Table_4_Diversity and Genome Analysis of Australian and Global Oilseed Brassica napus L. Germplasm Using Transcriptomics and Whole Genome Re-sequencing.XLSX

Intensive breeding of Brassica napus has resulted in relatively low diversity, such that B. napus would benefit from germplasm improvement schemes that sustain diversity. As such, samples representative of global germplasm pools need to be assessed for existing population structure, diversity and linkage disequilibrium (LD). Complexity reduction genotyping-by-sequencing (GBS) methods, including GBS-transcriptomics (GBS-t), enable cost-effective screening of a large number of samples, while whole genome re-sequencing (WGR) delivers the ability to generate large numbers of unbiased genomic single nucleotide polymorphisms (SNPs), and identify structural variants (SVs). Furthermore, the development of genomic tools based on whole genomes representative of global oilseed diversity and orientated by the reference genome has substantial industry relevance and will be highly beneficial for canola breeding. As recent studies have focused on European and Chinese varieties, a global diversity panel as well as a substantial number of Australian spring types were included in this study. Focusing on industry relevance, 633 varieties were initially genotyped using GBS-t to examine population structure using 61,037 SNPs. Subsequently, 149 samples representative of global diversity were selected for WGR and both data sets used for a side-by-side evaluation of diversity and LD. The WGR data was further used to develop genomic resources consisting of a list of 4,029,750 high-confidence SNPs annotated using SnpEff, and SVs in the form of 10,976 deletions and 2,556 insertions. These resources form the basis of a reliable and repeatable system allowing greater integration between canola genomics studies, with a strong focus on breeding germplasm and industry applicability.

甘蓝型油菜（Brassica napus）的集约化育种已导致其遗传多样性相对匮乏，亟需通过维持多样性的种质改良方案来提升该物种的育种潜力。鉴于此，需对代表全球种质库的样本开展现有种群结构、多样性及连锁不平衡（linkage disequilibrium, LD）的评估。
简化基因组测序（complexity reduction genotyping-by-sequencing, GBS）类方法（包括转录组简化测序（GBS-transcriptomics, GBS-t））可实现对大量样本的低成本筛选；而全基因组重测序（whole genome re-sequencing, WGR）则能够产生大量无偏倚的基因组单核苷酸多态性（single nucleotide polymorphisms, SNPs），并可用于鉴定结构变异（structural variants, SVs）。此外，基于覆盖全球油料作物多样性的全基因组数据并结合参考基因组（reference genome）进行锚定开发的基因组工具，具有重要的产业应用价值，将对油菜育种提供极大助力。
由于既往研究多聚焦于欧洲和中国品种，本研究纳入了全球多样性种质集合以及大量澳大利亚春性品种。出于产业应用考量，本研究首先采用GBS-t对633个品种进行基因分型，基于61037个SNPs开展种群结构分析。随后，选取代表全球多样性的149份样本进行WGR，并利用两组测序数据对多样性和LD进行平行评估。
本研究依托WGR数据开发了基因组资源：包括经SnpEff注释的4029750个高置信度SNPs列表，以及10976个缺失变异和2556个插入变异形式的结构变异。这些资源构建了一套可靠且可重复的研究体系，可为油菜基因组学研究的深度整合奠定基础，同时将研究重点聚焦于育种种质开发与产业应用。