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. We then highlight the potential of pangenomes in the discovery and functional characterization of noncoding regulatory sequences and their variations. 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. 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. Compared with single-reference genomes, pangenomes provide a more accurate representation of the genetic variation present in a species.
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, rice ( Oryza sativa L.), wheat ( Triticum aestivum L.), and barley ( Hordeum vulgare L.).
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