Journal
FRONTIERS IN PLANT SCIENCE
Volume 9, Issue -, Pages -Publisher
FRONTIERS MEDIA SA
DOI: 10.3389/fpls.2018.01660
Keywords
polyploidy; plant genomics; genome assembly; third generation sequencing; reference genome
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Funding
- Nouvelles Initiatives (Project International) grant from the Centre SEVE (Fonds de recherche du Quebec - Nature et technologies (FRQ-NT))
- Natural Sciences and Engineering Research Council of Canada (NSERC) [283303]
- Agriculture and Agri-Food Canada
- McGill Department of Plant Science Graduate Excellence Fund
- CGIAR Genebank Platform
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Polyploidy or duplication of an entire genome occurs in the majority of angiosperms. The understanding of polyploid genomes is important for the improvement of those crops, which humans rely on for sustenance and basic nutrition. As climate change continues to pose a potential threat to agricultural production, there will increasingly be a demand for plant cultivars that can resist biotic and abiotic stresses and also provide needed and improved nutrition. In the past decade, Next Generation Sequencing (NGS) has fundamentally changed the genomics landscape by providing tools for the exploration of polyploid genomes. Here, we review the challenges of the assembly of polyploid plant genomes, and also present recent advances in genomic resources and functional tools in molecular genetics and breeding. As genomes of diploid and less heterozygous progenitor species are increasingly available, we discuss the lack of complexity of these currently available reference genomes as they relate to polyploid crops. Finally, we review recent approaches of haplotyping by phasing and the impact of third generation technologies on polyploid plant genome assembly.
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