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PLANT GENOMICS

Graph pangenomes find missing heritability

Nature Genetics (2022)Cite this article

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The use of association studies to identify candidate genes for complex biological traits in plants has been challenging due to a reliance on single reference genomes, leading to missing heritability. Graphical pangenomes and the identification of causal variants help overcome this and provide an important advance for crop breeding.

The inability to identify all genetic variation in a genome, due to reliance on single reference genomes, has limited trait association studies in crops, and the subsequent ability to apply genomics approaches to accelerate crop improvement. The recent Article in Nature by Zhou et al.1 represents a milestone in genomics and provides a solution to this problem, through a culmination of advances in genome sequencing technology, and an understanding of plant genome diversity and its association with heritable traits. The authors constructed a graph pangenome for tomato on the basis of 32 high-quality genome assemblies and use this as a reference for the mapping of genomic sequence data from 332 tomato accessions. They demonstrate the increased value of using this graph pangenome compared with traditional linear reference genomes in capturing missing heritability1.

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Fig. 1: Graph pangenomes capture the genomic diversity that underlies the observed phenotypic diversity and maintains this structural variation information within the context of linear chromosomes.

References

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Authors and Affiliations

  1. School of Biological Sciences and Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, Australia

    David Edwards

  2. School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia

    Jacqueline Batley

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  1. David Edwards
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  2. Jacqueline Batley
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Correspondence to David Edwards or Jacqueline Batley.

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The authors declare no competing interests.

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Edwards, D., Batley, J. Graph pangenomes find missing heritability. Nat Genet (2022). https://doi.org/10.1038/s41588-022-01099-8

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  • DOI: https://doi.org/10.1038/s41588-022-01099-8

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