Zanini Silvia F, Bayer Philipp E, Wells Rachel, Snowdon Rod J, Batley Jacqueline, Varshney Rajeev K, Nguyen Henry T, Edwards David, Golicz Agnieszka A
Dep. of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig Univ. Giessen, Giessen, 35392, Germany.
School of Biological Sciences and Institute of Agriculture, Univ. of Western Australia, Perth, Western Australia, Australia.
Plant Genome. 2022 Mar;15(1):e20177. doi: 10.1002/tpg2.20177. Epub 2021 Dec 13.
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.
自2014年首次报道作物泛基因组以来，高通量且经济高效的DNA测序技术取得进展，推动了多项此类研究，包括油菜（甘蓝型油菜）、大豆[大豆（L.）Merr.]、水稻（稻）、小麦（普通小麦）和大麦（大麦）的泛基因组研究。与单参考基因组相比，泛基因组能更准确地呈现一个物种中存在的遗传变异。通过整合多个种质的基因组数据，泛基因组能够检测和注释复杂的DNA多态性，如结构变异（SVs），这是物种内遗传多样性的主要决定因素之一。在本综述中，我们总结了关于作物泛基因组学的当前文献，重点关注其在寻找与农艺性状相关的候选SVs方面的应用。然后，我们强调泛基因组在非编码调控序列及其变异的发现和功能表征方面的潜力。我们最后总结并展望了代表植物泛基因组完整内容的创新数据结构，包括编码和非编码元件的注释以及转录组学和表观基因组学实验的结果。
