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

Author

Listed:
  • Robert VanBuren

    (Michigan State University
    Michigan State University)

  • Ching Man Wai

    (Michigan State University
    Michigan State University)

  • Xuewen Wang

    (University of Georgia)

  • Jeremy Pardo

    (Michigan State University
    Michigan State University
    Michigan State University)

  • Alan E. Yocca

    (Michigan State University
    Michigan State University)

  • Hao Wang

    (University of Georgia)

  • Srinivasa R. Chaluvadi

    (University of Georgia)

  • Guomin Han

    (University of Georgia)

  • Douglas Bryant

    (Donald Danforth Plant Science Center)

  • Patrick P. Edger

    (Michigan State University)

  • Joachim Messing

    (Rutgers University)

  • Mark E. Sorrells

    (Cornell University)

  • Todd C. Mockler

    (Donald Danforth Plant Science Center)

  • Jeffrey L. Bennetzen

    (University of Georgia)

  • Todd P. Michael

    (J. Craig Venter Institute)

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.

Suggested Citation

  • 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 &, 2020. "Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-14724-z
    DOI: 10.1038/s41467-020-14724-z
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    Cited by:

    1. Taikui Zhang & Weichen Huang & Lin Zhang & De-Zhu Li & Ji Qi & Hong Ma, 2024. "Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages," Nature Communications, Nature, vol. 15(1), pages 1-27, December.
    2. Katrien M. Devos & Peng Qi & Bochra A. Bahri & Davis M. Gimode & Katharine Jenike & Samuel J. Manthi & Dagnachew Lule & Thomas Lux & Liliam Martinez-Bello & Thomas H. Pendergast & Chris Plott & Dipnar, 2023. "Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Man Xing & Bo Hong & Mengjie Lv & Xueyi Lan & Danhui Zhang & Chunlei Shu & Shucheng Qi & Zechuan Peng & Chunyun Guan & Xinghua Xiong & Luyao Huang, 2024. "Analysis of BnGPAT9 Gene Expression Patterns in Brassica napus and Its Impact on Seed Oil Content," Agriculture, MDPI, vol. 14(8), pages 1-18, August.
    4. Oluwaseyi Shorinola & Rose Marks & Peter Emmrich & Chris Jones & Damaris Odeny & Mark A. Chapman, 2024. "Integrative and inclusive genomics to promote the use of underutilised crops," Nature Communications, Nature, vol. 15(1), pages 1-4, December.
    5. Min-Rui-Xuan Xu & Zhen-Yang Liao & Jordan R. Brock & Kang Du & Guo-Yin Li & Zhi-Qiang Chen & Ying-Hao Wang & Zhong-Nan Gao & Gaurav Agarwal & Kevin H-C Wei & Feng Shao & Shuai Pang & Adrian E. Platts , 2023. "Maternal dominance contributes to subgenome differentiation in allopolyploid fishes," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    6. Justine K. Kitony & Kelly Colt & Bradley W. Abramson & Nolan T. Hartwick & Semar Petrus & Emadeldin H. E. Konozy & Nisa Karimi & Levi Yant & Todd P. Michael, 2024. "Chromosome-level baobab genome illuminates its evolutionary trajectory and environmental adaptation," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    7. Adam M. Session & Daniel S. Rokhsar, 2023. "Transposon signatures of allopolyploid genome evolution," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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