Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff

Robert VanBuren; Ching Man Wai; Xuewen Wang; Jeremy Pardo; Alan E. Yocca; Hao Wang; Srinivasa R. Chaluvadi; Guomin Han; Douglas Bryant; Patrick P. Edger; Joachim Messing; Mark E. Sorrells; Todd C. Mockler; Jeffrey L. Bennetzen; Todd P. Michael

doi:10.1038/s41467-020-14724-z

Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff

Robert VanBuren^*, Ching Man Wai, Xuewen Wang, Jeremy Pardo, Alan E. Yocca, Hao Wang, Srinivasa R. Chaluvadi, Guomin Han, Douglas Bryant, Patrick P. Edger, Joachim Messing, Mark E. Sorrells, Todd C. Mockler, Jeffrey L. Bennetzen, Todd P. Michael

^*Corresponding author for this work

Biochemistry and Molecular Genetics

Research output: Contribution to journal › Article › peer-review

115 Scopus citations

Abstract

Teff (Eragrostis tef) is a cornerstone of food security in the Horn of Africa, where it is prized for stress resilience, grain nutrition, and market value. Here, we report a chromosome-scale assembly of allotetraploid teff (variety Dabbi) and patterns of subgenome dynamics. The teff genome contains two complete sets of homoeologous chromosomes, with most genes maintaining as syntenic gene pairs. TE analysis allows us to estimate that the teff polyploidy event occurred ~1.1 million years ago (mya) and that the two subgenomes diverged ~5.0 mya. Despite this divergence, we detect no large-scale structural rearrangements, homoeologous exchanges, or biased gene loss, in contrast to many other allopolyploids. The two teff subgenomes have partitioned their ancestral functions based on divergent expression across a diverse expression atlas. Together, these genomic resources will be useful for accelerating breeding of this underutilized grain crop and for fundamental insights into polyploid genome evolution.

Original language	English (US)
Article number	884
Journal	Nature communications
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41467-020-14724-z
State	Published - Dec 1 2020

Funding

We are indebted to Tsegaye Dabi at the Salk Institute for Biological Studies for introducing us to this amazing plant, and for inspiring generations of plant biologists. We thank Elliott Meer for assistance with PacBio sequencing, and the Monsanto Genomics Team (Randy Kerstetter, Mitch Sudkamp, Phil Latreille, Zijin Du, and Joe Zhou) for full-length sequenced fosmids. We thank James Schnable for his helpful comments and suggestions on the manuscript. This work is supported by funding from the National Science Foundation (MCB\u20101817347 to R.V.), Department of Energy (DE-SC0012639 to T.C.M. and T.P.M.), and partial support from the Bill & Melinda Gates Foundation (T.C. M. and D.B.). This work is supported by the USDA National Institute of Food and Agriculture Hatch project to RV.

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

UN SDGs

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10.1038/s41467-020-14724-z

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VanBuren, R., Man Wai, C., Wang, X., Pardo, J., Yocca, A. E., Wang, H., Chaluvadi, S. R., Han, G., Bryant, D., Edger, P. P., Messing, J., Sorrells, M. E., Mockler, T. C., Bennetzen, J. L., & Michael, T. P. (2020). Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff. Nature communications, 11(1), Article 884. https://doi.org/10.1038/s41467-020-14724-z

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abstract = "Teff (Eragrostis tef) is a cornerstone of food security in the Horn of Africa, where it is prized for stress resilience, grain nutrition, and market value. Here, we report a chromosome-scale assembly of allotetraploid teff (variety Dabbi) and patterns of subgenome dynamics. The teff genome contains two complete sets of homoeologous chromosomes, with most genes maintaining as syntenic gene pairs. TE analysis allows us to estimate that the teff polyploidy event occurred ~1.1 million years ago (mya) and that the two subgenomes diverged ~5.0 mya. Despite this divergence, we detect no large-scale structural rearrangements, homoeologous exchanges, or biased gene loss, in contrast to many other allopolyploids. The two teff subgenomes have partitioned their ancestral functions based on divergent expression across a diverse expression atlas. Together, these genomic resources will be useful for accelerating breeding of this underutilized grain crop and for fundamental insights into polyploid genome evolution.",

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VanBuren, R, Man Wai, C, Wang, X, Pardo, J, Yocca, AE, Wang, H, Chaluvadi, SR, Han, G, Bryant, D, Edger, PP, Messing, J, Sorrells, ME, Mockler, TC, Bennetzen, JL & Michael, TP 2020, 'Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff', Nature communications, vol. 11, no. 1, 884. https://doi.org/10.1038/s41467-020-14724-z

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AU - Messing, Joachim

AU - Sorrells, Mark E.

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AU - Bennetzen, Jeffrey L.

AU - Michael, Todd P.

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Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff

Abstract

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UN SDGs

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