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Plant pangenomes for crop improvement, biodiversity and evolution

Nature Reviews Genetics (2024)Cite this article

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Abstract

Plant genome sequences catalogue genes and the genetic elements that regulate their expression. Such inventories further research aims as diverse as mapping the molecular basis of trait diversity in domesticated plants or inquiries into the origin of evolutionary innovations in flowering plants millions of years ago. The transformative technological progress of DNA sequencing in the past two decades has enabled researchers to sequence ever more genomes with greater ease. Pangenomes — complete sequences of multiple individuals of a species or higher taxonomic unit — have now entered the geneticists’ toolkit. The genomes of crop plants and their wild relatives are being studied with translational applications in breeding in mind. But pangenomes are applicable also in ecological and evolutionary studies, as they help classify and monitor biodiversity across the tree of life, deepen our understanding of how plant species diverged and show how plants adapt to changing environments or new selection pressures exerted by human beings.

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Fig. 1: Pangenomics: assembly and comparison of genome sequences.
Fig. 2: Pangenomics in crop plants.
Fig. 3: A tiered strategy for pangenomics.
Fig. 4: Pangenomics at different taxonomic levels.

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Acknowledgements

The authors’ research activities in barley and its wild relatives are supported by grants from, respectively, the German Federal Ministry of Education and Research (BMBF) (SHAPE-P3, 031B1302A to N.S. and M.M.) and the European Research Council (Starting Grant TRANSFER, action number 949873 to M.M.). M.J.’s work on faba bean genomics is funded by the Leibniz Association (REPLACE, J118/2021).

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  1. Department of Biology, University of Marburg, Marburg, Germany

    Mona Schreiber

  2. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany

    Murukarthick Jayakodi, Nils Stein & Martin Mascher

  3. Martin Luther University Halle–Wittenberg, Halle (Saale), Germany

    Nils Stein

  4. German Centre for Integrative Biodiversity Research (iDiv) Halle–Jena–Leipzig, Leipzig, Germany

    Martin Mascher

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10,000 Plant Genome Project: https://db.cngb.org/10kp/

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Schreiber, M., Jayakodi, M., Stein, N. et al. Plant pangenomes for crop improvement, biodiversity and evolution. Nat Rev Genet (2024). https://doi.org/10.1038/s41576-024-00691-4

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