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

OAR@ICRISAT

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Relation http://oar.icrisat.org/12595/
https://acsess.onlinelibrary.wiley.com/doi/full/10.1002/tpg2.20177
https://doi.org/10.1002/tpg2.20177
 
Title Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs
 
Creator Zanini, S F
Bayer, P E
Wells, R
Snowdon, R J
Batley, J
Varshney, R K
Nguyen, H T
Edwards, D
Golicz, A A
 
Subject Crop Improvement
Rice
Wheat
 
Description 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.
 
Publisher Wiley Open Access
 
Date 2021-12-13
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights cc_attribution
 
Identifier http://oar.icrisat.org/12595/1/The%20Plant%20Genome_15_1-18_2021.pdf
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