Exploring the structural variant landscape in the highly dynamic genome of a recent allopolyploid crop species

探索最近异源多倍体作物物种的高度动态基因组中的结构变异景观

• 批准号: 458716530
• 负责人: Professor Dr. Rod Snowdon
• 金额: --
• 依托单位: Lehrstuhl für Pflanzenzüchtung
• 依托单位国家: 德国
• 项目类别: Research Grants
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/458716530?language=en
• 关键词: Exploring; structural; variant; landscape; highly

The recent allopolyploid crop species Brassica napus (oilseed rape, canola) has an unusually dynamic genome. Using long-read sequencing, we recently discovered that up to 10% of all genes in any given B. napus genotype are affected by functionally relevant, genome-wide gene conversions and deletions with high relevance for crop evolution and breeding. Because of their predominant size range (100bp~5kb), the great majority of genome-wide structural variants (SV) were undetectable by short-read sequencing in the highly-duplicated B. napus genome, hence their mechanisms and evolutionary consequences have not yet been studied. Based on robust methods developed in extensive preliminary work, we plan a detailed survey of the SV landscape in the B. napus pangenome, using long-read sequencing in 100 genetically diverse, homozygous accessions from a well-characterised global species collection. Assembly of a B. napus “Pangemome SV Atlas” will provide a valuable public tool to address the mechanisms of small-scale SV in polyploid genomes and re-visit extensive short-read datasets from previous studies. By identifying sequence motifs associated with genome-wide SV breakpoints and investigating SV patterns in the context of 3D genome structure and chromatin interactions, we aim for novel biological insight into the mechanisms underlying small-scale homoeologous exchanges, as a basis for predictive models that help to potentially harness the power of SV in breeding. In a practical case study, we will use the SV Atlas to associate SV in floweringpathway genes to ecogeographical adaptation traits. This will give novel insight into the role of SV in polyploid evolution and adaptation.

最近的异源多倍体作物物种甘蓝型油菜（油菜，油菜）具有异常动态的基因组。使用长读序测序，我们最近发现，在任何给定的B中，高达10%的基因。欧洲油菜基因型受到功能相关的、全基因组的基因转换和缺失的影响，这些基因转换和缺失与作物进化和育种高度相关。由于高度重复的B中的结构变异（SV）的主要大小范围（100 bp ~ 5 kb），绝大多数SV在高度重复的B中不能被短读段测序检测到。油菜基因组，因此其机制和进化后果尚未研究。基于广泛的前期工作中开发的稳健方法，我们计划对B的SV景观进行详细调查。napus pangenome，使用来自一个充分表征的全球物种收集的100个遗传多样性纯合种质的长读序测序。组装一个B。napus“Pangemome SV Atlas”将提供一个有价值的公共工具，以解决多倍体基因组中小规模SV的机制，并重新访问以前研究的广泛短读数据集。通过识别与全基因组SV断点相关的序列基序，并在3D基因组结构和染色质相互作用的背景下研究SV模式，我们的目标是对小规模同源交换机制的新的生物学见解，作为预测模型的基础，有助于潜在地利用SV在育种中的力量。在一个实际的案例研究中，我们将使用SV图谱将开花途径基因中的SV与生态地理适应性状联系起来。这将为SV在多倍体进化和适应中的作用提供新的见解。