S.R. was supported by Chan Zuckerberg BioHub, internal funds at the Okinawa Institute of Science and Technology, and the Marthella Foskett-Brown Chair in Biological Science at UC Berkeley. This research used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
Publisher Copyright:
© 2022, This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.
ID: 310386328