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

Silvia F. Zanini; Philipp E. Bayer; Rachel Wells; Rod J. Snowdon; Jacqueline Batley; Rajeev K. Varshney; Henry T. Nguyen; David Edwards; Agnieszka A. Golicz

doi:10.1002/tpg2.20177

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

Journal article

Open access

Peer reviewed

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

Silvia F. Zanini, Philipp E. Bayer, Rachel Wells, Rod J. Snowdon, Jacqueline Batley, Rajeev K. Varshney, Henry T. Nguyen, David Edwards and Agnieszka A. Golicz

The plant genome, Vol.15(1), e20177

2022

DOI: https://doi.org/10.1002/tpg2.20177

PMID: 34904403

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Abstract

Genetics & Heredity

Life Sciences & Biomedicine

Plant Sciences

Science & Technology

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.

Details

Title: Pangenomics in crop improvement-from coding structural variations to finding regulatory variants with pangenome graphs
Authors/Creators: Silvia F. Zanini - Justus-Liebig-Universität Gießen
Philipp E. Bayer - The University of Western Australia
Rachel Wells - Norwich Research Park
Rod J. Snowdon - Justus-Liebig-Universität Gießen
Jacqueline Batley - The University of Western Australia
Rajeev K. Varshney - International Crops Research Institute for the Semi-Arid Tropics
Henry T. Nguyen - University of Missouri
David Edwards - The University of Western Australia
Agnieszka A. Golicz - Justus-Liebig-Universität Gießen
Publication Details: The plant genome, Vol.15(1), e20177
Publisher: Wiley Periodicals LLC on behalf of Crop Science Society of America
Number of pages: 18
Grant note: Alexander von Humboldt Foundation
Identifiers: 991005609294007891
Murdoch Affiliation: Centre for Crop and Food Innovation; State Agricultural Biotechnology Centre; Food Futures Institute
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Genetics & Heredity; Plant Sciences
ESI research areas: Plant & Animal Science