Polyploid plant genomes complexity and the challenges of sequencing

Main conclusion: Whole-genome duplication is an important evolutionary mechanism for many agriculturally important plants. We discuss selected polyploid genomic studies, limitations, and practical applications in plant breeding. Abstract: Polyploids are highly represented among agriculturally important plant species. Understanding how plant genomes change in response to whole-genome duplication is important for streamlining the use of diploid germplasm in polyploid breeding programs to introduce new alleles, genes, or desirable traits. The complexity of polyploid genomes stemming from their diverse evolutionary histories poses challenges for assembling high-quality, haplotype-resolved genome sequences, a necessary step for optimizing plant breeding efforts. In this review, we examined genomic studies that yielded high-quality reference genomes through novel approaches in various polyploid crop species. Examples include using references of progenitor species in peanut and blueberry, tackling the mixed-ploidy levels of sugarcane and dealing with species complexes in wheat and alfalfa. We also highlighted the new and innovative approaches to polyploid genome sequencing used in these studies as well as others. These methods and tools can be especially useful in species where genomic studies are not advanced, to provide insights on adapting techniques in other polyploid species to create more refined genomic studies crop improvement.