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Review
. 2020 Feb;25(2):148-158.
doi: 10.1016/j.tplants.2019.10.012. Epub 2019 Nov 29.

Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement

Aamir W Khan  1 , Vanika Garg  2 , Manish Roorkiwal  2 , Agnieszka A Golicz  3 , David Edwards  4 , Rajeev K Varshney  5
Affiliations
Review

Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement

Aamir W Khan et al. Trends Plant Sci. 2020 Feb.

Abstract

The pangenome provides genomic variations in the cultivated gene pool for a given species. However, as the crop's gene pool comprises many species, especially wild relatives with diverse genetic stock, here we suggest using accessions from all available species of a given genus for the development of a more comprehensive and complete pangenome, which we refer to as a super-pangenome. The super-pangenome provides a complete genomic variation repertoire of a genus and offers unprecedented opportunities for crop improvement. This opinion article focuses on recent developments in crop pangenomics, the need for a super-pangenome that should include wild species, and its application for crop improvement.

Keywords: copy number variations; crop wild relatives; genomics-assisted breeding; pangenome; presence/absence variations; structural variations.

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Figures

Figure 1
Figure 1
The Concept of the Pangenome and Super-Pangenome and Their Use for Crop Improvement. During the process of domestication and breeding, a number of alleles were lost. Therefore, it is important to have a catalog of all possible alleles in a crop species pangenome or genus-level super-pangenome. The pangenome and super-pangenome can be used for the development of markers using genome-wide association studies. These molecular markers can be used for crop improvement using genomics-assisted breeding approaches. Abbreviations: CWRs, crop wild relatives; SVs, structural variations.
Figure 2
Figure 2
Key Figure. Approaches for the Construction of a Super-Pangenome The figure presents a schema for the construction of a super-pangenome using diverse accessions of all of the species of a given genus. A minimum of ten different accessions for each species can be used to construct a species-level pangenome, and combining these species pangenomes would result in a super-pangenome, which would ultimately have the capacity to represent the complete genetic repertoire of the genus, thus providing a vast resource for the acceleration of crop improvement. Abbreviations: Acc, accession; SP, species of a given genus.
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