Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs

Zanini, S F and Bayer, P E and Wells, R and Snowdon, R J and Batley, J and Varshney, R K and Nguyen, H T and Edwards, D and Golicz, A A (2021) Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs. The Plant Genome, 15 (1). pp. 1-18. ISSN 1940-3372

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Since the first reported crop pangenome in 2014, advances in high-throughput and cost-effective DNA sequencing technologies facilitated multiple such studies including the pangenomes of oilseed rape (Brassica napus L.), soybean [Glycine max (L.) Merr.], rice (Oryza sativa L.), wheat (Triticum aestivum L.), and barley (Hordeum vulgare L.). Compared with single-reference genomes, pangenomes provide a more accurate representation of the genetic variation present in a species. By combining the genomic data of multiple accessions, pangenomes allow for the detection and annotation of complex DNA polymorphisms such as structural variations (SVs), one of the major determinants of genetic diversity within a species. In this review we summarize the current literature on crop pangenomics, focusing on their application to find candidate SVs involved in traits of agronomic interest. We then highlight the potential of pangenomes in the discovery and functional characterization of noncoding regulatory sequences and their variations.We conclude with a summary and outlook on innovative data structures representing the complete content of plant pangenomes including annotations of coding and noncoding elements and outcomes of transcriptomic and epigenomic experiments.

Item Type: Article
Divisions: Center of Excellence in Genomics and Systems Biology
Uncontrolled Keywords: crop improvement, oilseed rape, soybean, rice, wheat, barley
Subjects: Others > Crop Improvement
Others > Rice
Others > Wheat
Depositing User: Mr Nagaraju T
Date Deposited: 25 Mar 2024 06:38
Last Modified: 25 Mar 2024 06:38
Official URL:
Acknowledgement: This work was supported by Alexander von Humboldt Foundation in the framework of the Sofja Kovalevskaja Award endowed by the Federal Ministry of Education and Research to Agnieszka A. Golicz.
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